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 16:45:19 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 T0462
--> 154 residues, sequence name: T0462
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 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 2 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 5.91 | 17.03 | 6.82 | 13.73 |
2 | 5.91 | 0.00 | 16.89 | 6.41 | 13.13 |
3 | 17.03 | 16.89 | 0.00 | 17.54 | 15.03 |
4 | 6.82 | 6.41 | 17.54 | 0.00 | 13.22 |
5 | 13.73 | 13.13 | 15.03 | 13.22 | 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 | 36.96 | 19.57 | 20.29 | 29.10 |
2 | 36.96 | 100.00 | 16.78 | 23.78 | 20.00 |
3 | 19.57 | 16.78 | 100.00 | 15.38 | 25.19 |
4 | 20.29 | 23.78 | 15.38 | 100.00 | 17.78 |
5 | 29.10 | 20.00 | 25.19 | 17.78 | 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 | 42.75 | 57.97 | 61.19 |
2 | 100.00 | 100.00 | 32.87 | 96.50 | 56.30 |
3 | 42.75 | 32.87 | 100.00 | 26.57 | 41.48 |
4 | 57.97 | 96.50 | 26.57 | 100.00 | 45.93 |
5 | 61.19 | 56.30 | 41.48 | 45.93 | 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: 15.75% helical, 40.16% extended, 44.09% loops/other (query: 15.58% 36.36% 48.05%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase]
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.
1F9Z_A d.32.1.1 27.11.11.1 NONE -39.877 0 1 83.12% 8.70% OPTM -439.607 -339.120 1.157 0.547 0.490 0.883 0.950 6.300 -29.6 1.680 12.500 -37.0 0.860 -1.000 -84.0 -0.980 -3.340 5.0 -0.540 0.990 -24.4 0.710 3.950 15.2 0.350 2.650 -21.1 6.580 22.390 -20.7 5.940 7.920 -39.7 -30.000 36.000 -84.0 -30.000 28.000 -98.0 1.580 48.000 7.0 0.200 8.000 -45.0 1.740 19.000 6.0 0.830 5.000 -41.0 5.000 0.9 -0.055 -33.3 -43.000 207.0 5.000 0.5 0.279 1.2 0.11 0.92
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---EEEEEEE---HHHHHHHHH-------EEEEEEE------EEEEE---EEEE-HHHHHEEEEEE-------E------
Query: 8 PGVPARIKRLEVSGELHEKLVGMGFVPGEEIEIVQVAPLGDPIVCKIGNRNITLRKREADLIEVEVVGGELPLILADDGT 87
Sbjct: 1 MRLLHTMLRVGDLQRSIDFYTKVL---GMKLLRTSENPEYKYSLAFVGYG----PETEEAVIELTYNWGVDKYELGTAYG 73
----EEEEE---HHHHHHHHHH-- --EEEEEEEE----EEEEEEE-- ------EEEEEEE-------------
-EEEEE----HHHHHHHH-------EEEE-----EEEEEEEEE-----EEEEEEEE--
Query: 88 YEITKLNGGRRFLFRMKNLGIESGKKIQVSGRRYYIEGREIDLGYGEATKIWVRRVSD 145
Sbjct: 74 HIALSVDNAAEACEKIRQNGGNVTREAGPVKGG---TTVIAFVEDPDGYKIELIEEGN 128
-EEEE---HHHHHHHHHH---EEEEEEEE---- --EEEEEE-----EEEEEE---
128 residues (83.12%) 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: 15.38% helical, 37.06% extended, 47.55% loops/other (query: 15.58% 36.36% 48.05%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase]
