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:Mon Aug 11 18:09:49 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 T0425
--> 181 residues, sequence name: T0425
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 | 8 | 0 | 0 | 1 | 0 | 0 | 0 | 7 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 13.69 | 15.21 | 18.96 | 17.74 |
2 | 13.69 | 0.00 | 14.11 | 17.23 | 16.97 |
3 | 15.21 | 14.11 | 0.00 | 19.20 | 17.80 |
4 | 18.96 | 17.23 | 19.20 | 0.00 | 16.03 |
5 | 17.74 | 16.97 | 17.80 | 16.03 | 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 | 30.99 | 13.14 | 17.28 | 16.87 |
2 | 30.99 | 100.00 | 15.20 | 19.63 | 12.88 |
3 | 13.14 | 15.20 | 100.00 | 13.58 | 13.25 |
4 | 17.28 | 19.63 | 13.58 | 100.00 | 11.04 |
5 | 16.87 | 12.88 | 13.25 | 11.04 | 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 | 37.43 | 39.43 | 29.01 | 24.10 |
2 | 37.43 | 100.00 | 36.26 | 31.29 | 20.25 |
3 | 39.43 | 36.26 | 100.00 | 19.14 | 21.08 |
4 | 29.01 | 31.29 | 19.14 | 100.00 | 22.08 |
5 | 24.10 | 20.25 | 21.08 | 22.08 | 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: 40.68% helical, 22.03% extended, 37.29% loops/other (query: 38.12% 19.34% 42.54%)
SCOP classification: [Alpha and beta proteins (a/b)]/[Phosphorylase/hydrolase-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.
1JWQ_A c.56.5.6 69.1.1.1 NONE -46.190 0 1 96.69% 24.00% OPTM -596.380 -419.510 5.150 0.606 0.851 0.936 0.957 33.150 -60.0 7.960 171.500 -168.0 9.990 108.000 -175.0 1.040 0.690 -16.6 0.310 4.880 -41.9 2.480 14.540 -7.1 4.630 17.490 -41.3 11.590 66.750 -68.1 22.420 39.660 -84.1 -30.000 88.000 -145.0 -30.000 57.000 -145.0 14.570 263.000 -212.0 25.270 177.000 -219.0 12.960 105.000 -177.0 16.710 100.000 -183.0 5.000 -13.4 0.030 -24.0 21.000 166.0 5.000 -13.4 0.591 -7.0 0.74 0.89
alignment source: OPTM
-EEEEE--------------- --HHHHHHHHHHHHHHHHHH----EEEEE--------HHHHHHHH- ---EEEEEE
Query: 2 SKIICLTAGHSNTDPGAVNGS--DREADLAQDMRNIVASILRNDYGLTVKTDGTGKGNMPLRDAVKLIR--GSDVAIEFH 77
Sbjct: 1 MKVVVIDAGHGAKDSGAVGISRKNYEKTFNLAMALKVESILKQNPKLEVVLTRSDDTFLELKQRVKVAENLKANVFVSIH 80
-EEEEEEE-----------------HHHHHHHHHHHHHHHHH----EEEEE---------HHHHHHHHHH----EEEEEE
----------EEEEEE--- -HHHHHHHHHHHHHH-------------------EEEEEE---EEEEEEE----HHHHHH
Query: 78 TNAAANKTATGIEALSTPK-NKRWCQVLGKAVAKKTGWKLRGEDGFKPDNAGQHSRLAYAQAGGIVFEPFFISNDTDLAL 156
Sbjct: 81 ANSSGSSASNGTETYYQRSASKAFANVMHKYFAPATGLTDRGIRYGNFHVIRET------TMPAVLLEVGYLSNAKEEAT 154
EE---------EEEEE-----HHHHHHHHHHHHHHH---EEEEEE---HHHH-- ---EEEEEEEE---HHHHHH
H--H HHHHHHHHHHHHHHHH
Query: 157 FKTT--KWGICRAIADAIAMEL 176
Sbjct: 155 LFDEDFQNRVAQGIADGITEYL 176
H--HHHHHHHHHHHHHHHHHHH
175 residues (96.69%) 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: 46.36% helical, 19.21% extended, 34.44% loops/other (query: 38.12% 19.34% 42.54%)
