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 08 09:05:10 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 = 200 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 T0397
--> 150 residues, sequence name: T0397
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 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 3 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 15.54 | 17.14 | 17.40 | 15.64 |
2 | 15.54 | 0.00 | 16.33 | 17.92 | 15.61 |
3 | 17.14 | 16.33 | 0.00 | 16.10 | 18.07 |
4 | 17.40 | 17.92 | 16.10 | 0.00 | 18.11 |
5 | 15.64 | 15.61 | 18.07 | 18.11 | 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 | 12.60 | 11.76 | 18.88 | 12.33 |
2 | 12.60 | 100.00 | 14.29 | 17.89 | 14.63 |
3 | 11.76 | 14.29 | 100.00 | 15.97 | 10.08 |
4 | 18.88 | 17.89 | 15.97 | 100.00 | 9.09 |
5 | 12.33 | 14.63 | 10.08 | 9.09 | 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 | 18.90 | 23.53 | 25.87 | 23.29 |
2 | 18.90 | 100.00 | 21.01 | 28.46 | 24.39 |
3 | 23.53 | 21.01 | 100.00 | 26.89 | 21.01 |
4 | 25.87 | 28.46 | 26.89 | 100.00 | 24.48 |
5 | 23.29 | 24.39 | 21.01 | 24.48 | 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: 2.40% helical, 45.51% extended, 52.10% loops/other (query: 8.00% 46.67% 45.33%)
SCOP classification: [All beta proteins]/[Immunoglobulin-like beta-sandwich]
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.
1SY6_A b.1.1.4 80.27.15.8 NONE -999.000 0 1 100.00% 12.67% OPTM -366.744 -238.450 1.402 0.534 0.323 0.735 0.815 1.050 -30.0 2.010 44.000 -51.5 0.460 -2.500 -80.5 1.990 14.680 -18.8 -0.110 -5.470 -30.3 2.630 20.450 -4.7 0.080 -10.060 -19.4 4.120 11.700 -34.6 5.450 -1.330 -52.3 -30.000 7.000 -92.0 -30.000 6.000 -97.0 2.860 36.000 -12.0 0.730 8.000 -44.0 3.790 27.000 -60.0 4.970 21.000 -70.0 5.000 0.2 3.016 -31.4 27.000 154.0 5.000 0.3 0.556 -0.4 0.73 0.86
alignment source: OPTM
----EEEEE-------EEEEE----EEEEE----- -----EEEHHHHHHHHHHHH------EEEEEEE-----E
Query: 1 MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEE------YSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTL 74
Sbjct: 17 QEDGSVLLTCDA-EAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMYQCKG-------SQNKSKPLQVYYRMQTPYK 88
---EEEEEE--- --EEEEEE--EEEEEEE-----EEEEE-----EEEEEEE-- ------EEEEEE-----EE
EEE----EEEEEEE--EEEEEEEE---EE----EEEEEEE---EEEEE---- -EEEEEE-- -------EEEEEE-
Query: 75 TYLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPV---SGTVIFMNE--IPSERANYVFYMLE 149
Sbjct: 89 VSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRAR 168
EEE--EEEEE--------EEEEE--EEE--------EEEE--EEEE----HHHH-EEEEEEE----------EEEEEE--
-
Query: 150 E 150
Sbjct: 169 V 169
V
150 residues (100.00%) 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: 13.27% helical, 38.05% extended, 48.67% loops/other (query: 8.00% 46.67% 45.33%)
SCOP classification: [Alpha and beta proteins (a/b)]/[P-loop containing nucleoside triphosphate hydrolases]
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.
1F2T_A c.37.1.12 2.1.1.1 NONE -999.000 0 1 74.67% 20.47% OPTM -303.312 -182.430 1.118 0.385 0.262 0.680 0.769 10.710 -27.4 4.660 68.500 -122.5 3.800 41.000 -123.5 1.400 3.520 -21.6 -0.370 1.980 -26.8 3.240 13.290 -17.2 0.640 3.660 -22.0 4.700 20.030 -34.7 5.670 9.500 -40.6 -30.000 20.000 -67.0 -30.000 17.000 -78.0 4.080 67.000 -71.0 3.000 22.000 -73.0 -0.070 3.000 19.0 1.000 -1.000 -38.0 5.000 0.3 -0.784 -24.4 125.000 141.0 5.000 -0.3 1.114 -2.5 0.74 0.72
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----EEEEE-------EEEEE----EEEEE----------EEEHHHHHHHHHHHH-- ----EEEEEEE-- ---EE
Query: 1 MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSL----DTLKKDVLIQYPD-KHTLT 75
Sbjct: 1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQ-----NGSG---KSSLLDAILVGLYWPLRIKDIKKD---EFTKVGARDT 69
-EEEEEEEE-------EEEE----------- ---- HHHHHHHHHHHHH----------- ---------E
EE----EEEEEEE--EEEEEEEE---EE----EEEEEEE---EEEEE-----
Query: 76 YLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVS 127
Sbjct: 70 YI-----DLIFEKDGTKYRITR----RFLKGEIHAMKRLVGNEWKHVTEPSS 112
EE EEEEEE--EEEEEEE EE---EEEEEEEEE--EEEE-----H
112 residues (74.67%) 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: 8.73% helical, 45.24% extended, 46.03% loops/other (query: 8.00% 46.67% 45.33%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Thioesterase/thiol ester dehydrase-isomerase]
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.
