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 10:33:51 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 T0414
--> 140 residues, sequence name: T0414
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 | 4 | 0 | 0 | 0 | 1 | 1 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 15.26 | 8.13 | 5.87 | 14.71 |
2 | 15.26 | 0.00 | 15.22 | 14.29 | 12.83 |
3 | 8.13 | 15.22 | 0.00 | 6.73 | 14.04 |
4 | 5.87 | 14.29 | 6.73 | 0.00 | 14.06 |
5 | 14.71 | 12.83 | 14.04 | 14.06 | 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 | 21.74 | 33.33 | 47.86 | 20.69 |
2 | 21.74 | 100.00 | 25.00 | 17.98 | 23.86 |
3 | 33.33 | 25.00 | 100.00 | 24.58 | 26.50 |
4 | 47.86 | 17.98 | 24.58 | 100.00 | 23.02 |
5 | 20.69 | 23.86 | 26.50 | 23.02 | 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 | 39.13 | 78.33 | 100.00 | 52.59 |
2 | 39.13 | 100.00 | 30.43 | 41.57 | 43.18 |
3 | 78.33 | 30.43 | 100.00 | 82.20 | 45.30 |
4 | 100.00 | 41.57 | 82.20 | 100.00 | 44.44 |
5 | 52.59 | 43.18 | 45.30 | 44.44 | 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: 17.65% helical, 49.02% extended, 33.33% loops/other (query: 14.29% 42.86% 42.86%)
SCOP classification: [All beta proteins]/[PH domain-like barrel]
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.
b.55.1.4.2_A b.55.1.4 182.43.43.6 NONE -35.633 0 1 72.14% 9.17% OPTM -439.208 -254.730 1.017 0.424 0.577 0.809 0.920 12.170 -30.6 2.080 43.500 14.5 1.540 21.000 -61.5 0.370 1.620 5.8 0.620 0.860 -38.9 0.550 -0.990 25.8 0.670 3.040 -27.4 5.940 17.880 -4.8 7.710 10.450 -44.9 -30.000 24.000 -54.0 -30.000 11.000 -72.0 2.270 34.000 44.0 1.400 13.000 -42.0 -0.850 -6.000 18.0 0.850 -3.000 -50.0 5.000 -1.3 -2.353 -35.1 0.000 -9.3e+061 5.000 -1.3 1.279 -0.8 0.40 0.81
alignment source: OPTM
E---EEEEEEE--------HHHEEEE-----EEEEEE---EEEEEE-----EEEEEEEEE---EEEEE---EEEEE----
Query: 21 KNEKWLVCIKNWKPDNDIEGIAHLEIHHSTDEQFILSAGKAILITAEKENDKFNIELTLMEKGKVYNVPAECWFYSITQK 100
Sbjct: 10 SYARVRAVVMTRDDSSGG----WLQLGGGGLSSVTVSKTEFLVHGERLRDKTVVLECVLRRDLVYNKVTPTFHHWRIGDK 85
--EEEEEEEEEE------ EEE------EEEEEE----EEEEEE-----EEEEEE-----EEEEEE--EEEEEE--E
--EEEEEE----------EEE--HHHHHHHHHHHHHHHHH
Query: 101 DTKMMYVQDSNCSMDNSDFCDLSKEEIEYIQTNARKLFEK 140
Sbjct: 86 --KFGLTFQS-------------PADARAFDRGIRRAIED 110
EEEEEE-- HHHHHHHHHHHHHHHHH
101 residues (72.14%) 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: 18.42% helical, 31.58% extended, 50.00% loops/other (query: 14.29% 42.86% 42.86%)
SCOP classification: [All beta proteins]/[PH domain-like barrel]
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.
1Y5O_A b.55.1.9 182.43.43.2 NONE -35.777 0 1 65.71% 7.61% OPTM -317.505 -114.430 0.727 0.473 0.593 0.734 0.902 7.920 -27.1 2.030 41.500 -43.0 0.590 6.500 -72.0 1.540 2.050 -8.0 1.780 3.510 -30.2 2.160 6.130 3.1 -0.110 -5.540 -18.4 5.930 9.850 -19.2 5.830 2.670 -40.7 -30.000 31.000 -68.0 -30.000 14.000 -80.0 1.540 36.000 4.0 0.060 -6.000 -38.0 -2.010 -20.000 40.0 0.170 2.000 -28.0 5.000 0.1 -1.034 -33.1 2.000 151.0 5.000 0.1 0.279 -0.1 0.31 0.69
alignment source: OPTM
---EEEEEE---EEEEEE-----EEEEEEEEE---EEEEE-- -EEEEE------EEEEEE----------
Query: 49 STDEQFILSAGKAILITAEKENDKFNIELTLMEKGKVYNVPA----ECWFYSITQKDTKMMYVQDSNCSMDNSD------ 118
Sbjct: 1 PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEV 80
---EEEEE----EEEEEEE------EEEEEE-----EEEEE-----EEEE-------EEEEEEE----------------
EEE- -HHHHHHHHHHHHHHHHH
Query: 119 -------FCDL-SKEEIEYIQTNARKLFEK 140
Sbjct: 81 VPKPQRHMFSFNNRTVMDNIKMTLQQIISR 110
----EEEEEEE--HHHHHHHHHHHHHHHHH
92 residues (65.71%) 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: 17.31% helical, 44.23% extended, 38.46% loops/other (query: 14.29% 42.86% 42.86%)
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.
