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 16 13:52:47 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 T0439
    --> 223 residues, sequence name: T0439
   Database: T:\CBSU\blastdb\20080108\nr


 -> 229 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          0         16        119         43         64          3          3          1   

5 dynamic database entries created: 2A5L_A 1YDG_A 1YRH_A 2ARK_A 2OHH_A 




RESULTS

secondary structure prediction shows 37.22% helical, 15.25% extended and 47.53% loops/other

homologs/domains used:
  0 query sequence T0439
all homologs found

total number of entries processed: 305

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    3B6I_A               not_found     108.108.108.62          NONE   -56.829     0       1  88.34%  59.09%   OPTM     -791.074     -672.830        9.997        0.702        0.848        0.988        0.993     70.850     -97.1    25.150   504.000    -542.0    46.710   623.500    -733.5     0.620    -1.620       3.4    -0.710     1.800     -43.0    12.900    78.400     -50.7    37.100    82.630    -115.6    16.640    65.760     -75.6    34.730    80.080    -137.3   -30.000    57.000    -140.0   -30.000    64.000    -165.0    30.850   661.000    -599.0    87.230   720.000    -763.0     2.320    37.000     -62.0     8.440    58.000    -136.0     5.000     -82.0    -7.284     -14.8     0.000 -9.3e+061     5.000     -83.0    -0.538     -60.7    0.18  0.90
2    1ZWK_A               c.23.5.8      139.55.33.7            NONE   -57.396     0       1  75.34%  37.95%   OPTM     -521.053     -574.190        6.451        0.660        0.693        0.854        0.984     53.750     -75.8    12.290   287.500    -259.5    23.180   295.500    -372.5     0.250     6.380      41.7     1.340     6.790     -34.6     3.800    28.280      45.7    18.650    44.770     -63.8     9.630    44.890      -6.8    20.040    46.480     -86.0   -30.000    46.000    -105.0   -30.000    34.000    -131.0    25.750   595.000    -488.0    73.840   562.000    -604.0    -0.730    24.000      31.0    -0.860    -5.000     -66.0     5.000     -63.1    -1.503     -20.7     0.000 -9.3e+061     5.000     -71.0     0.041     -36.7    0.15  0.85
3    c.23.5.8.2_A         c.23.5.8      139.55.33.7            NONE   -57.571     0       1  74.44%  37.88%   OPTM     -743.320     -573.240        6.175        0.649        0.618        0.828        0.981     42.710     -61.0    14.140   334.500    -308.0    27.670   302.000    -383.0    -1.020    -0.580      32.2    -0.100    -0.490     -29.8    12.520    43.470      18.9     8.290    22.100     -39.5    19.140    50.480     -24.6    14.310    27.160     -66.8   -30.000    40.000     -91.0   -30.000    21.000    -116.0    27.400   594.000    -495.0    61.360   532.000    -571.0    -0.140    17.000      56.0    -1.180   -12.000     -47.0     5.000     -55.5    -4.053     -19.7     0.000 -9.3e+061     5.000     -55.5     0.531     -29.0    0.18  0.97
4    2A5L_A               c.23.5.8      139.55.33.7            NONE   -57.571     0       1  74.44%  37.88%   OPTM     -743.320     -573.240        6.175        0.649        0.617        0.828        0.981     42.710     -61.0    14.140   334.500    -308.0    27.670   302.000    -383.0    -1.020    -0.580      32.2    -0.100    -0.490     -29.8    12.520    43.470      18.9     8.290    22.100     -39.5    19.140    50.480     -24.6    14.310    27.160     -66.8   -30.000    40.000     -91.0   -30.000    21.000    -116.0    27.400   594.000    -495.0    61.360   532.000    -571.0    -0.140    17.000      56.0    -1.180   -12.000     -47.0     5.000     -55.5    -4.053     -19.7     0.000 -9.3e+061     5.000     -55.5     0.531     -29.0    0.18  0.97
5    2ZKI_A               not_found     108.108.108.62          NONE   -57.573     0       1  87.00%  31.50%   OPTM     -644.425     -649.960        7.922        0.633        0.717        0.966        0.986     48.620     -72.7    11.880   277.000    -278.0    21.690   315.500    -396.0    -1.040    -6.860      20.2     0.240    -1.260     -59.0     4.750    31.490       8.7    12.550    48.200     -87.5     9.580    36.440     -38.6    27.020    50.620    -104.7   -30.000    42.000    -135.0   -30.000    51.000    -159.0    28.320   634.000    -598.0    76.640   674.000    -719.0     1.600    28.000     -44.0     5.720    43.000    -116.0     5.000     -63.4    -5.092     -20.1     0.000 -9.3e+061     5.000     -63.4    -0.310     -28.4    0.14  0.98



