LOOPP results

LOOPP parallel driver v5.0 (06/13/08 15:45 EDT) with LOOPP v3.0 (compiled Jul 11 2008 17:20:20)
     [NEWSABLE]     [HSHFL]     [ENE]     [NEWALICHOICE]

This is HTML output, the other options are plain text, CASP AL and CASP TS formats.

If an error occured during execution it is logged in plain text version only,
there is no need to look for an error if this file ends with 'DONE' statement.

STARTING:Sun Aug 10 06:48:45 2008 EST

INPUT:
   sim_min =  40.0% minimum sequence identity (%)
   sim_max =  80.0% maximum sequence identity (%)
   len_dif =  20.0% maximum length difference (% of query sequence length) 
                    between query and homolog
   nmax    =  1     maximum number of homologous sequences (including query sequence)
   maxout  =  5     maximum number of outputted matches
   strict  =  0     all alignments will be accepted from LOOPP results
                    for homologs; they will be translated to query sequence 
                    alignments using BLAST results
   casp    =  5     maximum number of outputted matches in CASP format
   align   =  'g'   only corresponding global alignments will be reported
   maxdiff =  50.0% only alignments differing no more than  50.0% from the query
                    sequence will be reported, or when reject=0, corresponding local
                    alignments will be reported
   reject  =  1     alignments shorter more than  50.0% from the query sequence
                    will be rejected
   seccut  =  0.00  structures with sec. str. score below seccut will be rejected
    secdb  = 1      type of secondary structure description: 1 - DSSB, 0 - phi/psi map
   tasktb  = 11111111111111111111  type of initial calculations
   pdbcut  =  60.0% pdb sequence identity threshold (%)
  pdbstop  = 0      stop if PDB structure with similarity above pdbcut found
  domains  = 0      query sequence will be decomposed into putative domains if =1
   maxall  = 300      maximum number of models evaluated in the second stage       
   refstr  = 0      if equal to 1 rmsd distances between all hits and a reference structure
                   will be reported
   maxpdb  = 5      number of top PDB hits added to the second stage scoring 
   maxdyn  = 5      number of dynamic domain entries from database added to the second stage scoring 
 beautify  = 0      use pdb beautifier 
rmsdtables  = 1     compute rmsd tables between hits 

   local LOOPP/BLAST database will be used

   input file T0420
    --> 189 residues, sequence name: T0420
   Database: T:\CBSU\blastdb\20080108\nr


 -> 3 homolog sequences with sequence identity from  40.0% to  80.0% satisfying length constraints found
 -> 0 representatives will be used in search (nmax=1 including query sequence)
 Histogram of all homolog sequences found by BLAST (e-value cutoff 0.01, length constr.) by sequence identity:
  00%-10%    10%-20%    20%-30%    30%-40%    40%-50%    50%-60%    60%-70%    70%-80%    80%-90%    90%-100% 

       0          0         72         48          0          2          1          0          0          1   

5 dynamic database entries created: 1HJJ_A 1HJL_A 1HV9_A 1E5K_A 1FR9_A 




RESULTS

secondary structure prediction shows 38.10% helical, 19.58% extended and 42.33% loops/other

homologs/domains used:
  0 query sequence T0420
all homologs found

total number of entries processed: 167

Amino acid profile calculated versus nr database is here
  (Amino acid profile BLAST run output is here)
Results of BLAST versus pdbaa database using the nr profile are here
  (Results of BLAST versus pdbaa database with no profile are here)
Transitive BLAST output calculted with this profile is here

Phase 1 scoring data: input and output
Phase 2 scoring data: input and output


HITS:

