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:Sat Aug 09 04:22:54 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 T0411
    --> 139 residues, sequence name: T0411
   Database: T:\CBSU\blastdb\20080108\nr


 -> 8 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         44         30          5          3          0          0          0          1   

5 dynamic database entries created: 1TQ1_A 1UAR_A 1QXN_A 1H4K_X 1DP2_A 




RESULTS

secondary structure prediction shows 36.69% helical, 12.23% extended and 51.08% loops/other

homologs/domains used:
  0 query sequence T0411
all homologs found

total number of entries processed: 85

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    c.46.1.4.1_A         c.46.1.4      22.15.15.2             NONE   -35.455     0       1  84.17%  11.11%   OPTM     -332.212     -263.240        1.435        0.582        0.725        0.791        0.907     16.550     -31.4     1.620    39.500     -32.0     0.220    20.500     -66.0     0.660    -0.130     -13.5     1.010     1.280     -26.8     0.560     3.550       3.6     3.610     3.530     -24.1     3.570     8.060     -28.9     6.640     5.780     -39.0   -30.000    -1.000     -72.0   -30.000     5.000     -85.0     0.210    31.000      33.0     5.380    28.000     -69.0     1.700    20.000     -32.0     6.940    28.000     -72.0     5.000      -3.2   -11.967     -63.2     0.000 -9.3e+061     5.000      -3.2     0.813      -1.4    0.38  0.96
2    1GMX_A               c.46.1.3      22.15.15.3             NONE   -35.488     0       1  75.54%  14.05%   OPTM     -289.031     -161.090        1.958        0.413        0.671        0.831        0.935     17.810     -33.6     2.410    49.500     -27.5     2.180    14.500     -85.0     3.120     4.700       9.3     2.520     3.220     -24.2     5.130     9.500      17.0     2.900     3.090     -19.0    10.380    20.610     -13.6    11.680    18.300     -41.9   -30.000    23.000     -60.0   -30.000    24.000     -78.0     7.110   132.000     -65.0    14.530    89.000    -125.0     1.100    22.000       5.0     2.660    12.000     -52.0     5.000     -13.0    -7.899     -61.7     6.000     173.0     5.000     -13.0    -0.553      -2.7    0.22  0.75
3    2OUC_A               not_found     23.23.23.23            NONE   -35.630     0       1  83.45%  14.66%   OPTM     -261.842     -248.280        0.888        0.524        0.581        0.797        0.901     14.850     -29.1     0.010    15.000     -12.5     1.210     6.000     -78.5    -1.210    -4.520      -1.3     0.990    -1.170     -27.4    -1.370    -8.660      16.5     2.000     3.510     -22.0     2.840    11.370     -22.6     5.430     4.430     -36.2   -30.000    10.000     -73.0   -30.000     9.000     -79.0    -0.140    -9.000      50.0     4.980    32.000     -68.0    -0.930     8.000      -8.0     2.060    15.000     -52.0     5.000      -6.3    -4.794     -66.2     0.000 -9.3e+061     5.000      -6.0     5.000      -1.8    0.26  0.85
4    1URH_A               c.46.1.2      22.15.15.6             NONE   -35.653     0       1  78.42%  21.10%   OPTM     -251.676     -174.090        1.331        0.527        0.504        0.407        0.949     13.930     -30.1    -0.610   -11.000     330.0     1.700    26.000     -94.5    -1.010    -1.900     750.2     0.170     0.890     -27.0    -1.490    -6.630     769.2     1.020     3.260     -19.6     2.410     2.970     409.9     6.350     8.930     -47.4   -30.000     4.000      -7.0   -30.000     8.000     -93.0    -0.250   -17.500     406.5    17.880    93.000    -148.0     3.400    21.000     168.0     3.260    20.000     -67.0     5.000     -16.2   -10.584     -67.8   -35.000     261.0     5.000     -17.4     0.204      -3.7    0.33  0.80
5    2J6P_A               not_found     23.23.23.23            NONE   -35.688     0       1  85.61%  20.17%   OPTM     -282.376     -154.960        1.438        0.529        0.551        0.728        0.876     14.560     -29.6    -1.460    -4.500      16.0     3.580    18.000     -99.5     0.270    -7.010     -12.8     0.960     1.390     -23.3     0.180    -3.020       3.4     0.330    -0.560     -13.9     1.440    -6.300     -19.4     8.340     7.980     -40.6   -30.000    -1.000     -56.0   -30.000     5.000     -76.0     1.080    38.000      13.0    15.630    96.000    -136.0    -0.720    -2.000     -12.0     2.640    10.000     -60.0     5.000       1.5   -14.080     -66.0     0.000 -9.3e+061     5.000       1.5    -1.108       0.3    0.18  0.81



