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:Fri Aug 15 03:40:25 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 T0454
    --> 203 residues, sequence name: T0454
   Database: T:\CBSU\blastdb\20080108\nr


 -> 5 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         97         11          0          1          4          0          0          1   

5 dynamic database entries created: 1ZKG_A 2ID6_A 1Z77_A 2QTQ_A 2UXH_A 




RESULTS

secondary structure prediction shows 72.41% helical,  1.48% extended and 26.11% loops/other

homologs/domains used:
  0 query sequence T0454
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    1VI0_A               a.4.1.9       198.40.30.28           NONE   -52.543     0       1  86.21%  14.53%   OPTM     -766.159     -402.730        4.761        0.614        0.665        0.940        0.966     22.880     -48.5     4.100    86.500     -99.0     6.490    76.500    -154.5     2.930     5.500     -28.4     2.660     6.500     -50.2     7.100    20.100     -26.2     8.930    20.170     -50.8    11.920    28.850     -77.5    15.680    21.390     -94.5   -30.000    22.000    -139.0   -30.000    13.000    -147.0    13.930   231.000    -235.0    25.310   210.000    -271.0     6.370    43.000     -73.0    10.770    37.000    -119.0     5.000     -22.4    -2.176     -14.1   -16.000     242.0     5.000     -22.5     0.230      -0.9    0.51  0.84
2    1PB6_A               a.4.1.9       198.40.30.28           NONE   -52.555     0       1  96.55%  20.41%   OPTM     -891.509     -526.020        5.922        0.629        0.648        0.984        0.994     30.710     -62.9     9.280   164.000    -219.5     9.100   113.500    -225.0     3.580     4.480     -40.5     6.350    11.850     -57.4     8.960    34.010     -51.1    14.510    38.150     -69.8    13.110    41.350    -106.0    22.610    45.260    -116.6   -30.000    41.000    -169.0   -30.000    33.000    -173.0    17.820   283.000    -306.0    28.880   261.000    -331.0     6.580    52.000    -108.0     8.610    31.000    -125.0     5.000     -38.2    -2.057     -26.1    11.000     197.0     5.000     -38.4     0.362     -12.3    0.76  0.92
3    1T56_A               a.4.1.9       198.40.30.28           NONE   -52.565     0       1  95.07%  17.95%   OPTM     -899.034     -489.280        4.294        0.623        0.630        0.962        0.972     30.410     -62.2     2.760    70.000     -82.0     2.480    51.000    -123.5     0.510     6.720     -25.7     2.480     5.140     -51.6     3.930    30.550     -21.6     7.240    17.240     -53.4     8.180    39.400     -86.0    15.580    38.540    -110.7   -30.000    34.000    -164.0   -30.000    29.000    -173.0     8.470   171.000    -155.0    14.650   132.000    -198.0     5.870    66.000     -89.0     9.380    41.000    -120.0     5.000     -14.0    -2.243     -20.8    55.000     160.0     5.000     -13.7     0.959       1.5    0.73  0.87
4    2HYJ_A               not_found     84.84.84.38            NONE   -52.594     0       1  92.61%  18.09%   OPTM     -928.970     -554.330        4.501        0.673        0.718        0.952        0.977     24.270     -57.3     5.680    96.500    -136.5     6.060    68.500    -154.5     3.370     8.660     -36.5     2.300     8.740     -47.5     7.210    30.850     -34.8     7.600    17.730     -44.8    10.080    29.410     -83.7    15.100    32.720     -98.4   -30.000    28.000    -150.0   -30.000    29.000    -160.0     9.820   164.000    -173.0    16.080   133.000    -193.0     6.500    57.000     -97.0    10.760    48.000    -137.0     5.000     -13.2    -1.372     -20.7     0.000 -9.3e+061     5.000      -6.7    -0.237       0.7    0.86  0.96
5    2EH3_A               not_found     84.84.84.38            NONE   -52.597     0       1  82.76%  15.68%   OPTM     -914.776     -409.800        4.249        0.575        0.633        0.879        0.955     18.260     -48.5     5.680   104.500     -78.5     7.760    68.000    -136.5     3.770     7.230     -18.3     3.120     3.660     -48.0     6.540    16.080      -9.9     6.490    14.390     -45.9    10.900    21.330     -57.5     7.780     8.920     -79.4   -30.000    11.000    -122.0   -30.000     9.000    -134.0    12.540   196.000    -169.0    24.270   153.000    -214.0     5.540    49.000     -64.0     8.960    40.000    -121.0     5.000     -18.3    -1.417     -22.6     0.000 -9.3e+061     5.000     -18.7    -0.409      -8.7    0.55  0.89