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.23.5.1.3_A c.23.5.1 69.22.7.4 NONE -47.591 0 1 82.32% 12.21% OPTM -395.816 -177.670 0.806 0.325 0.574 0.706 0.792 8.610 -34.8 1.710 41.500 -13.5 -0.220 -11.000 -65.0 1.180 4.900 2.1 -0.700 -3.340 -28.2 2.160 12.710 20.9 1.120 0.090 -24.6 5.060 11.160 -6.0 3.200 0.450 -31.1 -30.000 8.000 -73.0 -30.000 -4.000 -85.0 2.780 107.000 -4.0 0.760 10.000 -47.0 0.050 11.000 -26.0 -0.240 -12.000 -68.0 5.000 -0.7 -2.178 -32.3 0.000 -9.3e+061 5.000 -0.7 0.519 1.7 0.86 0.83
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--EEEEE-----------------HHHHHHHHHHHHHHHHHH----EEEEE--------HHHHHHHH----EEEEEE---
Query: 1 MSKIICLTAGHSNTDPGAVNGSDREADLAQDMRNIVASILRNDYGLTVKTDGTGKGNMPLRDAVKLIRGSDVAIEFHTNA 80
Sbjct: 252 TNKVVIFYDSMWH--------------STEKMARVLAESFRDE-GCTVKLMWCKA--CHHSQIMSEISDAGAVIVGSPTH 314
-EEEEEE-----H HHHHHHHHHHHHHH-- -EEEEEE---- -HHHHHHHHH---EEEEE-----
-------EEEEEE----HHHHHHHHHHHHHH-------------------EEEEEE---EEEE
Query: 81 -----------------AANKTATGIEALSTPKNKRWCQVLGKAVAKKTGWKLRGEDGFKPDNAGQHSRLAYAQAGGIVF 143
Sbjct: 315 NNGILPYVAGTLQYIKGLRPQNKIGGAFGSFGWSGESTKVLAEWLTGM-GFDMPATP------------VKVKNV----- 376
----HHHHHHHHHHHH------EEEEEEEE----HHHHHHHHHHHH-- -------E EEE---
EEE----HHHHHHH--HHHHHHHHHHHHH
Query: 144 EPFFISNDTDLALFKTTKWGICRAIADAI 172
Sbjct: 377 -----PTHADYEQLKTMAQTIARALKAKL 400
-HHHHHHHHHHHHHHHHHHHHHH-
149 residues (82.32%) 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: 34.21% helical, 18.42% extended, 47.37% loops/other (query: 38.12% 19.34% 42.54%)
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.
1J2Y_A c.23.13.1 69.22.3.3 NONE -999.000 0 1 83.43% 11.11% OPTM -333.702 -216.600 1.204 0.372 0.132 0.670 0.757 3.780 -30.2 1.510 43.500 -37.0 0.770 10.500 -79.5 0.740 2.440 2.3 -0.550 0.490 -28.6 1.780 7.090 18.8 -0.820 -0.610 -23.4 8.170 38.810 -26.0 5.850 12.690 -40.1 -30.000 49.000 -104.0 -30.000 22.000 -106.0 3.840 72.000 -9.0 0.510 0.000 -43.0 2.110 36.000 -29.0 2.840 0.000 -77.0 5.000 -0.2 -3.349 -32.6 0.000 233.0 5.000 -0.2 -0.137 -0.1 0.81 0.90
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-EEEEE------ -----------HHHHHHHHHHHHHHHHHH- ---EEEEE--------HHHHHHHH----EEEEE
Query: 2 SKIICLTAGHSN----TDPGAVNGSDREADLAQDMRNIVASILRND-YGLTVKTDGTGKGNMPLRDAVKLIRGSDVAIEF 76
Sbjct: 1 MKILVIQGPNLNMLGHRDPRLYGMVTLD-----QIHEIMQTFVKQGNLDVELEFFQTN-FEGEIIDKIQESVGSDYEGII 74
-EEEEEE--------------------- HHHHHHHHHHHH-----EEEEEE-- -HHHHHHHHHH-----EEEEE
E----------EEEEEE----HHHHHHHHHHHHHH-- --------- --------EEEEEE---EEEEEEE--
Query: 77 HTNAAANKTATGIEALSTPKNKRWCQVLGKAVAKKTG-------WKLRGEDGF-KPDNAGQHSRLAYAQAGGIVFEPFFI 148
Sbjct: 75 INPGAFSHTS---------------IAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFG--------- 130
EE-------- HHHHHHHHH----EEEEE---------------------EEEE---
--HHHHHHH--HHHHHHHHHHHHHHHHHHHHHH
Query: 149 SNDTDLALFKTTKWGICRAIADAIAMELGAAKV 181
Sbjct: 131 ------------PLGYNMALMAMVNILAEMKAF 151
-HHHHHHHHHHHHHHHHHHHH
151 residues (83.43%) 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: 29.56% helical, 36.48% extended, 33.96% loops/other (query: 38.12% 19.34% 42.54%)
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.