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

	1	2	3	4	5
1	0.00	4.39	4.99	6.20	4.67
2	4.39	0.00	5.46	6.41	5.41
3	4.99	5.46	0.00	4.23	4.34
4	6.20	6.41	4.23	0.00	6.08
5	4.67	5.41	4.34	6.08	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	42.74	43.97	43.12	43.59
2	42.74	100.00	41.38	37.61	39.50
3	43.97	41.38	100.00	50.00	43.10
4	43.12	37.61	50.00	100.00	41.28
5	43.59	39.50	43.10	41.28	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	98.17	100.00
2	100.00	100.00	100.00	93.58	100.00
3	100.00	100.00	100.00	100.00	100.00
4	98.17	93.58	100.00	100.00	99.08
5	100.00	100.00	100.00	99.08	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: 35.07% helical, 12.69% extended, 52.24% loops/other (query: 36.69% 12.23% 51.08%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Rhodanese/Cell cycle control phosphatase]

 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.46.1.4.1_A         c.46.1.4      22.15.15.2             NONE   -35.455     0       1  84.17%  11.11%   OPTM     -332.212     -263.240        1.435        0.582        0.725        0.791        0.907     16.550     -31.4     1.620    39.500     -32.0     0.220    20.500     -66.0     0.660    -0.130     -13.5     1.010     1.280     -26.8     0.560     3.550       3.6     3.610     3.530     -24.1     3.570     8.060     -28.9     6.640     5.780     -39.0   -30.000    -1.000     -72.0   -30.000     5.000     -85.0     0.210    31.000      33.0     5.380    28.000     -69.0     1.700    20.000     -32.0     6.940    28.000     -72.0     5.000      -3.2   -11.967     -63.2     0.000 -9.3e+061     5.000      -3.2     0.813      -1.4    0.38  0.96

alignment source: OPTM
            ----HHHHHHHHH-----EEEEEE--HHHHHH------EE---         HHHHHH----HHHHHHH----------E
Query:   23 QSYSFEDMKRIVGKHDPNVVLVDVREPSEYSIVHIPASINVPY---------RSHPDAFALDPLEFEKQIGIPKPDSAKE   93
Sbjct:  181 GAITAKELYTMMTDKNISLIIMDARRMQDYQDSCILHSLSVPEEAISPGVTASWIEAHLPDDSKDTWKKRG-----NVEY  255
            -EE-HHHHHHHHH-----EEEEE---HHHHHH------EE-----------HHHHHH---HHHHHHHH---     ---E

            EEEEE--        -HHHHHHHHHHHH----     -EEE----HHHHHH--------
Query:   94 LIFYCAS--------GKRGGEAQKVASSHGYS-----NTSLYPGSMNDWVSHGGDKLDL  139
Sbjct:  256 VVLLDWFSSAKDLQIGTTLRSLKDALFKWESKTVLRNEPLVLEGGYENWLLCYPQYTTN  314
            EEEE-------------HHHHHHHHHH------------EEE--HHHHHHHH-------

117 residues (84.17%) 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: 42.45% helical, 18.87% extended, 38.68% loops/other (query: 36.69% 12.23% 51.08%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Rhodanese/Cell cycle control phosphatase]