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.32.1.10.1_A d.32.1.10 27.11.11.1 NONE -999.000 0 1 90.91% 7.43% OPTM -327.125 -244.720 1.395 0.503 0.290 0.918 0.943 9.870 -31.1 0.210 22.500 -25.5 -0.440 -9.000 -67.5 1.170 1.200 -13.9 -0.240 -0.700 -28.3 1.260 4.760 1.3 -0.960 0.050 -17.0 6.830 31.720 -42.8 9.370 9.480 -45.9 -30.000 46.000 -107.0 -30.000 38.000 -108.0 1.460 31.000 -2.0 -0.180 5.000 -41.0 5.540 31.000 -30.0 4.690 7.000 -51.0 5.000 0.2 -0.709 -30.2 0.000 -9.3e+061 5.000 0.2 1.230 0.4 0.19 0.98
alignment source: OPTM
----EEEEEEE---HHHHHHHHH-------EEEEEEE------EEEEE---EEEE-HHHHHEEEEEE-------E-----
Query: 7 VPGVPARIKRLEVSGELHEKLVGMGFVPGEEIEIVQVAPLGDPIVCKIGNRNITLRKREADLIEVEVVGGELPLILADDG 86
Sbjct: 4 IKGHHHISMVTKNANENNHFYKNV--LGLRRVKMTVNQDDPSMYHLFYGDKTGSPGT----ELSFFEIPLVGRTYRGTNA 77
----EEEEEE--HHHHHHHHH--- --EEEEEEEE--EEEEEEEEEE--------E EEEEE--------------
--EEEEE----HHHHHHHH-------EEEE-----EEEEEEEEE-----EEEEEEEE-----------
Query: 87 TYEITKLNGGRRFLFRMKNLGIESGKKIQVSGRRYYIEGREIDLGYGEATKIWVRRVSDAGEESHPQK 154
Sbjct: 78 ITRIGLLVPSEDSLHYWKERFEKFD--VKHSEMTTYANRPALQFEDAEGLRLVLLVSNGEKVEHWETW 143
--EEEEE--HHHHHHHHHHHHH--- EE---EEE--EEEEEEE-----EEEEEE-------------
140 residues (90.91%) 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: 13.79% helical, 51.03% extended, 35.17% loops/other (query: 15.58% 36.36% 48.05%)
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.
2FJT_A not_found 84.84.84.84 NONE -999.000 0 1 93.51% 13.70% OPTM -395.855 -235.990 1.173 0.524 0.290 0.645 0.766 6.470 -30.1 0.140 24.000 -12.5 1.860 20.500 -95.0 -0.320 -0.330 1.8 4.370 7.620 -37.5 -0.580 -7.190 25.3 4.090 5.360 -28.8 0.570 -13.120 1.8 10.980 11.240 -51.4 -30.000 3.000 -72.0 -30.000 16.000 -94.0 0.940 -1.000 16.0 2.430 13.000 -71.0 0.220 -4.000 -31.0 -1.290 -18.000 -48.0 5.000 0.1 -3.865 -24.5 0.000 -9.3e+061 5.000 0.1 5.000 -1.1 0.34 0.67
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
H----- -EEEEEEE---HHHHHHHHH- ------EEEEEEE------ EEEEE---EEEE-HHHHHEE
Query: 4 SRLVPG---VPARIKRLEVSGELHEKLVGM---GFVPGEEIEIVQVAPLGDP--------IVCKIGNRNITLRKREADLI 69
Sbjct: 2 SEHFVGKYEVELKFRVMDL-TTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLADQQISMVLREMNPSGI--------RL 72
-------EEEEEEEEE--- HHHHHHHHH---EEEEEEEEEEEEEEE-----------EEEEEEEE---- EE
EEEE-------E-------EEEEE----HHHHHHHH-------EEEE-----EEEEEEEEE---- -EEEEEEEE----
Query: 70 EVEVVGGELPLILADDGTYEITKLNGGRRFLFRMKNLGIESGKKIQVSGRRYYIEGREIDLGYGE--ATKIWVRRVSDAG 147
Sbjct: 73 WIVKGPGA---------EREASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDA 143
EEEE---- ---EEE---HHHHHHHHHH---EEEEEEEEEEEEEEE--EEEEEEEE---EEEEEEEEEE---
--
Query: 148 EE 149
Sbjct: 144 TE 145
--
144 residues (93.51%) 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: 18.38% helical, 33.82% extended, 47.79% loops/other (query: 15.58% 36.36% 48.05%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase]
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.
