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 00:36:29 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 T0406
--> 167 residues, sequence name: T0406
Database: T:\CBSU\blastdb\20080108\nr
-> 10 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 | 1 | 2 | 6 | 2 | 2 | 0 | 1 | 8 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 5.22 | 4.88 | 5.64 | 7.59 |
2 | 5.22 | 0.00 | 6.90 | 7.11 | 6.93 |
3 | 4.88 | 6.90 | 0.00 | 8.31 | 7.26 |
4 | 5.64 | 7.11 | 8.31 | 0.00 | 6.39 |
5 | 7.59 | 6.93 | 7.26 | 6.39 | 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 | 43.17 | 41.22 | 41.55 | 39.44 |
2 | 43.17 | 100.00 | 40.13 | 33.11 | 37.50 |
3 | 41.22 | 40.13 | 100.00 | 32.45 | 38.03 |
4 | 41.55 | 33.11 | 32.45 | 100.00 | 38.13 |
5 | 39.44 | 37.50 | 38.03 | 38.13 | 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 | 68.31 |
2 | 100.00 | 100.00 | 64.47 | 95.27 | 71.32 |
3 | 100.00 | 64.47 | 100.00 | 92.05 | 70.42 |
4 | 100.00 | 95.27 | 92.05 | 100.00 | 75.54 |
5 | 68.31 | 71.32 | 70.42 | 75.54 | 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: 57.34% helical, 0.00% extended, 42.66% loops/other (query: 60.48% 0.00% 39.52%)
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.
2HKV_A not_found 43.43.43.43 NONE -43.062 0 1 85.03% 14.86% OPTM -487.289 -167.870 2.671 0.581 0.545 0.937 0.956 12.300 -41.0 1.990 33.000 -45.5 3.820 41.500 -117.0 1.790 8.270 -5.5 2.420 -1.870 -36.0 3.410 11.150 6.8 6.920 9.820 -36.5 7.520 21.480 -39.7 12.860 13.000 -70.7 -30.000 17.000 -100.0 -30.000 5.000 -115.0 5.160 89.000 -54.0 8.500 59.000 -109.0 5.410 47.000 -57.0 7.930 20.000 -101.0 5.000 -6.7 -3.291 -23.4 0.000 -9.3e+061 5.000 -6.7 0.000 -0.1 0.80 0.94
alignment source: OPTM
---HHHHHHHHHHHHHHHHHHHHHH--HHH-----------HHHHHHHHHHHHHHHHH----------------HHHHHH
Query: 1 MYQTIEGFLQSWTYETESTQKMLDVLTDESLSQEIAPGHWTLGRVAWHIVTAIPVILSGTGLKFEGETKDYPVPTSAKTI 80
Sbjct: 3 GTDWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEAQFYAVPVLPEQL 82
--HHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHH-------------------H
HHHHHHHHHHHHHHHHHH--HHHHHHHHH-------HHHHHHHHHH------HHHHHHHHH-------
Query: 81 ADGYRKVNTAFVEALQSEWTDKDLTTINDFFGRPMPNSIFLMTLINHQNHHRGQMTVLMRQAGLTVPG 148
Sbjct: 83 VDRLDQSWQYYQDRLADFSTE------TTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIKL 144
HHHHHHHHHHHHHH------- ---------HHHHHHHHHHHHHHHHHHHHHHHHH-------
142 residues (85.03%) 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: 56.62% helical, 2.94% extended, 40.44% loops/other (query: 60.48% 0.00% 39.52%)
SCOP classification: [All alpha proteins]/[DinB/YfiT-like putative metalloenzymes]
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.