 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.
1GMX_A               c.46.1.3      22.15.15.3             NONE   -35.488     0       1  75.54%  14.05%   OPTM     -289.031     -161.090        1.958        0.413        0.671        0.831        0.935     17.810     -33.6     2.410    49.500     -27.5     2.180    14.500     -85.0     3.120     4.700       9.3     2.520     3.220     -24.2     5.130     9.500      17.0     2.900     3.090     -19.0    10.380    20.610     -13.6    11.680    18.300     -41.9   -30.000    23.000     -60.0   -30.000    24.000     -78.0     7.110   132.000     -65.0    14.530    89.000    -125.0     1.100    22.000       5.0     2.660    12.000     -52.0     5.000     -13.0    -7.899     -61.7     6.000     173.0     5.000     -13.0    -0.553      -2.7    0.22  0.75

alignment source: OPTM
 +++ there is a problem with all-atom model, click here for details
            --------HHHHHHHHH-----EEEEEE--HHHHHH------EE---HHHHHH----HHHHHHH----------EEEEEE
Query:   19 VSNIQSYSFEDMKRIVGKHDPNVVLVDVREPSEYSIVHIPASINVPYRSHPDAFALDPLEFEKQIGIPKPDSAKELIFYC   98
Sbjct:    1 MDQFECINVADAHQKLQEKEA--VLVDIRDPQSFAMGHAVQAFHLT----NDT----LGAFMRDNDFDTP------VMVM   64
            ----EEE-HHHHHHHHH----  EEEE---HHHHHH-EE---EE--    HHH    HHHHHHH------      EEE-

            ---HHHHHHHHHHHH-----EEE----HHHHHH--------
Query:   99 ASGKRGGEAQKVASSHGYSNTSLYPGSMNDWVSHGGDKLDL  139
Sbjct:   65 YHGNSSKGAAQYLLQQGYDVVYSIDGGFEAWQRQFPAEVAY  105
            ----HHHHHHHHHHHH----EEEE--HHHHHHHH----EE-

105 residues (75.54%) 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: 40.31% helical, 16.28% extended, 43.41% loops/other (query: 36.69% 12.23% 51.08%)

  SCOP classification: 


 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.
2OUC_A               not_found     23.23.23.23            NONE   -35.630     0       1  83.45%  14.66%   OPTM     -261.842     -248.280        0.888        0.524        0.581        0.797        0.901     14.850     -29.1     0.010    15.000     -12.5     1.210     6.000     -78.5    -1.210    -4.520      -1.3     0.990    -1.170     -27.4    -1.370    -8.660      16.5     2.000     3.510     -22.0     2.840    11.370     -22.6     5.430     4.430     -36.2   -30.000    10.000     -73.0   -30.000     9.000     -79.0    -0.140    -9.000      50.0     4.980    32.000     -68.0    -0.930     8.000      -8.0     2.060    15.000     -52.0     5.000      -6.3    -4.794     -66.2     0.000 -9.3e+061     5.000      -6.0     5.000      -1.8    0.26  0.85

alignment source: OPTM
            ----HHHHHHHHH-----EEEEEE--HHHHHH------EE---  HHHHHH----HHHHHHH--------      --EE
Query:   23 QSYSFEDMKRIVGKHDPNVVLVDVREPSEYSIVHIPASINVPY--RSHPDAFALDPLEFEKQIGIPKPDS------AKEL   94
Sbjct:  148 KIIYPNDLAKKMTKP----VIIDCRPFMEYNKSHIQGAVHINCADKISRRRLQQGKITVLDLISCREGKDSFKRIFSKEI  223
            -EE-HHHHHHHHH--    EEEE---HHHHHHEEE---EE-----HHHHHHHH-----HHHHHH------HHHHHHH--E

            EEEE--         -HHHHHHHHHHHH-----EEE----HHHHHH-------
Query:   95 IFYCAS---------GKRGGEAQKVASSHGYSNTSLYPGSMNDWVSHGGDKLD  138
Sbjct:  224 IVYDENTNEPSRVMPSQPLHIVLESLKREGK-EPLVLKGGLSSFKQNHENLCD  275
            EEE--------------HHHHHHHHHHH--- --EEE--HHHHH-------EE

116 residues (83.45%) 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: 27.34% helical, 11.51% extended, 61.15% loops/other (query: 36.69% 12.23% 51.08%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Rhodanese/Cell cycle control phosphatase]