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

	1	2	3	4	5
1	0.00	4.78	4.29	4.18	4.90
2	4.78	0.00	4.95	4.69	5.54
3	4.29	4.95	0.00	4.55	5.30
4	4.18	4.69	4.55	0.00	5.66
5	4.90	5.54	5.30	5.66	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	55.87	55.87	41.34	43.02
2	55.87	100.00	45.13	43.85	43.24
3	55.87	45.13	100.00	39.25	55.14
4	41.34	43.85	39.25	100.00	40.98
5	43.02	43.24	55.14	40.98	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: 66.11% helical,  0.00% extended, 33.89% loops/other (query: 72.41%  1.48% 26.11%)

  SCOP classification:  [All alpha proteins]/[DNA/RNA-binding 3-helical bundle]

 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.
1VI0_A               a.4.1.9       198.40.30.28           NONE   -52.543     0       1  86.21%  14.53%   OPTM     -766.159     -402.730        4.761        0.614        0.665        0.940        0.966     22.880     -48.5     4.100    86.500     -99.0     6.490    76.500    -154.5     2.930     5.500     -28.4     2.660     6.500     -50.2     7.100    20.100     -26.2     8.930    20.170     -50.8    11.920    28.850     -77.5    15.680    21.390     -94.5   -30.000    22.000    -139.0   -30.000    13.000    -147.0    13.930   231.000    -235.0    25.310   210.000    -271.0     6.370    43.000     -73.0    10.770    37.000    -119.0     5.000     -22.4    -2.176     -14.1   -16.000     242.0     5.000     -22.5     0.230      -0.9    0.51  0.84

alignment source: OPTM
 +++ there is a problem with all-atom model, click here for details
            HHHHHHHHHHH-------HHHHHHH-----HHEEE----HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Query:   10 LMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTI   89
Sbjct:   10 IIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFKEKGQFIEREEDIKEKA-TAKEKLALVISKHF   88
            HHHHHHHHHHH------HHHHHHHH---HHHHHHH---HHHHHHHHHHH--HHHH---------- HHHHHHHHHHHHHH

            HHHH--HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHH-
Query:   90 QRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATE  169
Sbjct:   89 SLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEGIQSGEIKEGLDV---RLARQIFGTIDETVTTWVN  165
            HHH--HHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HH   HHH--HHHHHHHHHHH---

            -------HHHHHHHHHHHH
Query:  170 GLTSHSPDQDEELIRQYVA  188
Sbjct:  166 DQKYDLVALSNSVLELLVS  184
            --------HHHHHHHHHH-

175 residues (86.21%) 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: 75.13% helical,  0.00% extended, 24.87% loops/other (query: 72.41%  1.48% 26.11%)

  SCOP classification:  [All alpha proteins]/[DNA/RNA-binding 3-helical bundle]

 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.
1PB6_A               a.4.1.9       198.40.30.28           NONE   -52.555     0       1  96.55%  20.41%   OPTM     -891.509     -526.020        5.922        0.629        0.648        0.984        0.994     30.710     -62.9     9.280   164.000    -219.5     9.100   113.500    -225.0     3.580     4.480     -40.5     6.350    11.850     -57.4     8.960    34.010     -51.1    14.510    38.150     -69.8    13.110    41.350    -106.0    22.610    45.260    -116.6   -30.000    41.000    -169.0   -30.000    33.000    -173.0    17.820   283.000    -306.0    28.880   261.000    -331.0     6.580    52.000    -108.0     8.610    31.000    -125.0     5.000     -38.2    -2.057     -26.1    11.000     197.0     5.000     -38.4     0.362     -12.3    0.76  0.92