table legend
no    name                SCOP           SCOP_stat         confidence    score homolog  hits  length   seq.   align    ENE             TE13        old        CGenergy      SIFT2        tma1         tma2      |-------OPTM------| |-------SEQ  (global)-------| |-------SEQ   (local)-------| |-------TRD  (global)-------| |-------TRD   (local)-------| |-------TRS  (global)-------| |-------TRS   (local)-------| |-------TSS  (global)-------| |-------TSS   (local)-------| |-------TSC  (global)-------| |-------TSC   (local)-------| |-------PSM  (global)-------| |-------PSM   (local)-------| |-------SRF  (global)-------| |-------SRF   (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------|  sec. str.
                                                                                               (%)    ident.  src.    all-atom      all-atom      score      all-atom     all-atom     all-atom     all-atom   r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy    pos. comp.
1    1VPA_A               c.68.1.13     55.21.21.10            NONE   -48.551     0       1  98.94%  18.72%   OPTM     -896.087     -634.010        3.783        0.715        0.799        0.820        0.966     28.170     -49.1     3.620    87.500     -80.5     3.520    37.500    -127.0     2.220    12.770      -6.5     1.690     7.610     -49.1     3.190    20.460      15.8     0.650     2.030     -32.4     9.640    36.220     -28.7    11.450    16.490     -61.1   -30.000    47.000    -128.0   -30.000    31.000    -129.0    10.550   228.000    -123.0    17.880   117.000    -168.0     6.490    90.000    -108.0     8.260    35.000    -126.0     5.000     -13.0     0.258     -22.1    79.000     211.0     5.000     -13.0     0.146      -1.5    0.76  0.65
2    c.68.1.5.2_A         c.68.1.5      55.21.21.4             NONE   -48.654     0       1  98.41%  18.82%   OPTM    -1005.107     -693.780        3.420        0.756        0.865        0.716        0.953     28.930     -51.1     3.780    54.500     -29.0     8.770    80.500    -176.0    -0.730    -1.650     167.0     0.160     6.820     -56.0     0.450    -0.530     184.6     2.250     5.160     -45.1     2.830    10.160      89.5    13.330    16.770     -74.7   -30.000    48.000    -105.0   -30.000    19.000    -125.0     7.190   176.000      -2.0    15.780   118.000    -163.0     3.080    40.000     -39.0     3.880    23.000    -115.0     5.000     -19.5    -0.456     -18.5     2.000     224.0     5.000     -19.5     0.301      -5.5    0.64  0.73
3    1HJJ_A               c.68.1.8      55.21.21.4             NONE   -48.669     0       1  96.83%  20.22%   OPTM     -830.938     -502.600        4.793        0.699        0.609        0.930        0.955     29.740     -49.7     6.280   193.000    -158.0     8.120    78.000    -170.5     3.110    20.050     -57.4     0.460     0.110     -66.5     5.820    40.890     -50.4     2.900    15.450     -57.7    14.090    56.340     -88.4    17.670    44.630     -92.7   -30.000    54.000    -141.0   -30.000    46.000    -144.0    11.480   263.000    -197.0    24.490   176.000    -209.0     9.110    99.000    -137.0    11.930    66.000    -147.0     5.000     -24.0    -0.173     -28.3     0.000 -9.3e+061     5.000     -24.0     0.176      -2.7    0.72  0.80
4    c.68.1.5.1_A         c.68.1.5      55.21.21.4             NONE   -48.721     0       1  98.94%  18.72%   OPTM     -929.075     -724.910        3.393        0.800        0.771        0.731        0.964     25.180     -47.9     3.580   102.500     -21.5     7.860    77.500    -161.0     0.520    -0.420     156.4     3.650    10.090     -55.4     1.770    -0.240     174.5     5.810    13.450     -44.0     4.720    15.640      82.1    14.500    25.340     -72.2   -30.000    48.000    -106.0   -30.000    24.000    -121.0     6.570   138.000       0.0    15.700   122.000    -162.0     4.330    35.000     -53.0     3.360    23.000    -116.0     5.000     -23.7    -1.953     -18.7   -37.000     253.0     5.000     -23.7    -0.292      -4.5    0.75  0.66
5    1E5K_A               c.68.1.8      55.21.21.4             NONE   -48.727     0       1  96.83%  19.67%   OPTM     -791.106     -532.930        4.774        0.703        0.601        0.926        0.950     29.090     -49.7     5.970   187.500    -151.0     7.280    71.000    -163.5     2.190    18.430     -46.1     0.490     3.300     -59.5     5.360    41.410     -42.7     2.160     5.610     -50.3    13.500    58.060     -85.0    20.160    44.420     -90.2   -30.000    55.000    -142.0   -30.000    47.000    -145.0    11.270   265.000    -198.0    25.560   175.000    -210.0     9.070   101.000    -137.0    11.820    64.000    -147.0     5.000     -23.5    -0.222     -28.2     0.000 -9.3e+061     5.000     -23.5     0.176      -2.7    0.72  0.81