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

	1	2	3	4	5
1	0.00	4.50	3.51	3.51	1.85
2	4.50	0.00	4.57	4.57	4.76
3	3.51	4.57	0.00	0.00	4.09
4	3.51	4.57	0.00	0.00	4.09
5	1.85	4.76	4.09	4.09	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	49.74	74.24	74.24	100.00
2	49.74	100.00	49.74	49.74	49.23
3	74.24	49.74	100.00	100.00	50.00
4	74.24	49.74	100.00	100.00	50.00
5	100.00	49.23	50.00	50.00	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: 35.20% helical, 18.37% extended, 46.43% loops/other (query: 37.22% 15.25% 47.53%)

  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.
3B6I_A               not_found     108.108.108.62          NONE   -56.829     0       1  88.34%  59.09%   OPTM     -791.074     -672.830        9.997        0.702        0.848        0.988        0.993     70.850     -97.1    25.150   504.000    -542.0    46.710   623.500    -733.5     0.620    -1.620       3.4    -0.710     1.800     -43.0    12.900    78.400     -50.7    37.100    82.630    -115.6    16.640    65.760     -75.6    34.730    80.080    -137.3   -30.000    57.000    -140.0   -30.000    64.000    -165.0    30.850   661.000    -599.0    87.230   720.000    -763.0     2.320    37.000     -62.0     8.440    58.000    -136.0     5.000     -82.0    -7.284     -14.8     0.000 -9.3e+061     5.000     -83.0    -0.538     -60.7    0.18  0.90

alignment source: OPTM
 +++ there is a problem with all-atom model, click here for details
            -EEEEEEE-----HHHHHHHHHHHHHH- ---EEEEE------HHHHHH-------------HHHHHH--EEEEE--HH-
Query:   26 TKVLVLYYSSYGHIETMAYAVAEGVEST-GAEAVVKRVPELVPEEVAKSSHFKMDQPAPVATVDELAEYDAIIVGAGTRF  104
Sbjct:    2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGK-TQTAPVATPQELADYDAIIFGTPTRF   80
            -EEEEEE-----HHHHHHHHHHHHHH-----EEEEEE------HHHHHH---- ----------------EEEEEEEEE-

            ----HHHHHHHHHH--HH--------EEEEEEEE------HHHHHHHHHHHHHH---EEE--------------------
Query:  105 GTVASQMRNFWDQTGGLWFSGKLVGKVGSAFTSSATQHGGQESTILGFIPTFLHHGMAVVGLPYAFQGQMGVDEIKGGSP  184
Sbjct:   81 GNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGT-GGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTP  159
            -EE-HHHHHHH---HHHHHH------EEEEEEEE-- ---HHHHHHHHHHHHHH---EE---------------------

            EEEEEE----------HHHHHHHHHHHHHHHHHHHHH--
Query:  185 YGASTITDGDGSRQPSAIELDAARYQGAHVAKLAAKLSA  223
Sbjct:  160 YGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG  198
            ---EEE----------HHHHHHHHHHHHHHHHHHHHHH-

197 residues (88.34%) 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: 40.48% helical, 19.64% extended, 39.88% loops/other (query: 37.22% 15.25% 47.53%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Flavodoxin-like]

 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.
1ZWK_A               c.23.5.8      139.55.33.7            NONE   -57.396     0       1  75.34%  37.95%   OPTM     -521.053     -574.190        6.451        0.660        0.693        0.854        0.984     53.750     -75.8    12.290   287.500    -259.5    23.180   295.500    -372.5     0.250     6.380      41.7     1.340     6.790     -34.6     3.800    28.280      45.7    18.650    44.770     -63.8     9.630    44.890      -6.8    20.040    46.480     -86.0   -30.000    46.000    -105.0   -30.000    34.000    -131.0    25.750   595.000    -488.0    73.840   562.000    -604.0    -0.730    24.000      31.0    -0.860    -5.000     -66.0     5.000     -63.1    -1.503     -20.7     0.000 -9.3e+061     5.000     -71.0     0.041     -36.7    0.15  0.85

alignment source: OPTM
            -EEEEEEE-----HHHHHHHHHHHHHH----EEEEE------HHHHHH-------------HHHHHH--EEEEE--HH--
Query:   26 TKVLVLYYSSYGHIETMAYAVAEGVESTGAEAVVKRVPELVPEEVAKSSHFKMDQPAPVATVDELAEYDAIIVGAGTRFG  105
Sbjct:    4 PYILVLYYSRHGATAEMARQIARGVEQGGFEARVRTVPAV------------STEGALYATLEDLKNCAGLALGSPTRFG   71
            -EEEEEE-----HHHHHHHHHHHHHHH---EEEEE-----            ---------HHHHHH--EEEEEEE----