1TWU_A d.32.1.8 27.11.11.1 NONE -999.000 0 1 85.71% 9.79% OPTM -285.032 -286.260 1.158 0.483 0.439 0.884 0.921 8.680 -28.1 0.490 -33.500 -24.5 2.450 11.000 -91.0 1.360 2.810 -8.2 0.370 0.480 -24.3 1.430 4.240 7.5 -0.520 -0.570 -13.3 9.750 31.850 -38.8 9.470 18.350 -45.2 -30.000 47.000 -98.0 -30.000 35.000 -101.0 1.050 -4.000 19.0 -0.680 -3.000 -32.0 2.970 16.000 -21.0 2.440 10.000 -58.0 5.000 -0.3 3.650 -41.3 -64.000 237.0 5.000 -0.3 -0.523 1.4 0.13 0.89
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----EEEEEEE---HHHHHHHHH-------EEEEEEE------EEEEE---EEEE-HHHHHEEEEEE-------E-----
Query: 7 VPGVPARIKRLEVSGELHEKLVGMGFVPGEEIEIVQVAPLGDPIVCKIGNRNITLRKREADLIEVEVVGGELPLILADDG 86
Sbjct: 8 FQAAQIRIARPTGQLDEIIRFYEEGLCLKRIGEFSQHNGY-DGVMFGLPHADY--------HLEFTQYEGGSTAPVPHPD 78
----EEEEEE---HHHHHHHH-------EEEEEEEE--EE EEEEE-----EE EEEEEE-------------
--EEEEE----HHHHHHHH-------EEEE-----EEEEEEEEE-----EEEEEEEE------
Query: 87 TYEITKLNGGRRFLFRMKNLGIESGKKIQVSGRRYYIEGREIDLGYGEATKIWVRRVSDAGEE 149
Sbjct: 79 SLLVFYVPNAVELAAITSKLKHMGYQEVESENPYWSNGGVTIEDPDG--WRIVFMNSKGISGK 139
EEEEE---HHHHHHHHHHHHH----EE----HHHH--EEEEE----- EEEEE--------K
132 residues (85.71%) 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: 18.75% helical, 46.09% extended, 35.16% loops/other (query: 15.58% 36.36% 48.05%)
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.
2QH0_A not_found 84.84.84.84 NONE -999.000 0 1 83.77% 11.11% OPTM -293.884 -209.930 0.969 0.498 0.260 0.873 0.912 6.940 -24.6 0.760 5.000 -28.5 0.540 -7.000 -82.5 -2.310 -6.860 4.8 -0.450 1.580 -23.9 -0.360 -2.360 16.1 1.530 4.640 -20.1 7.140 27.730 -21.3 5.990 9.150 -39.0 -30.000 43.000 -75.0 -30.000 23.000 -89.0 1.960 37.000 -5.0 1.320 -23.000 -58.0 0.400 15.000 4.0 1.790 -1.000 -44.0 5.000 0.0 1.326 -47.7 0.000 -9.3e+061 5.000 0.1 -1.000 0.6 0.03 0.74
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----EEEEEEE---HHHHHHHHH-------EEEEEEE------EEEEE---EEEE-HHHHHEEEEEE------ -E
Query: 7 VPGVPARIKRLEVSGELHEKLVGMGFVPGEEIEIVQVAPLGDPIVCKIGNRNITLRKREADLIEVEVVGGELP-----LI 81
Sbjct: 2 SLKVHHIGYAVKNIDSALKKFKRLGYVEES--EVVRDEVRKVYIQFVINGGY---------RVELVAPDGEDSPINKTIK 70
--EEEEEEEE---HHHHHHHHHHH--EE-- --EEE----EEEEEEEE--E EEEEEEE------HHHH--
-------EEEEE----HHHHHHHH-------EEEE-----EEEEEEEEE-----EEEEEE
Query: 82 LADDGTYEITKLNGGRRFLFRMKNLGIESGKKIQVSGRRYYIEGREIDLGYGEATKIWVR 141
Sbjct: 71 KGSTPYHICYEVEDIQKSIEEMSQIGYTLFKKAEIAPAIDNRKVAFLFSTDIGLIELLEK 130
---EEEEEEEEE--HHHHHHHHH----EEEEEEEEE-----EEEEEEE------EEEEE-
129 residues (83.77%) of query sequence aligned
DONE: Sat Aug 16 21:24:52 2008 EST