RMSD table between hits
(RMSDs are shaded according to similarity, up to 10Å )

	1	2	3	4	5
1	0.00	2.93	4.34	3.46	4.30
2	2.93	0.00	3.93	2.24	3.88
3	4.34	3.93	0.00	4.10	0.61
4	3.46	2.24	4.10	0.00	4.06
5	4.30	3.88	0.61	4.06	0.00



Similarity table for hits: percentage of chain fitting below 3Å RMSD
(Cells are shaded according to similarity starting at 30%)

	1	2	3	4	5
1	100.00	100.00	25.68	49.20	26.78
2	100.00	100.00	33.52	100.00	32.42
3	25.68	33.52	100.00	57.92	100.00
4	49.20	100.00	57.92	100.00	56.83
5	26.78	32.42	100.00	56.83	100.00



Similarity table for hits: percentage of chain fitting below 6Å RMSD
(Cells are shaded according to similarity starting at 50%)

	1	2	3	4	5
1	100.00	100.00	100.00	100.00	100.00
2	100.00	100.00	100.00	100.00	100.00
3	100.00	100.00	100.00	100.00	100.00
4	100.00	100.00	100.00	100.00	100.00
5	100.00	100.00	100.00	100.00	100.00





ALIGNMENTS

--> hit 1 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]


  secondary structure: 28.57% helical, 27.65% extended, 43.78% loops/other (query: 38.10% 19.58% 42.33%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Nucleotide-diphospho-sugar transferases]

 name                SCOP           SCOP_stat         confidence    score homolog  hits  length   seq.   align    ENE             TE13        old        CGenergy      SIFT2        tma1         tma2      |-------OPTM------| |-------SEQ  (global)-------| |-------SEQ   (local)-------| |-------TRD  (global)-------| |-------TRD   (local)-------| |-------TRS  (global)-------| |-------TRS   (local)-------| |-------TSS  (global)-------| |-------TSS   (local)-------| |-------TSC  (global)-------| |-------TSC   (local)-------| |-------PSM  (global)-------| |-------PSM   (local)-------| |-------SRF  (global)-------| |-------SRF   (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------|  sec. str.
                                                                                          (%)    ident.  src.    all-atom      all-atom      score      all-atom     all-atom     all-atom     all-atom   r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy    pos. comp.
1VPA_A               c.68.1.13     55.21.21.10            NONE   -48.551     0       1  98.94%  18.72%   OPTM     -896.087     -634.010        3.783        0.715        0.799        0.820        0.966     28.170     -49.1     3.620    87.500     -80.5     3.520    37.500    -127.0     2.220    12.770      -6.5     1.690     7.610     -49.1     3.190    20.460      15.8     0.650     2.030     -32.4     9.640    36.220     -28.7    11.450    16.490     -61.1   -30.000    47.000    -128.0   -30.000    31.000    -129.0    10.550   228.000    -123.0    17.880   117.000    -168.0     6.490    90.000    -108.0     8.260    35.000    -126.0     5.000     -13.0     0.258     -22.1    79.000     211.0     5.000     -13.0     0.146      -1.5    0.76  0.65

alignment source: OPTM
 +++ there is a problem with all-atom model, click here for details
            --EEEEEE-----------  HHHHH----HHHHHHHHHHH----   EEEE--  -HHHHHHHH----EEE--------
Query:    1 MNIGVIILAAGEGKRFGGD--KLLAKIDNTPIIMRTIRIYGDLEK---IIIVGK--YVNEMLPLLMDQIVIYNPFWNEGI   73
Sbjct:    4 HMNVAILLAAGKGERMSENVPKQFLEIEGRMLFEYPLSTFLKSEAIDGVVIVTRREWFEVVEKRVFHEKVLGIVEGGDTR   83
            -EEEEEEE----------------EE--EE--HHHHHHHHH-----EEEEEE----HHHHH-------EEEEEE----HH