 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.
1URH_A               c.46.1.2      22.15.15.6             NONE   -35.653     0       1  78.42%  21.10%   OPTM     -251.676     -174.090        1.331        0.527        0.504        0.407        0.949     13.930     -30.1    -0.610   -11.000     330.0     1.700    26.000     -94.5    -1.010    -1.900     750.2     0.170     0.890     -27.0    -1.490    -6.630     769.2     1.020     3.260     -19.6     2.410     2.970     409.9     6.350     8.930     -47.4   -30.000     4.000      -7.0   -30.000     8.000     -93.0    -0.250   -17.500     406.5    17.880    93.000    -148.0     3.400    21.000     168.0     3.260    20.000     -67.0     5.000     -16.2   -10.584     -67.8   -35.000     261.0     5.000     -17.4     0.204      -3.7    0.33  0.80

alignment source: OPTM
            HHHHH--  ---EEEEEE--          HHHHHH------EE---HHHHHH--      --HHHHHHH----------
Query:   31 KRIVGKH--DPNVVLVDVRE----------PSEYSIVHIPASINVPYRSHPDAFA------LDPLEFEKQIGIPKPDSAK   92
Sbjct:    8 ADWLAEHIDDPEIQIIDARMASPGQEDRNVAQEYLNGHIPGAVFFDIEALSDHTSPLPHMLPRPETFAVAMRELGVNQDK   87
            HHHH-------EEEEE------------HHHHHHH------EE-------------------HHHHHHHHHH-------E

            EEEEEE-- -HHHHHHHHHHHH-----EEE----HHHHHH--    ------
Query:   93 ELIFYCAS-GKRGGEAQKVASSHGYSNTSLYPGSMNDWVSHG----GDKLDL  139
Sbjct:   88 HLIVYDEGNLFSAPRAWWMLRTFGVEKVSILGGGLAGWQRDDLLLEEGAVEL  139
            EEEE-------HHHHHHHHHH-----EEEE--HHHHHHH-------------

109 residues (78.42%) 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: 42.28% helical, 16.26% extended, 41.46% loops/other (query: 36.69% 12.23% 51.08%)

  SCOP classification: 


 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.
2J6P_A               not_found     23.23.23.23            NONE   -35.688     0       1  85.61%  20.17%   OPTM     -282.376     -154.960        1.438        0.529        0.551        0.728        0.876     14.560     -29.6    -1.460    -4.500      16.0     3.580    18.000     -99.5     0.270    -7.010     -12.8     0.960     1.390     -23.3     0.180    -3.020       3.4     0.330    -0.560     -13.9     1.440    -6.300     -19.4     8.340     7.980     -40.6   -30.000    -1.000     -56.0   -30.000     5.000     -76.0     1.080    38.000      13.0    15.630    96.000    -136.0    -0.720    -2.000     -12.0     2.640    10.000     -60.0     5.000       1.5   -14.080     -66.0     0.000 -9.3e+061     5.000       1.5    -1.108       0.3    0.18  0.81

alignment source: OPTM
            ------HHHHHHHHH----  -EEEEEE--HHHHHH------EE---HHHHHH----HHHHHHH----------EEEEEE
Query:   21 NIQSYSFEDMKRIVGKHDP--NVVLVDVREPSEYSIVHIPASINVPYRSHPDAFALDPLEFEKQIGIPKPDSAKELIFYC   98
Sbjct:    3 NYTYIKPEELVELLDNPDSLVKAAVIDCRD-SDRDCGFIVNSINMPT------ISCTEEMYEKLAKTLFEEKKELAVFHC   75
            --EEE-HHHHHHHHH-HHHHH-EEEEE--- -----------EE---      ----HHHHHHHHHHHHH----EEEEE-

            ---     HHHHHHHHHHHH-----  EEE----HHHHHH---- ----
Query:   99 ASG-----KRGGEAQKVASSHGYSN--TSLYPGSMNDWVSHGGD-KLDL  139
Sbjct:   76 AQSLVRAPKGANRFALAQKKLGYVLPAVYVLRGGWEAFYHMYGDVRPDL  124
            -----HHHHHHHHHHHHHHHH-----EEEEE--HHHHHHHHH-------

119 residues (85.61%) of query sequence aligned




DONE: Sat Aug 09 06:34:07 2008 EST

00%-10%	10%-20%	20%-30%	30%-40%	40%-50%	50%-60%	60%-70%	70%-80%	80%-90%	90%-100%
0	0	44	30	5	3	0	0	0	1