            ---HHHHHHHHHH--HH--------EEEEEEEE------HHHHHHHHHHHHHH---EEE--------------------E
Query:  106 TVASQMRNFWDQTGGLWFSGKLVGKVGSAFTSSATQHGGQESTILGFIPTFLHHGMAVVGLPYAFQGQMGVDEIKGGSPY  185
Sbjct:   72 NMASPLKYFLDGTSSLWLTGSLVGKPAAVFTSTASLHGGQETTQLSMLLPLLHHGMLVLGIP---------------TPY  136
            ---HHHHHHHH--HHHHH-------EEEEEEEE------HHHHHHHHHHHHHH---EE----               ---

            EEEEE----------HHHHHHHHHHHHHHHHHHHH
Query:  186 GASTITDGDGSRQPSAIELDAARYQGAHVAKLAAK  220
Sbjct:  137 GASHFAGADGKRSLDEHELTLCRALGKRLAETAGK  171
            EEEEE----------HHHHHHHHHHHHHHHHHHHH

168 residues (75.34%) 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: 36.75% helical, 14.46% extended, 48.80% loops/other (query: 37.22% 15.25% 47.53%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Flavodoxin-like]

 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.23.5.8.2_A         c.23.5.8      139.55.33.7            NONE   -57.571     0       1  74.44%  37.88%   OPTM     -743.320     -573.240        6.175        0.649        0.618        0.828        0.981     42.710     -61.0    14.140   334.500    -308.0    27.670   302.000    -383.0    -1.020    -0.580      32.2    -0.100    -0.490     -29.8    12.520    43.470      18.9     8.290    22.100     -39.5    19.140    50.480     -24.6    14.310    27.160     -66.8   -30.000    40.000     -91.0   -30.000    21.000    -116.0    27.400   594.000    -495.0    61.360   532.000    -571.0    -0.140    17.000      56.0    -1.180   -12.000     -47.0     5.000     -55.5    -4.053     -19.7     0.000 -9.3e+061     5.000     -55.5     0.531     -29.0    0.18  0.97

alignment source: OPTM
            -EEEEEEE-----HHHHHHHHHHHHHH----EEEEE------HHHHHH-------------HHHHHH--EEEEE--HH--
Query:   26 TKVLVLYYSSYGHIETMAYAVAEGVESTGAEAVVKRVPELVPEEVAKSSHFKMDQPAPVATVDELAEYDAIIVGAGTRFG  105
Sbjct:    4 PYILVLYYSRHGATAE-ARQIARGVEQGGFEARVRTVPAV--------------STALYATLEDLKNCAGLALGSPTRFG   68
            EEEEEE---------- HHHHHHHHH---EEEEE------              ------HHHHH---EEEEEEE-----

            ---HHHHHHHHHH--HH--------EEEEEEEE------HHHHHHHHHHHHHH---EEE--------------------E
Query:  106 TVASQMRNFWDQTGGLWFSGKLVGKVGSAFTSSATQHGGQESTILGFIPTFLHHGMAVVGLPYAFQGQMGVDEIKGGSPY  185
Sbjct:   69 N-ASPLKYFLDGTSSLWLTGSLVGKPAAVFTSTASLHGGQETTQLSLLP-LLHHGL-VLGIPY--------------TPY  131
            - HHHHHHHH--HHHHHH-------EEEEEE-------HHHHHH--HHH HH---- ------              ---

            EEEEE----------HHHHHHHHHHHHHHHHHHHHH--
Query:  186 GASTITDGDGSRQPSAIELDAARYQGAHVAKLAAKLSA  223
Sbjct:  132 GASHFAGADGKRSLDEHELTLCRALGKRLAETAGKLGS  169
            --------------HHHHHHHHHHHHHHHHHHHHHH-S

166 residues (74.44%) 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: 36.75% helical, 14.46% extended, 48.80% loops/other (query: 37.22% 15.25% 47.53%)

  SCOP classification:  [Alpha and beta proteins (a/b)]/[Flavodoxin-like]

 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.
2A5L_A               c.23.5.8      139.55.33.7            NONE   -57.571     0       1  74.44%  37.88%   OPTM     -743.320     -573.240        6.175        0.649        0.617        0.828        0.981     42.710     -61.0    14.140   334.500    -308.0    27.670   302.000    -383.0    -1.020    -0.580      32.2    -0.100    -0.490     -29.8    12.520    43.470      18.9     8.290    22.100     -39.5    19.140    50.480     -24.6    14.310    27.160     -66.8   -30.000    40.000     -91.0   -30.000    21.000    -116.0    27.400   594.000    -495.0    61.360   532.000    -571.0    -0.140    17.000      56.0    -1.180   -12.000     -47.0     5.000     -55.5    -4.053     -19.7     0.000 -9.3e+061     5.000     -55.5     0.531     -29.0    0.18  0.97

alignment source: OPTM
            -EEEEEEE-----HHHHHHHHHHHHHH----EEEEE------HHHHHH-------------HHHHHH--EEEEE--HH--
Query:   26 TKVLVLYYSSYGHIETMAYAVAEGVESTGAEAVVKRVPELVPEEVAKSSHFKMDQPAPVATVDELAEYDAIIVGAGTRFG  105
Sbjct:    4 PYILVLYYSRHGATAE-ARQIARGVEQGGFEARVRTVPAV--------------STALYATLEDLKNCAGLALGSPTRFG   68
            EEEEEE---------- HHHHHHHHH---EEEEE------              ------HHHHH---EEEEEEE-----

