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 22:25:34 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 T0412
    --> 178 residues, sequence name: T0412
   Database: T:\CBSU\blastdb\20080108\nr


 -> 1 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          1         25          4          1          0          0          0          0          1   

5 dynamic database entries created: 2O9A_A 1TF1_A 1TD5_A 2O99_A 1YSQ_A 




RESULTS

secondary structure prediction shows 39.89% helical, 19.10% extended and 41.01% loops/other

homologs/domains used:
  0 query sequence T0412
all homologs found

total number of entries processed: 186

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    1YSQ_A               not_found     62.62.62.16            NONE   -45.554     0       1  96.07%  19.30%   OPTM     -662.296     -403.750        4.591        0.645        0.654        0.937        0.975     29.230     -56.3     4.380    61.500    -125.0     5.680    54.000    -144.5     2.550     6.710     -31.1     1.150     0.460     -36.2     5.870    28.420     -34.0     8.880    20.150     -41.2    15.340    47.920     -87.9    25.960    44.900     -92.1   -30.000    60.000    -146.0   -30.000    45.000    -147.0    10.710   172.000    -146.0    16.910   115.000    -166.0    10.060    61.000    -116.0    12.570    66.000    -141.0     5.000     -20.4    -0.404     -30.7     0.000 -9.3e+061     5.000     -20.4    -0.229       1.6    0.35  0.94
2    2O9A_A               d.110.2.2     43.12.8.6              NONE   -45.620     0       1  92.13%  14.02%   OPTM     -621.396     -358.500        4.891        0.632        0.683        0.914        0.992     26.310     -58.2     5.300    68.500    -119.0     5.510    52.000    -146.0     2.530     9.190     -35.0     0.290     2.320     -52.2     5.330    21.480     -32.9     2.970     7.770     -47.0    15.700    33.640     -84.4    28.050    38.430     -92.5   -30.000    41.000    -146.0   -30.000    40.000    -151.0    12.290   195.000    -158.0    21.930   142.000    -189.0    12.070    85.000    -132.0    14.490    78.000    -148.0     5.000     -26.1    -3.431     -27.1     0.000 -9.3e+061     5.000     -26.1     5.000      -4.3    0.37  0.86
3    d.110.2.2.2_A        d.110.2.2     43.12.8.6              NONE   -45.621     0       1  92.13%  14.02%   OPTM     -621.396     -358.500        4.899        0.632        0.684        0.904        0.992     26.470     -58.3     5.060    67.000    -120.0     5.360    51.000    -145.0     2.250     8.490     -34.1     0.290     3.000     -52.2     5.630    23.160     -33.1     2.970     7.770     -47.0    15.700    37.320     -86.3    26.840    38.180     -92.3   -30.000    43.000    -148.0   -30.000    40.000    -151.0    12.850   197.000    -161.0    21.930   142.000    -188.0    12.630    90.000    -141.0    14.300    77.000    -151.0     5.000     -26.0    -3.733     -26.9     0.000 -9.3e+061     5.000     -26.0     5.000      -4.3    0.37  0.86
4    1TF1_A               d.110.2.2     43.12.8.6              NONE   -45.638     0       1  97.75%  14.94%   OPTM     -602.912     -386.520        4.899        0.662        0.771        0.968        0.996     27.070     -59.3     3.990    42.000    -111.5     4.490    50.000    -134.0     0.840     1.250     -25.3     1.010     5.500     -37.2     4.070    21.180     -25.1     5.140    11.160     -34.4    14.320    40.260     -85.0    26.270    36.490     -88.4   -30.000    42.000    -147.0   -30.000    38.000    -150.0    13.120   183.000    -163.0    23.030   141.000    -188.0    11.980   103.000    -152.0    15.050    91.000    -167.0     5.000     -26.0    -0.146     -30.9     0.000 -9.3e+061     5.000     -26.0    -0.114      -3.7    0.64  0.88
5    1MKM_A               d.110.2.2     43.12.8.6              NONE   -45.699     0       1  93.82%  14.37%   OPTM     -664.878     -402.390        4.025        0.627        0.739        0.677        0.996     26.590     -60.5     0.410    35.000      53.5     7.430    82.500    -163.5     0.430    -1.690     166.0     0.990     2.980     -38.3    -0.460    -0.210     193.1     7.410    19.570     -39.4     0.870   -12.000     107.2    27.950    35.700     -93.5   -30.000    16.000     -83.0   -30.000    35.000    -152.0     2.190    62.500     103.5    21.030   144.000    -188.0     3.490    40.000      -8.0    14.930    65.000    -158.0     5.000     -27.0    -0.241     -26.6   -95.000     380.0     5.000     -27.0     1.204      -4.7    0.37  0.68