            HHHHHHHHHHH---  -EEEEEE-------HHHHHHHHHHH-----EEEEE---               ---     --E
Query:   74 STSLKLGLRFFKDY--DAVLVALGDMPFVTKEDVNKIINTFKPNCKAVIPTHKG---------------ERG-----NPV  131
Sbjct:   84 SQSVRSALEFLEKFSPSYVLVHDSARPFLRKKHVSEVLRRARETGAATLALKNSDALVRVENDRIEYIPRKGVYRILTPQ  163
            HHHHHHHHHH------EEEEEE-------HHHHHHHHHHHHHH-EEEEEEE----EEEEE--EEEEE-----EEEEEEEE

            E--HHHHHHHHH----- EHHHHHHH----EEEEEE----EEEE---HHHHHHHHHH
Query:  132 LISKSLFNEIEKLRGDV-GARVILNKIKIEELCFIECSEGVLIDIDKKEDLMRLRDF  187
Sbjct:  164 AFSYEILKKAHENGGEWADDTEPVQKLGVKIALVEGDPLCF--KVTFKEDLELARII  218
            EEHHHHHHHH---------HHHHH------EEEE-------  -----HHHHHHHHH

187 residues (98.94%) of query sequence aligned



--> hit 2 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]


  secondary structure: 28.99% helical, 23.95% extended, 47.06% loops/other (query: 38.10% 19.58% 42.33%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Nucleotide-diphospho-sugar transferases]

 name                SCOP           SCOP_stat         confidence    score homolog  hits  length   seq.   align    ENE             TE13        old        CGenergy      SIFT2        tma1         tma2      |-------OPTM------| |-------SEQ  (global)-------| |-------SEQ   (local)-------| |-------TRD  (global)-------| |-------TRD   (local)-------| |-------TRS  (global)-------| |-------TRS   (local)-------| |-------TSS  (global)-------| |-------TSS   (local)-------| |-------TSC  (global)-------| |-------TSC   (local)-------| |-------PSM  (global)-------| |-------PSM   (local)-------| |-------SRF  (global)-------| |-------SRF   (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------|  sec. str.
                                                                                          (%)    ident.  src.    all-atom      all-atom      score      all-atom     all-atom     all-atom     all-atom   r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy    pos. comp.
c.68.1.5.2_A         c.68.1.5      55.21.21.4             NONE   -48.654     0       1  98.41%  18.82%   OPTM    -1005.107     -693.780        3.420        0.756        0.865        0.716        0.953     28.930     -51.1     3.780    54.500     -29.0     8.770    80.500    -176.0    -0.730    -1.650     167.0     0.160     6.820     -56.0     0.450    -0.530     184.6     2.250     5.160     -45.1     2.830    10.160      89.5    13.330    16.770     -74.7   -30.000    48.000    -105.0   -30.000    19.000    -125.0     7.190   176.000      -2.0    15.780   118.000    -163.0     3.080    40.000     -39.0     3.880    23.000    -115.0     5.000     -19.5    -0.456     -18.5     2.000     224.0     5.000     -19.5     0.301      -5.5    0.64  0.73

alignment source: OPTM
            -EEEEEE-----------  HHHHH----HHHHHHHHHHH----   EEEE---HHHHHHHH----EEE--------HHH
Query:    2 NIGVIILAAGEGKRFGGD--KLLAKIDNTPIIMRTIRIYGDLEK---IIIVGKYVNEMLPLLMDQIVIYNPFWNEGISTS   76
Sbjct:    2 SNFAIILAAGKGTRMKSDLPKVLHKVAGISMLEHVFRSVGAIQPEKTVTVVGHKAELVEEVLAGQTEFVTQSEQLGTGHA   81
            -EEEEEE-----------------EE--EEHHHHHHHHH------EEEEEE---HHHHHHH-----EEEE------HHHH

            HHHHHHHH---- EEEEEE-------HHHHHHHHHHH- ----EEEEE--------                        
Query:   77 LKLGLRFFKDYD-AVLVALGDMPFVTKEDVNKIINTFK-PNCKAVIPTHKGERGNP------------------------  130
Sbjct:   82 VMMTEPILEGLSGHTLVIAGDTPLITGESLKNLIDFHINHKNVATILTAETDNPFGYGRIVRNDNAEVLRIVEQKDATDF  161
            HH--HHHH-----EEEEEE-------HHHHHHHHHHHHH----EEEEEEE--------EEEE-----EEEEE------HH