alignment source: OPTM
            --HHHHHHHHHHHHHHHHH-------HHHHHHH-----HHEEE----HHHHHHHHHHHHHHHHHHHHHHHH----HHHHH
Query:    2 TRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVM   81
Sbjct:   14 AVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAI   93
            -HHHHHHHHHHHHHHHHHHH------HHHHHHH----HHHHHHH---HHHHHHHHHHHHHHHH-HHHHH------HHHHH

            HHHHHHHHHHHH--HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHH
Query:   82 TAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYF  161
Sbjct:   94 KEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYA  173
            HHHHHHHHHHHHH-HHHHHHHHHHHH------HHHHH-HHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHH

            HHHHHHH-  -------HHHHHHHHHHHHHHHHHH---
Query:  162 FLSTLATE--GLTSHSPDQDEELIRQYVAIFTRGIMAD  197
Sbjct:  174 DFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR  211
            H-HHHHHHHH------HHHHHHHHHHHHHHHH------

196 residues (96.55%) 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: 77.60% helical,  0.00% extended, 22.40% loops/other (query: 72.41%  1.48% 26.11%)

  SCOP classification:  [All alpha proteins]/[DNA/RNA-binding 3-helical bundle]

 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.
1T56_A               a.4.1.9       198.40.30.28           NONE   -52.565     0       1  95.07%  17.95%   OPTM     -899.034     -489.280        4.294        0.623        0.630        0.962        0.972     30.410     -62.2     2.760    70.000     -82.0     2.480    51.000    -123.5     0.510     6.720     -25.7     2.480     5.140     -51.6     3.930    30.550     -21.6     7.240    17.240     -53.4     8.180    39.400     -86.0    15.580    38.540    -110.7   -30.000    34.000    -164.0   -30.000    29.000    -173.0     8.470   171.000    -155.0    14.650   132.000    -198.0     5.870    66.000     -89.0     9.380    41.000    -120.0     5.000     -14.0    -2.243     -20.8    55.000     160.0     5.000     -13.7     0.959       1.5    0.73  0.87

alignment source: OPTM
 +++ there is a problem with all-atom model, click here for details
            -HHHHHHHHHHHHHHHHH-------HHHHHHH-----HHEEE----HHHHHHHHHHHHHHHHH HHHHHHH---  -HHH
Query:    3 RADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFG-QLDDIRGQAG--DPLA   79
Sbjct:   22 GDDRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAENPADTDREN  101
            -HHHHHHHHHHHHHHHHH-------HHHHHHHH---HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH------HHH

            HHHHHHHHHHHHHH--HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHH
Query:   80 VMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVN  159
Sbjct:  102 MWRTGINVFFETFGSH-KAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNE  180
            HHHHHHHHHHHHHH-- HHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHH

            HHHHHHHHH--------HHHHHHHHHHHHHHHHHH---
Query:  160 YFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMAD  197
Sbjct:  181 RTLFASFAGEQPSVP----EARVLDTLVHIWVTSIYGE  214
            HHHHHHHH-------    HHHHHHHHHHHHHHHHH--

193 residues (95.07%) 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: 72.92% helical,  0.00% extended, 27.08% loops/other (query: 72.41%  1.48% 26.11%)

  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.
2HYJ_A               not_found     84.84.84.38            NONE   -52.594     0       1  92.61%  18.09%   OPTM     -928.970     -554.330        4.501        0.673        0.718        0.952        0.977     24.270     -57.3     5.680    96.500    -136.5     6.060    68.500    -154.5     3.370     8.660     -36.5     2.300     8.740     -47.5     7.210    30.850     -34.8     7.600    17.730     -44.8    10.080    29.410     -83.7    15.100    32.720     -98.4   -30.000    28.000    -150.0   -30.000    29.000    -160.0     9.820   164.000    -173.0    16.080   133.000    -193.0     6.500    57.000     -97.0    10.760    48.000    -137.0     5.000     -13.2    -1.372     -20.7     0.000 -9.3e+061     5.000      -6.7    -0.237       0.7    0.86  0.96