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

	1	2	3	4	5
1	0.00	1.85	1.85	2.02	1.90
2	1.85	0.00	0.00	1.31	1.77
3	1.85	0.00	0.00	1.31	1.77
4	2.02	1.31	1.31	0.00	1.76
5	1.90	1.77	1.77	1.76	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	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



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: 40.56% helical, 21.67% extended, 37.78% loops/other (query: 39.89% 19.10% 41.01%)

  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.
1YSQ_A               not_found     62.62.62.16            NONE   -45.554     0       1  96.07%  19.30%   OPTM     -662.296     -403.750        4.591        0.645        0.654        0.937        0.975     29.230     -56.3     4.380    61.500    -125.0     5.680    54.000    -144.5     2.550     6.710     -31.1     1.150     0.460     -36.2     5.870    28.420     -34.0     8.880    20.150     -41.2    15.340    47.920     -87.9    25.960    44.900     -92.1   -30.000    60.000    -146.0   -30.000    45.000    -147.0    10.710   172.000    -146.0    16.910   115.000    -166.0    10.060    61.000    -116.0    12.570    66.000    -141.0     5.000     -20.4    -0.404     -30.7     0.000 -9.3e+061     5.000     -20.4    -0.229       1.6    0.35  0.94

alignment source: OPTM
            HHHHHHHHHHHHH----EEEEEE---EEEEEEEE-- ----EEE------------HHHHHHHH---HHHHHHHHHH---
Query:    8 RDILEVLQDIHMETGETVAIATKNDIYLQYIQIIES-VHALRFHVDENAIRPLTMSSNGWMLMSTMNDKAIDNTVRRANT   86
Sbjct:   10 HIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTTGMLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESHQH   89
            HHHHHHHHHHHHH--EEEEEEEE--EEEEEEEE---------------EEE----HHHHHHHH---HHHHHHHHHH----

            ----  ------HHHHHHHHHHHHH---EEE--------EEEEEEEE------EEEEEE---HHH--HH HHHHHHHHHH
Query:   87 ITQK--DGIRFEVDDMMARIRQVREQGYASAEHIPFVGGGTICVLLPMTIQGQPVTMGLGGALDRIKQN-YDRYLELLLN  163
Sbjct:   90 EIQPLTRNTITELPAMFDELAHIRESGAAMDREENELGVSCIAVPVFDIHGRVPYAVSISLSTSRLKQVGEKNLLKPLRE  169
            -----------HHHHHHHHHHHHHH--EEEE------EEEEEEEE--------EEEEEEEEHHHHHHH-HHHHHHHHHHH

            HHHHHHHH-------
Query:  164 GVQQLKKSDSFHQPI  178
Sbjct:  170 TAQAISNELGFTAIT  184
            HHHHHHHHHH-----

171 residues (96.07%) 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: 36.93% helical, 23.30% extended, 39.77% loops/other (query: 39.89% 19.10% 41.01%)

  SCOP classification:  [Alpha and beta proteins (a+b)]/[Profilin-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.
2O9A_A               d.110.2.2     43.12.8.6              NONE   -45.620     0       1  92.13%  14.02%   OPTM     -621.396     -358.500        4.891        0.632        0.683        0.914        0.992     26.310     -58.2     5.300    68.500    -119.0     5.510    52.000    -146.0     2.530     9.190     -35.0     0.290     2.320     -52.2     5.330    21.480     -32.9     2.970     7.770     -47.0    15.700    33.640     -84.4    28.050    38.430     -92.5   -30.000    41.000    -146.0   -30.000    40.000    -151.0    12.290   195.000    -158.0    21.930   142.000    -189.0    12.070    85.000    -132.0    14.490    78.000    -148.0     5.000     -26.1    -3.431     -27.1     0.000 -9.3e+061     5.000     -26.1     5.000      -4.3    0.37  0.86

alignment source: OPTM
            HHHHHHHHHHHHH----EEEEEE-  --EEEEEEEE------EEE------------HHHHHHHH---HHHHHHHHHH--
Query:    8 RDILEVLQDIHMETGETVAIATKN--DIYLQYIQIIESVHALRFHVDENAIRPLTMSSNGWMLMSTMNDKAIDNTVRRAN   85
Sbjct:    9 AIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKG   88
            HHHHHHHHHHHHH--EEEEEEEE----EEEEEEEE--------------EE-----HHHHHHH----HHHHHHHHH----