1IXL_A d.38.1.5 18.1.1.1 NONE -999.000 0 1 77.33% 16.81% OPTM -348.711 -232.370 1.086 0.523 0.253 0.877 0.934 9.990 -26.4 1.430 30.000 -46.5 1.020 20.000 -88.0 -0.180 3.290 -5.6 -0.040 0.870 -32.8 0.220 4.320 9.8 1.090 3.340 -26.3 5.760 18.730 -26.0 8.670 20.370 -51.4 -30.000 36.000 -79.0 -30.000 35.000 -90.0 2.270 38.000 -16.0 1.970 18.000 -57.0 -1.160 11.000 5.0 -0.200 7.000 -53.0 5.000 -0.8 0.014 -27.2 13.000 178.0 5.000 -0.8 -0.569 -2.1 0.46 0.96
alignment source: OPTM
E-------EEEEE----EEEEE----------EEEHHHHHHHHHHHH------EEEEEEE-----EEEE----EEEEEEE
Query: 9 EGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTLTYLKAGTKLISVPA 88
Sbjct: 12 TSRILVGKPILIKE-GYAEVELETIDEKVDEKGLVHGGFTFGLADYAALAVNEPTVVLGKAEVRFTKPVKVGDKLVAKAK 90
------EEEEEE-- EEEEEEE-------------HHHHHHHHHHH--------EEEEEEEEEE--------EEEEEEEE
--EEE EEEEE---EE----EEEEEEE---EEEEE-----
Query: 89 EGYKV--YPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVS 127
Sbjct: 91 IIEDLGKKKIVEVKVYREE----EVVLEGKFYCYVLEKHVL 127
EEEE--EEEEEEEEEE--E EEEEEEEEEEE-------
116 residues (77.33%) 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: 14.97% helical, 38.92% extended, 46.11% loops/other (query: 8.00% 46.67% 45.33%)
SCOP classification: [Alpha and beta proteins (a+b)]/[MHC antigen-recognition domain]
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.
1D9K_C d.19.1.1 18.2.2.2 NONE -999.000 0 1 95.33% 12.59% OPTM -262.031 -169.040 1.025 0.465 0.178 0.580 0.711 7.330 -26.9 0.080 -7.500 -6.5 0.530 18.500 -86.0 -0.020 -3.720 5.9 -0.770 -1.710 -27.8 1.520 5.060 23.3 1.120 3.730 -21.0 6.270 21.030 -15.4 8.450 11.720 -47.9 -30.000 27.000 -85.0 -30.000 22.000 -96.0 -0.390 -22.000 71.0 0.050 -2.000 -44.0 2.890 44.000 -15.0 2.960 12.000 -55.0 5.000 0.0 0.785 -36.3 0.000 -9.3e+061 5.000 0.0 1.322 0.3 0.43 0.71
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
EEEEE-------EEEEE----EEEEE--------- -EEEHHHHHHHHHHHH- -----EEE
Query: 5 KIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGN--------GKLLYQVIYDDLAKYMS------------LDTLKKDV 64
Sbjct: 13 GITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGGLQNIATGKHNLEILTKRSNSTPATNEAPQ 92
EEEEE----EEEEEEEE--EEEEEEE----EEEE----HHHH----HHHHHHHHHHHHHHHHHHHHH-------------
EEEE-----EEEE----EEEEEEE--E EEEEEEE---EE----EEEEEEE---EEEEE-----EEEEEE-------
Query: 65 LIQYPDKHTLTYLKAGTKLISVPAEGY----KVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSER 140
Sbjct: 93 ATVFPKSPVL---LGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFFVNR-------DYSFHKLSYLTFIPSDD 162
-EEE------ ---EEEEEEEEEE-----EEEEEE---EE---EEE---EE--- --EEEEEEEEE------
--EEEEE
Query: 141 ANYVFYM 147
Sbjct: 163 DIYDCKV 169
-EEEEEE
143 residues (95.33%) 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: 0.00% helical, 42.25% extended, 57.75% loops/other (query: 8.00% 46.67% 45.33%)
SCOP classification: [All beta proteins]/[beta-Trefoil]
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.
1J0S_A b.42.1.2 80.1.1.1 NONE -999.000 0 1 89.33% 13.01% OPTM -225.187 -220.230 1.022 0.464 0.151 0.733 0.785 1.380 -27.6 1.720 23.000 -58.0 0.940 11.000 -89.5 0.600 -1.940 -22.5 -0.420 -1.770 -30.0 0.940 -1.340 -7.8 -0.260 -1.430 -22.4 3.580 5.300 -45.6 3.800 -1.850 -48.3 -30.000 7.000 -94.0 -30.000 4.000 -94.0 2.240 34.000 -11.0 0.930 15.000 -52.0 3.280 19.000 -37.0 3.160 -4.000 -49.0 5.000 0.1 1.487 -27.9 -63.000 214.0 5.000 0.1 1.602 -0.4 0.25 0.75
alignment source: OPTM
EEEEE-------EEEEE----EEEEE----------EEEHHHHHHHHHHHH------EEEEEEE----- EEEE--
Query: 5 KIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHT-----LTYLKA 79
Sbjct: 8 KLSVIRNLND--QVLFIDQGNRPLFEDMTDSDCRDN---------------APRTI--FIISMYKDSQPRGMAVTISVKC 68
EEEEE----E EEEE-----EEEEE---------- ----- EEEEE-------EEE-EEE---
--EEEEEEE--EEEEEEEE---EE----E EEEEEE--- EEEEE-----EEEEEE---------EEEEEE--
Query: 80 GTKLISVPAEGYKVYPIMDFGFRVLKGYR--LATLESKKG---DLRYVNSPVSGTVIFMNEIPSERANYVFYMLEE 150
Sbjct: 69 EKISTLSCENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLACEKERD---LFKLILKKE 141
--EEEEE----EEEE----------------EEEEE------EEEEEE------EEEEEEE--E EEEEEE---
134 residues (89.33%) of query sequence aligned
DONE: Fri Aug 08 12:32:05 2008 EST