                        EE--HHHHHHHHH----        -EHHHHHHH----EEEEEE----EEEE---HHHHHHHHHH
Query:  131 ------------VLISKSLFNEIEKLRGD--------VGARVILNKIKIEELCFIECSEGVLIDIDKKEDLMRLRDF  187
Sbjct:  162 EKQIKEINTGTYVFDNERLFEALKNINTNNAQGEYYITDVIGIFRETGEKVGAYTLKDFDESLGVNDRVALATAESV  238
            HH---EEEEEEEEEEHHHHHHHH----------------HHHHHHH----EEEEE------------HHHHHHHHHH

186 residues (98.41%) of query sequence aligned



--> hit 3 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]


  secondary structure: 29.95% helical, 21.39% extended, 48.66% loops/other (query: 38.10% 19.58% 42.33%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Nucleotide-diphospho-sugar transferases]

 name                SCOP           SCOP_stat         confidence    score homolog  hits  length   seq.   align    ENE             TE13        old        CGenergy      SIFT2        tma1         tma2      |-------OPTM------| |-------SEQ  (global)-------| |-------SEQ   (local)-------| |-------TRD  (global)-------| |-------TRD   (local)-------| |-------TRS  (global)-------| |-------TRS   (local)-------| |-------TSS  (global)-------| |-------TSS   (local)-------| |-------TSC  (global)-------| |-------TSC   (local)-------| |-------PSM  (global)-------| |-------PSM   (local)-------| |-------SRF  (global)-------| |-------SRF   (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------|  sec. str.
                                                                                          (%)    ident.  src.    all-atom      all-atom      score      all-atom     all-atom     all-atom     all-atom   r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy    pos. comp.
1HJJ_A               c.68.1.8      55.21.21.4             NONE   -48.669     0       1  96.83%  20.22%   OPTM     -830.938     -502.600        4.793        0.699        0.609        0.930        0.955     29.740     -49.7     6.280   193.000    -158.0     8.120    78.000    -170.5     3.110    20.050     -57.4     0.460     0.110     -66.5     5.820    40.890     -50.4     2.900    15.450     -57.7    14.090    56.340     -88.4    17.670    44.630     -92.7   -30.000    54.000    -141.0   -30.000    46.000    -144.0    11.480   263.000    -197.0    24.490   176.000    -209.0     9.110    99.000    -137.0    11.930    66.000    -147.0     5.000     -24.0    -0.173     -28.3     0.000 -9.3e+061     5.000     -24.0     0.176      -2.7    0.72  0.80

alignment source: OPTM
            --EEEEEE---------- -HHHHH----HHHHHHHHHHH- ---EEEE---HHHHHHHH----EEE--------HHHHH
Query:    1 MNIGVIILAAGEGKRFGG-DKLLAKIDNTPIIMRTIRIYGD-LEKIIIVGKYVNEMLPLLMDQIVIYNPFWNEGISTSLK   78
Sbjct:    5 TTITGVVLAGGKARRMGGVDKGLLELNGKPLWQHVADALMTQLSHVVVNANRHQEIYQAS-GLKVIEDSLADYPGPLAGM   83
            -EEEEEE----------------EE--EEHHHHHHHHHHHH---EEEE----HHHHH--- --EE---------HHHHHH

            HHHHHH----EEEEEE-------HHHHHHHHHHH-----EEEEE--------  EE--   HHHHHHHHH-----EHHHH
Query:   79 LGLRFFKDYDAVLVALGDMPFVTKEDVNKIINTFKPNCKAVIPTHKGERGNP--VLIS---KSLFNEIEKLRGDVGARVI  153
Sbjct:   84 LSVMQQEAGEWFLFCPCDTPYIPP-DLAARLNHQRKDAP-VVWVHDGERDHPTIALVNRAIEPLLLEYLQA-GERRVMVF  160
            HHHHH----EEEEEE--------- HHHHHHH------E EEEE----EEEEEEEEE---HHHHHHHHH-- ---HHHHH