2F22_A a.213.1.2 156.2.2.1 NONE -43.526 0 1 80.24% 17.76% OPTM -357.022 -303.840 1.983 0.541 0.513 0.816 0.902 9.240 -32.0 4.800 94.000 -91.0 5.140 53.000 -137.0 1.250 7.320 8.1 0.520 1.800 -26.1 1.570 4.470 27.4 4.960 7.610 -29.2 2.140 3.420 -9.1 5.310 -2.730 -48.3 -30.000 6.000 -79.0 -30.000 -4.000 -94.0 4.960 96.000 -43.0 8.010 54.000 -98.0 3.970 17.000 -17.0 8.820 28.000 -89.0 5.000 -4.7 -3.017 -22.6 0.000 -9.3e+061 5.000 -4.7 1.362 -6.0 0.36 0.86
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHHHHHHHH--HHH-----------HHHHHHHHHHHHHHHHH-- --------------HHHHHHHHHHHH
Query: 10 QSWTYETESTQKMLDVLTDESLSQEIAPGHWTLGRVAWHIVTAIPVILSGT---GLKFEGETKDYPVPTSAKTIADGYRK 86
Sbjct: 6 NGVLYAANTN-ALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPGRLASDEHR-----LLDELER 79
HHHHHH--HH HHHH----------------HHHHHHHHHHHHHHHHHHHHH---------------H HHHHHH-
HHHHHHHHHHHH--HHHHHHHHH-------HHHHHHHHHH------HHHHHHHHH------------HHHHHHH-
Query: 87 VNTAFVEALQSEWTDKDLTTINDFFGRPMPNSIFLMTLINHQNHHRGQMTVLMRQAGLTVPGVYGPAKEEWATAG 161
Sbjct: 80 SE-ELVFEFKQTTFN-------SIKGENYLSIELLGTVIQHEGIHQGQYYVALKQSGINLP-------KQWVQDW 139
-H HHHHHHH----E E-----EE--HHHHHHHHHHHHHHHHHHHHHHH-----H HHHHH-W
134 residues (80.24%) 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: 54.66% helical, 2.48% extended, 42.86% loops/other (query: 60.48% 0.00% 39.52%)
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.
2QE9_A not_found 43.43.43.43 NONE -999.000 0 1 94.01% 15.57% OPTM -303.959 -122.270 2.014 0.478 0.213 0.817 0.836 10.210 -34.8 2.720 65.000 -85.5 3.110 34.500 -124.0 -0.810 -1.140 -13.7 0.660 1.440 -27.9 2.810 11.240 -10.3 3.700 8.470 -25.4 5.180 22.570 -55.8 9.160 11.840 -63.7 -30.000 29.000 -112.0 -30.000 3.000 -116.0 5.630 104.000 -64.0 7.470 61.000 -101.0 3.150 19.000 -41.0 4.560 4.000 -79.0 5.000 0.8 0.117 -45.6 0.000 -9.3e+061 5.000 0.7 5.000 -4.0 0.85 0.83
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---HHHHHHHHHHHHHHHHHHHHHH- -HHH-----------HHHHHHHHHHHHHHHHH- ---------------H
Query: 1 MYQTIEGFLQSWTYETESTQKMLDVL---TDESLSQEIAPGHWTLGRVAWHIVTAIPVILSG--TGLKFEGETKDYPVPT 75
Sbjct: 18 HHENLYFQGKFFEYNWQVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQT-- 95
---HHHH--HHHHHHHHHHHHHHH-----HHHHH---------HHHHHHHHHHHHHHHHHHHH--------------H
HHHHHHHHHHHHHHHHHHHHHH H--HHHHHHHHH-------HHHHHHHHHH------HHHHHHHHH--------
Query: 76 SAKTIADGYRKVNTAFVEALQS------EWTDKDLTTINDFFGRPMPNSIFLMTLINHQNHHRGQMTVLMRQAGLTVPGV 149
Sbjct: 96 -LNKVKSLSNTFRTEIIDVLQTHELVSVPW----------ETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLS-PVS 163
HHHHHHHHHHHHHHHHHH-----EE---- ---EE-HHHHHHHHHHHHHHHHHHHHHHHHH----- ---
----HHHHHHH-------
Query: 150 YGPAKEEWATAGMEAPKM 167
Sbjct: 164 ASFI-------GRTLKPI 174
---- -------
157 residues (94.01%) 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: 52.75% helical, 4.40% extended, 42.86% loops/other (query: 60.48% 0.00% 39.52%)
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.