2NYI_A not_found 61.61.61.15 NONE -999.000 0 1 87.29% 12.88% OPTM -215.423 -116.550 1.122 0.465 0.144 0.530 0.546 5.770 -28.4 1.340 40.500 -57.0 1.210 32.000 -100.0 1.380 8.390 -14.6 1.130 6.040 -28.2 2.470 15.100 -0.7 -0.690 0.070 -13.8 7.270 25.720 -34.7 12.970 13.640 -47.4 -30.000 30.000 -85.0 -30.000 24.000 -98.0 2.950 79.000 -38.0 1.130 20.000 -58.0 3.080 31.000 4.0 3.780 8.000 -37.0 5.000 1.0 1.171 -31.8 0.000 -9.3e+061 5.000 1.1 5.000 1.4 0.69 0.49
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--EEEEE-----------------HHHHHHHHHHHHHHHHHH----EEEEE----- --- HHHHHHH
Query: 1 MSKIICLTAGHSNTDPGAVNGSDREADLAQDMRNIVASILRNDYGLTVKTDGTGKG----------NMP----LRDAVKL 66
Sbjct: 2 ETQSFVVSVAGSDRVG---------------IVHDFSWALKNIS-ANVESSRACLGGDFAIVLVSLNAKDGKLIQSALES 65
--EEEEEEEEEE---- HHHHHHHHHHH-- -EEEEE--EE--EE--EEEEE-----HHHHHHHHH
H- ---EEEEEE----------EEEEEE----HHHHHHHHHHHHHH-------------------EEEEEE---EEEEEE
Query: 67 IR-GSDVAIEFHTNAAANKTATGIEALSTPKNKRWCQVLGKAVAKKTGWKLRGEDGFKPDNAGQHSRLAYAQAGGIVFEP 145
Sbjct: 66 ALPGFQISTRRASSVVSPDTREYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFR----GSRVAFP 141
H----EEEEEE--------EEEEEEEEEEE----HHHHHHHHHHH---EEEEE---EEE------EEE- -EEEEEE
E----HHHHHHH--HHHH
Query: 146 FFISNDTDLALFKTTKWG 163
Sbjct: 142 FPLYQEVVTALSRVEEEF 159
---HHHHHHHHHHHHHHH
158 residues (87.29%) 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: 34.48% helical, 23.56% extended, 41.95% loops/other (query: 38.12% 19.34% 42.54%)
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.
1F5M_A d.110.2.1 88.6.2.2 NONE -999.000 0 1 91.71% 10.84% OPTM -305.750 -253.250 1.106 0.353 0.346 0.817 0.864 5.560 -32.7 1.820 40.500 -52.0 1.830 -1.500 -96.5 1.130 14.170 -15.5 -0.140 3.150 -32.8 1.080 12.810 3.4 -0.070 1.710 -25.3 6.700 46.710 -42.3 10.750 15.150 -51.4 -30.000 52.000 -105.0 -30.000 21.000 -114.0 0.120 -10.000 42.0 -0.460 -1.000 -35.0 0.700 21.000 -30.0 2.350 17.000 -75.0 5.000 1.6 -2.412 -29.8 106.000 117.0 5.000 1.6 -0.444 0.7 0.23 0.84
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---------------HHHHHHHHHHHHHHHHHH----EEEEE--------HHHHHHHH- ---EEEEEE------
Query: 10 GHSNTDPGAVNGSDREADLAQDMRNIVASILRNDYGLTVKTDGTGKGNMPLRDAVKLIR------GSDVAIEFHTNAAAN 83
Sbjct: 6 GFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQV----------NWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQAS 75
--------------HHHHHHHHHHHHHHHH----- HHHHHHHHHHHHHHHHHH----EEEEEEEEE----
----EEEEEE--- -HHHHHHHHHHHHHH----- --------------EEEEEE--- EEEEEEE---
Query: 84 KTATGIEALSTPK--------NKRWCQVLGKAVAKKTGWKL-RGEDGFKPDNAGQHSRLAYAQAG-----GIVFEPFFIS 149
Sbjct: 76 EENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDY 155
--EEEEEEEEE-----EEE---HHHHHHHHH---EEE-----------------EEEEEEEE-----EEEEEEEEE----
-HHHHHHH--HHHHHHHHHHHHHHHH
Query: 150 NDTDLALFKTTKWGICRAIADAIAME 175
Sbjct: 156 EG-----FDHVDKEFLEKLAKLINKS 176
-- -HHHHHHHHHHHHHHHHH-
166 residues (91.71%) of query sequence aligned
DONE: Mon Aug 11 23:32:12 2008 EST