alignment source: OPTM
            ---HHHHHHHHHHHHHHHHH-------HHHHHHH-----HHEEE----HHHHHHHHHHHHHHHHH HHHHHHH----HHH
Query:    1 MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFG-QLDDIRGQAGDPLA   79
Sbjct:    8 AEAQATRGRILGRAAEIASEEGLDGITIGRLAEELEMSKSGVHKHFGTKETLQISTLDKAFVDFWHRVVEPALAEPPGLR   87
            --HHHHHHHHHHHHHHHHHHH------HHHHHHHH---HHHHH-----HHHHHHHHHHHHHHHHHHHH----------HH

            HHHHHHHHHHHHHH--    HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHH
Query:   80 VMTAYLRWTIQRHRNN----PQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALA  155
Sbjct:   88 RLRAVCANSVGYLEEPLLPGGCLLTAALSEYDGRPGRVRDAVAEVWSRWREQLRADLTAAVDKGELPAGFDVEQALFEIV  167
            HHHHHHHHHHHHHH--------HHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHH

            HHHHHHHHHHHHH--------HHHHHHHHHHHH
Query:  156 GMVNYFFLSTLATEGLTSHSPDQDEELIRQYVA  188
Sbjct:  168 AAGLALNAAMQLQHDRT--AADRARRAIERALA  198
            HHHHHHHHHHHHH----  HHHHHHHHHHHHHH

188 residues (92.61%) 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: 76.33% helical,  0.00% extended, 23.67% loops/other (query: 72.41%  1.48% 26.11%)

  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.
2EH3_A               not_found     84.84.84.38            NONE   -52.597     0       1  82.76%  15.68%   OPTM     -914.776     -409.800        4.249        0.575        0.633        0.879        0.955     18.260     -48.5     5.680   104.500     -78.5     7.760    68.000    -136.5     3.770     7.230     -18.3     3.120     3.660     -48.0     6.540    16.080      -9.9     6.490    14.390     -45.9    10.900    21.330     -57.5     7.780     8.920     -79.4   -30.000    11.000    -122.0   -30.000     9.000    -134.0    12.540   196.000    -169.0    24.270   153.000    -214.0     5.540    49.000     -64.0     8.960    40.000    -121.0     5.000     -18.3    -1.417     -22.6     0.000 -9.3e+061     5.000     -18.7    -0.409      -8.7    0.55  0.89

alignment source: OPTM
 +++ there is a problem with all-atom model, click here for details
            HHHHHHHHHHHHHHH-------HHHHHHH-----HHEEE----HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHH
Query:    6 CRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYL   85
Sbjct:    3 TKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFKSKEELITEIIERTHKKIISLFEENKEK-TPEELLEF--   79
            HHHHHHHHHHHHHHH------HHHHHHHH---HHHHHHH---HHHHHHHHHHHHHHHHHHHHHH----- HHHHH--H  

            HHHHHHHH--HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHH
Query:   86 RWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLST  165
Sbjct:   80 ---LEVLYREKKVVYIFLFDLLCSEK-FRNIYFEKIEDAKRRFEKFLEKHFPSK----------AEILSEIILGFLRQLI  145
               HHHHH-HHHHHHHHHH------- HHHHHHHHHHHHHHHHHHHHHH----H          HHHHHHHHHHHHHHHH

            HHH--------HHHHHHHHHHHHHH
Query:  166 LATEGLTSHSPDQDEELIRQYVAIF  190
Sbjct:  146 LHYVIKEERELPFLKEKLREGLKLI  170
            HH-------HHHHHHHHHHHHHHH-

168 residues (82.76%) of query sequence aligned




DONE: Fri Aug 15 09:47:11 2008 EST

00%-10%	10%-20%	20%-30%	30%-40%	40%-50%	50%-60%	60%-70%	70%-80%	80%-90%	90%-100%
0	0	97	11	0	1	4	0	0	1