2RD9_A not_found 43.43.43.43 NONE -999.000 0 1 90.42% 16.56% OPTM -308.129 -272.110 1.864 0.500 0.306 0.668 0.804 13.410 -35.2 2.120 61.000 -80.0 2.720 23.500 -117.0 2.210 2.270 -14.6 3.430 5.000 -31.3 2.720 9.370 -1.7 4.040 6.010 -22.1 3.950 10.110 -39.8 9.810 11.790 -63.1 -30.000 2.000 -100.0 -30.000 3.000 -115.0 2.690 63.000 -33.0 3.430 38.000 -83.0 4.340 29.000 -13.0 6.340 24.000 -85.0 5.000 0.1 -3.813 -22.4 0.000 -9.3e+061 5.000 0.1 0.114 -0.9 0.51 0.76
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHHHHHHHHHHH--HHH-----------HHHHHHHHHHHHHH HHH---- ---------
Query: 7 GFLQSWTYETESTQKMLDVLTDESLSQEIAPGHWTLGRVAWHIVTAIPV--------ILSGTGL-------KFEGETKDY 71
Sbjct: 36 EAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSN 115
HHHHHHHHHHHHHHHH----HHHH----------HHHHHHHHHHHHHH-HHHHHHHHHHH--------------------
---HHHHHHHHHHHHHHHHHHHHHHHH-- HHHHHHHHH----- --HHHHHHHHHH------HHHHHHHHH-----
Query: 72 PVPTSAKTIADGYRKVNTAFVEALQSEWT-DKDLTTINDFFGRP----MPNSIFLMTLINHQNHHRGQMTVLMRQAGLTV 146
Sbjct: 116 AVP--ISERFKEFQQLRKENLNTLRSLVQSEADLER---TGAHPAFGVVKVRELLSAWVVH----DLTHIAQIVRSAKRY 186
--H HHHHHHHHHHHHHHHHHHHHH---HHHH--E EEE---EEEEHHHHHHHHHHHH HHHHHHHHH------
-------HHHH
Query: 147 PGVYGPAKEEW 157
Sbjct: 187 DTDVGPWKEYL 197
------HHHH-
151 residues (90.42%) of query sequence aligned
--> hit 5 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 55.06% helical, 0.00% extended, 44.94% loops/other (query: 60.48% 0.00% 39.52%)
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.
2QNL_A not_found 43.43.43.43 NONE -999.000 0 1 85.03% 16.90% OPTM -212.539 -180.180 1.849 0.593 0.495 0.771 0.859 12.500 -35.9 3.110 49.000 -86.0 7.280 96.500 -164.5 1.320 7.210 -15.0 0.630 1.320 -31.0 1.960 12.810 -0.4 4.410 10.700 -28.5 3.200 14.630 -44.9 8.190 17.760 -64.9 -30.000 12.000 -104.0 -30.000 11.000 -112.0 3.310 43.500 -37.0 9.060 59.000 -97.0 1.070 -1.000 -44.0 5.670 32.000 -96.0 5.000 -5.0 -4.336 -23.2 0.000 -9.3e+061 5.000 -5.0 -0.194 -5.4 0.69 0.89
alignment source: OPTM
HHHHHHHHHHHHHHHHHHHHHH--HHH-----------HHHHHHHHHHHHHHH HH----- ----------
Query: 4 TIEGFLQSWTYETESTQKMLDVLTDESLSQEIAPGHWTLGRVAWHIVTAIPVI----LSGTGLK------FEGETKDYPV 73
Sbjct: 10 FVRLALDAWNTQSSRTDKLIQSLSNEALAVETAPGRNSGTYLLGHLTAVHDALPLLELGDTLYPQLAPVFIQNPDKSGLE 89
HHHHHHHHHHHHHHHHHHHHH--HHHHH---------HHHHHHHHHHHHH--------------HHHHH-----------
-HHHHHHHHHHHHHHHHHHHHHHH H- -HHHHHHHHH-------HHHHHHHHHH------HHHHHHHHH-
Query: 74 PTSAKTIADGYRKVNTAFVEALQS----EW-------TDKDLTTINDFFGRPMPNSIFLMTLINHQNHHRGQMTVLMRQA 142
Sbjct: 90 KPEINDLRLYWSLVQERLANQFNQLQPADWFNKHAAISREDFLKE-----PHRNKLSVLINRTNHA-------YHLGQLA 157
--HHHHHHHHHHHHHHHHHHHHH--------------HHHHHH-- ---HHHHHHHHHH--H HHHHH--
---
Query: 143 GLT 145
Sbjct: 158 YLK 160
---
142 residues (85.03%) of query sequence aligned
DONE: Sun Aug 10 05:26:57 2008 EST