            HHH----EEEEEE----EEEE---HHHHHH
Query:  154 LNKIKIEELCFIECSEGVLIDIDKKEDLMR  183
Sbjct:  161 MRLAGGHAVDFSDHKD-AFVDVNTPEELAR  189
            HH---EEEE------- ------HHHHH--

183 residues (96.83%) of query sequence aligned



--> hit 4 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]


  secondary structure: 26.27% helical, 25.00% extended, 48.73% loops/other (query: 38.10% 19.58% 42.33%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Nucleotide-diphospho-sugar transferases]

 name                SCOP           SCOP_stat         confidence    score homolog  hits  length   seq.   align    ENE             TE13        old        CGenergy      SIFT2        tma1         tma2      |-------OPTM------| |-------SEQ  (global)-------| |-------SEQ   (local)-------| |-------TRD  (global)-------| |-------TRD   (local)-------| |-------TRS  (global)-------| |-------TRS   (local)-------| |-------TSS  (global)-------| |-------TSS   (local)-------| |-------TSC  (global)-------| |-------TSC   (local)-------| |-------PSM  (global)-------| |-------PSM   (local)-------| |-------SRF  (global)-------| |-------SRF   (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------|  sec. str.
                                                                                          (%)    ident.  src.    all-atom      all-atom      score      all-atom     all-atom     all-atom     all-atom   r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy    pos. comp.
c.68.1.5.1_A         c.68.1.5      55.21.21.4             NONE   -48.721     0       1  98.94%  18.72%   OPTM     -929.075     -724.910        3.393        0.800        0.771        0.731        0.964     25.180     -47.9     3.580   102.500     -21.5     7.860    77.500    -161.0     0.520    -0.420     156.4     3.650    10.090     -55.4     1.770    -0.240     174.5     5.810    13.450     -44.0     4.720    15.640      82.1    14.500    25.340     -72.2   -30.000    48.000    -106.0   -30.000    24.000    -121.0     6.570   138.000       0.0    15.700   122.000    -162.0     4.330    35.000     -53.0     3.360    23.000    -116.0     5.000     -23.7    -1.953     -18.7   -37.000     253.0     5.000     -23.7    -0.292      -4.5    0.75  0.66

alignment source: OPTM
            --EEEEEE-----------  HHHHH----HHHHHHHHHHH--  --EEEE---HHHHHHHH-  ---EEE--------H
Query:    1 MNIGVIILAAGEGKRFGGD--KLLAKIDNTPIIMRTIRIYGDL--EKIIIVGKYVNEMLPLLM--DQIVIYNPFWNEGIS   74
Sbjct:    4 NAMSVVILAAGKGTRMYSDLPKVLHTLAGKAMVQHVIDAANELGAAHVHLVYGHGGDLLKQALKDDNLNWVLQAEQLGTG   83
            --EEEEEEE----------------EE--EEHHHHHHHHHHHH----EEEEE---HHHHHHH-----EEEEE------HH

            HHHHHHHHHH----EEEEEE-------HHHHHHHHHHH-----EEEEE--------                        
Query:   75 TSLKLGLRFFKDYDAVLVALGDMPFVTKEDVNKIINTFKPNCKAVIPTHKGERGNP------------------------  130
Sbjct:   84 HAMQQAAPFFADDEDILMLYGDVPLISVETLQRLRD-AKPQGGIGLLTVKLDDPTGYGRITRENGKVTGIVEHKDATDEQ  162
            HHHHHH--------EEEEEE-------HHHHHHHHH H-----EEEEEEE--------EEEEE--EEEEEE---------

                       EE--HHHHHHHHH----        -EHHHHHHH----EEEEEE----EEEE---HHHHHHHHHH
Query:  131 -----------VLISKSLFNEIEKLRGD--------VGARVILNKIKIEELCFIECSEGVLIDIDKKEDLMRLRDF  187
Sbjct:  163 RQIQEINTGILIANGADMKRWLAKLTNNNAQGEYYITDIIALAYQEGREIVAVHPQRLSEVEGVNNRLQLSRLERV  238
            ----EEEEEEEEEEHHHHHHHH----------------HHHHHH-----EEEE-------------HHHHHHHHHH