            -----------HHHHHHHHHHHHH---EEE--------EEEEEEEE------EEEEEE---HHH-- HHHHHHHHHHHHH
Query:   86 TITQKDGIRFEVDDMMARIRQVREQGYASAEHIPFVGGGTICVLLPMTIQGQPVTMGLGGALDRIK-QNYDRYLELLLNG  164
Sbjct:   89 LHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKA  168
            ----------HHHHHHHHHHHHHH--EEEE------EEEEEEEEE-----EEEEEEEEEE-----HHHHHHHHHHHHHHH

            HHHHHHH
Query:  165 VQQLKKS  171
Sbjct:  169 AKEVTLA  175
            HHHHHHH

164 residues (92.13%) 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: 36.93% helical, 23.30% extended, 39.77% loops/other (query: 39.89% 19.10% 41.01%)

  SCOP classification:  [Alpha and beta proteins (a+b)]/[Profilin-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.
d.110.2.2.2_A        d.110.2.2     43.12.8.6              NONE   -45.621     0       1  92.13%  14.02%   OPTM     -621.396     -358.500        4.899        0.632        0.684        0.904        0.992     26.470     -58.3     5.060    67.000    -120.0     5.360    51.000    -145.0     2.250     8.490     -34.1     0.290     3.000     -52.2     5.630    23.160     -33.1     2.970     7.770     -47.0    15.700    37.320     -86.3    26.840    38.180     -92.3   -30.000    43.000    -148.0   -30.000    40.000    -151.0    12.850   197.000    -161.0    21.930   142.000    -188.0    12.630    90.000    -141.0    14.300    77.000    -151.0     5.000     -26.0    -3.733     -26.9     0.000 -9.3e+061     5.000     -26.0     5.000      -4.3    0.37  0.86

alignment source: OPTM
            HHHHHHHHHHHHH----EEEEEE-  --EEEEEEEE------EEE------------HHHHHHHH---HHHHHHHHHH--
Query:    8 RDILEVLQDIHMETGETVAIATKN--DIYLQYIQIIESVHALRFHVDENAIRPLTMSSNGWMLMSTMNDKAIDNTVRRAN   85
Sbjct:    9 AIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKG   88
            HHHHHHHHHHHHH--EEEEEEEE----EEEEEEEE--------------EE-----HHHHHHH----HHHHHHHHH----

            -----------HHHHHHHHHHHHH---EEE--------EEEEEEEE------EEEEEE---HHH-- HHHHHHHHHHHHH
Query:   86 TITQKDGIRFEVDDMMARIRQVREQGYASAEHIPFVGGGTICVLLPMTIQGQPVTMGLGGALDRIK-QNYDRYLELLLNG  164
Sbjct:   89 LHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKA  168
            ----------HHHHHHHHHHHHHH--EEEE------EEEEEEEEE-----EEEEEEEEEE-----HHHHHHHHHHHHHHH

            HHHHHHH
Query:  165 VQQLKKS  171
Sbjct:  169 AKEVTLA  175
            HHHHHHH

164 residues (92.13%) 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: 37.70% helical, 22.95% extended, 39.34% loops/other (query: 39.89% 19.10% 41.01%)