            ---HHHHHHHHHH--HH--------EEEEEEEE------HHHHHHHHHHHHHH---EEE--------------------E
Query:  106 TVASQMRNFWDQTGGLWFSGKLVGKVGSAFTSSATQHGGQESTILGFIPTFLHHGMAVVGLPYAFQGQMGVDEIKGGSPY  185
Sbjct:   69 N-ASPLKYFLDGTSSLWLTGSLVGKPAAVFTSTASLHGGQETTQLSLLP-LLHHGL-VLGIPY--------------TPY  131
            - HHHHHHHH--HHHHHH-------EEEEEE-------HHHHHH--HHH HH---- ------              ---

            EEEEE----------HHHHHHHHHHHHHHHHHHHHH--
Query:  186 GASTITDGDGSRQPSAIELDAARYQGAHVAKLAAKLSA  223
Sbjct:  132 GASHFAGADGKRSLDEHELTLCRALGKRLAETAGKLGS  169
            --------------HHHHHHHHHHHHHHHHHHHHHH-S

166 residues (74.44%) 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: 37.44% helical, 14.36% extended, 48.21% loops/other (query: 37.22% 15.25% 47.53%)

  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.
2ZKI_A               not_found     108.108.108.62          NONE   -57.573     0       1  87.00%  31.50%   OPTM     -644.425     -649.960        7.922        0.633        0.717        0.966        0.986     48.620     -72.7    11.880   277.000    -278.0    21.690   315.500    -396.0    -1.040    -6.860      20.2     0.240    -1.260     -59.0     4.750    31.490       8.7    12.550    48.200     -87.5     9.580    36.440     -38.6    27.020    50.620    -104.7   -30.000    42.000    -135.0   -30.000    51.000    -159.0    28.320   634.000    -598.0    76.640   674.000    -719.0     1.600    28.000     -44.0     5.720    43.000    -116.0     5.000     -63.4    -5.092     -20.1     0.000 -9.3e+061     5.000     -63.4    -0.310     -28.4    0.14  0.98

alignment source: OPTM
 +++ there is a problem with all-atom model, click here for details
            ---EEEEEEE-----HHHHHHHHHHHHHH----EEEEE------HHHHHH-------------HHHHHH--EEEEE--HH
Query:   24 RMTKVLVLYYSSYGHIETMAYAVAEGVESTGAEAVVKRVPELVPEEVAKSSHFKMDQPAPVATVDELAEYDAIIVGAGTR  103
Sbjct:    3 CKPNILVLFYG-YGSIVELAKEIGKGAEEAGAEVKIRRVRETLPPEFQSRIPFDKVKDIPEVTLDDMRWADGFAIGSPTR   81
            ---EEEEEE-- --HHHHHHHHHHHHHHHH--EEEEEE-------------------------HHHHHH--EEEEEEE--

            -----HHHHHHHHHH--HH--------EEEEEEEE------HHHHHHHHHHHHHH---EEE-------------------
Query:  104 FGTVASQMRNFWDQTGGLWFSGKLVGKVGSAFTSSATQHGGQESTILGFIPTFLHHGMAVVGLPYAFQGQMGVDEIKGGS  183
Sbjct:   82 YGNMAGGLKTFLDTTAILWKDNVLYGKPVTFFTEASTVHGGHETTILTMSTYAYHFGMIIVPIGYGIPELFQTT--TGGG  159
            -----HHHHHHHH--HHHHH-------EEEEEEE---------HHHHHH-HHHHHH--EE--------HHHH--  ----

            -EEEEEE----------HHHHHHHHHHHHHHHHHHHHH--
Query:  184 PYGASTITDGDGSRQPSAIELDAARYQGAHVAKLAAKLSA  223
Sbjct:  160 PYGATHLGS---KEELDEMERKIARFQGKRITEVAKAIKC  196
            ---------   -----HHHHHHHHHHHHHHHHHHHHHH-

194 residues (87.00%) of query sequence aligned




DONE: Sat Aug 16 21:14:33 2008 EST

00%-10%	10%-20%	20%-30%	30%-40%	40%-50%	50%-60%	60%-70%	70%-80%	80%-90%	90%-100%
0	0	0	16	119	43	64	3	3	1