187 residues (98.94%) of query sequence aligned



--> hit 5 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]


  secondary structure: 30.48% helical, 21.39% extended, 48.13% loops/other (query: 38.10% 19.58% 42.33%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Nucleotide-diphospho-sugar transferases]

 name                SCOP           SCOP_stat         confidence    score homolog  hits  length   seq.   align    ENE             TE13        old        CGenergy      SIFT2        tma1         tma2      |-------OPTM------| |-------SEQ  (global)-------| |-------SEQ   (local)-------| |-------TRD  (global)-------| |-------TRD   (local)-------| |-------TRS  (global)-------| |-------TRS   (local)-------| |-------TSS  (global)-------| |-------TSS   (local)-------| |-------TSC  (global)-------| |-------TSC   (local)-------| |-------PSM  (global)-------| |-------PSM   (local)-------| |-------SRF  (global)-------| |-------SRF   (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------|  sec. str.
                                                                                          (%)    ident.  src.    all-atom      all-atom      score      all-atom     all-atom     all-atom     all-atom   r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy    zscore  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy  r-energy    energy    pos. comp.
1E5K_A               c.68.1.8      55.21.21.4             NONE   -48.727     0       1  96.83%  19.67%   OPTM     -791.106     -532.930        4.774        0.703        0.601        0.926        0.950     29.090     -49.7     5.970   187.500    -151.0     7.280    71.000    -163.5     2.190    18.430     -46.1     0.490     3.300     -59.5     5.360    41.410     -42.7     2.160     5.610     -50.3    13.500    58.060     -85.0    20.160    44.420     -90.2   -30.000    55.000    -142.0   -30.000    47.000    -145.0    11.270   265.000    -198.0    25.560   175.000    -210.0     9.070   101.000    -137.0    11.820    64.000    -147.0     5.000     -23.5    -0.222     -28.2     0.000 -9.3e+061     5.000     -23.5     0.176      -2.7    0.72  0.81

alignment source: OPTM
            --EEEEEE---------- -HHHHH----HHHHHHHHHHH- ---EEEE---HHHHHHHH----EEE--------HHHHH
Query:    1 MNIGVIILAAGEGKRFGG-DKLLAKIDNTPIIMRTIRIYGD-LEKIIIVGKYVNEMLPLLMDQIVIYNPFWNEGISTSLK   78
Sbjct:    5 TTITGVVLAGGKARRMGGVDKGLLELNGKPLWQHVADALMTQLSHVVVNANRHQEIYQAS-GLKVIEDSLADYPGPLAGM   83
            -EEEEEE----------------EE--EEHHHHHHHHHHHH---EEEE----HHHHH--- --EE---------HHHHHH

            HHHHHH----EEEEEE-------HHHHHHHHHHH-----EEEEE--------  EE--   HHHHHHHHH-----EHHHH
Query:   79 LGLRFFKDYDAVLVALGDMPFVTKEDVNKIINTFKPNCKAVIPTHKGERGNP--VLIS---KSLFNEIEKLRGDVGARVI  153
Sbjct:   84 LSVMQQEAGEWFLFCPCDTPYIPP-DLAARLNHQRKDAP-VVWVHDGERDHPTIALVNRAIEPLLLEYLQA-GERRVMVF  160
            HHHHH----EEEEEE--------- HHHHHHH------E EEEE----EEEEEEEEE--HHHHHHHHHH-- ---HHHHH

            HHH----EEEEEE----EEEE---HHHHHH
Query:  154 LNKIKIEELCFIECSEGVLIDIDKKEDLMR  183
Sbjct:  161 MRLAGGHAVDFSDHKD-AFVNVNTPEELAR  189
            HH---EEEE------- ------HHHHH--

183 residues (96.83%) of query sequence aligned




DONE: Sun Aug 10 11:14:37 2008 EST

00%-10%	10%-20%	20%-30%	30%-40%	40%-50%	50%-60%	60%-70%	70%-80%	80%-90%	90%-100%
0	0	72	48	0	2	1	0	0	1