  SCOP classification:  [Alpha and beta proteins (a+b)]/[Profilin-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.
1TF1_A               d.110.2.2     43.12.8.6              NONE   -45.638     0       1  97.75%  14.94%   OPTM     -602.912     -386.520        4.899        0.662        0.771        0.968        0.996     27.070     -59.3     3.990    42.000    -111.5     4.490    50.000    -134.0     0.840     1.250     -25.3     1.010     5.500     -37.2     4.070    21.180     -25.1     5.140    11.160     -34.4    14.320    40.260     -85.0    26.270    36.490     -88.4   -30.000    42.000    -147.0   -30.000    38.000    -150.0    13.120   183.000    -163.0    23.030   141.000    -188.0    11.980   103.000    -152.0    15.050    91.000    -167.0     5.000     -26.0    -0.146     -30.9     0.000 -9.3e+061     5.000     -26.0    -0.114      -3.7    0.64  0.88

alignment source: OPTM
            HHHH-HHHHHHHHHHHHH----EEEEEE---EEEEEEEE------EEE------------HHHHHHHH---HHHHHHHHH
Query:    3 ALFSSRDILEVLQDIHMETGETVAIATKNDIYLQYIQIIESVHALRFHVDENAIRPLTMSSNGWMLMSTMNDKAIDNTVR   82
Sbjct:   10 HMDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIIL   89
            HHHHHHHHHHHHHHHHHH--EEEEEEEE--EEEEEEEE--------------EEE----HHHHHHH----HHHHHHHHHH

            H-------------HHHHHHHHHHHHH---EEE--------EEEEEEEE------EEEEEE---HHH-- HHHHHHHHHH
Query:   83 RANTITQKDGIRFEVDDMMARIRQVREQGYASAEHIPFVGGGTICVLLPMTIQGQPVTMGLGGALDRIK-QNYDRYLELL  161
Sbjct:   90 QTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELV  169
            H------------HHHHHHHHHHHHHH--EEEE------EEEEEEEEE-----EEEEEEEEEE--------HHHHHHHHH

            HHHHHHHHHH-----
Query:  162 LNGVQQLKKSDSFHQ  176
Sbjct:  170 RDTARDISTALGLKA  184
            HHHHHHHHHH----A

174 residues (97.75%) 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: 26.53% helical, 16.33% extended, 57.14% loops/other (query: 39.89% 19.10% 41.01%)

  SCOP classification:  [Alpha and beta proteins (a+b)]/[Profilin-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.
1MKM_A               d.110.2.2     43.12.8.6              NONE   -45.699     0       1  93.82%  14.37%   OPTM     -664.878     -402.390        4.025        0.627        0.739        0.677        0.996     26.590     -60.5     0.410    35.000      53.5     7.430    82.500    -163.5     0.430    -1.690     166.0     0.990     2.980     -38.3    -0.460    -0.210     193.1     7.410    19.570     -39.4     0.870   -12.000     107.2    27.950    35.700     -93.5   -30.000    16.000     -83.0   -30.000    35.000    -152.0     2.190    62.500     103.5    21.030   144.000    -188.0     3.490    40.000      -8.0    14.930    65.000    -158.0     5.000     -27.0    -0.241     -26.6   -95.000     380.0     5.000     -27.0     1.204      -4.7    0.37  0.68

alignment source: OPTM
            HHHHHHHHHHHHH----EEEEEE---EEEEEEEE------EEE------------HHHHHHHH---HHHHHHHHHH----
Query:    8 RDILEVLQDIHMETGETVAIATKNDIYLQYIQIIESVHALRFHVDENAIRPLTMSSNGWMLMSTMNDKAIDNTVRRANTI   87
Sbjct:   79 DIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELK  158
            HHHHHHHHHHH-----EEEEEE---EEEEEEEE--------------EEE----HHHHHHHHH--HHHHHHHHHH-----

            ---------HHHHHHHHHHHHH---EEE--------EEEEEEEE------EEEEEE---HHH-- HHHHHHHHHHHHHHH
Query:   88 TQKDGIRFEVDDMMARIRQVREQGYASAEHIPFVGGGTICVLLPMTIQGQPVTMGLGGALDRIK-QNYDRYLELLLNGVQ  166
Sbjct:  159 PKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKIEEYSDVLKEKAE  238
            --------HHHHHHHHHHHHHH--EEEE------EEEEEEEEE-----EEEEEEEEEE-----HHHHHHHHHHHHHHHHH

            HHHHH---
Query:  167 QLKKSDSF  174
Sbjct:  239 EISRKLGY  246
            HHHH---Y

167 residues (93.82%) of query sequence aligned




DONE: Mon Aug 11 02:36:28 2008 EST

00%-10%	10%-20%	20%-30%	30%-40%	40%-50%	50%-60%	60%-70%	70%-80%	80%-90%	90%-100%
0	1	25	4	1	0	0	0	0	1