2P0D_A not_found 33.33.33.33 NONE -35.787 0 1 71.43% 6.61% OPTM -260.937 -84.900 0.676 0.482 0.550 0.741 0.833 7.490 -28.3 0.660 6.500 33.5 1.680 16.000 -58.5 1.200 5.240 4.1 0.610 -1.200 -28.4 2.780 12.160 19.5 1.110 1.520 -19.9 6.410 19.750 -7.3 4.240 2.640 -34.3 -30.000 30.000 -55.0 -30.000 8.000 -70.0 1.140 22.000 33.0 1.290 -1.000 -43.0 0.810 18.000 17.0 0.340 -11.000 -37.0 5.000 1.5 -0.237 -33.2 0.000 -9.3e+061 5.000 5.0 5.000 5.0 0.32 0.91
alignment source: OPTM
EE---EEEEEEE--------HHHEEEE-----EEEEEE---EEEEEE-----EEEEEEEEE---EEEEE-- -EEE
Query: 20 YKNEKWLVCIKNWKPDNDIEGIAHLEIHHSTDEQFILSAGKAILITAEKENDKFNIELTLMEKGKVYNVPA-----ECWF 94
Sbjct: 323 VEKSGLLNMTKIAQGG--------RKLRKNWGPSWVVLTGNSLVFYREPRPE----SSVDLRGAALAHGRHLSSRRNVLH 390
EEEEEEEEEEEEE--E E-----EEEEEEEE--EEEEE------E EEE----EEEE---------EEEE
EE------EEEEEE----------EEE--HHHHHHHHHHHHHHHHH
Query: 95 YSITQKDTKMMYVQDSNCSMDNSDFCDLSKEEIEYIQTNARKLFEK 140
Sbjct: 391 IRTI-PGHEFLLQSD-------------HETELRAWHRALRTVIER 422
E--- --EEEEE--- HHHHHHHHHHHHHHHHHH
100 residues (71.43%) 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: 13.21% helical, 55.66% extended, 31.13% loops/other (query: 14.29% 42.86% 42.86%)
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.
2OQB_A not_found 33.33.33.33 NONE -35.881 0 1 75.00% 7.09% OPTM -309.072 -201.900 0.733 0.495 0.569 0.735 0.855 8.590 -28.5 0.960 28.500 10.5 0.350 -2.000 -58.5 1.580 6.250 -2.7 0.120 -0.370 -28.4 1.650 5.260 16.0 -0.260 -0.570 -20.1 7.740 19.840 -17.1 6.180 5.540 -39.8 -30.000 29.000 -65.0 -30.000 8.000 -72.0 1.120 37.000 31.0 0.160 0.000 -37.0 1.460 20.000 20.0 0.230 -4.000 -31.0 5.000 5.0 2.038 -41.7 0.000 -9.3e+061 5.000 5.0 0.176 -0.1 0.50 0.72
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-----EEEEEE---EEEEEEE--------HHHEEEE-----EEEEEE-- -EEEEEE-----EEEEEEEEE---EEEEE-
Query: 11 NNREGILCVYKNEKWLVCIKNWKPDNDIEGIAHLEIHHSTDEQFILSAG-KAILITAEKENDKFNIELTLMEKGKVYNVP 89
Sbjct: 24 GSHMATVSVFPG---ARLLTIGDANGEI-----QRHAEQQALRLEVRAGPDAAGIALYSHEDVCVFKCSVSRETECSRVG 95
-------EEEEE EEEEEEE------ EEEEEEEEEEEEEEE---EEEEEEE-----EEEEEEEE---EEEEE-
--EEEEE------EEEEEE----------EEE--HHHHHHHHHHHHHH
Query: 90 AECWFYSITQKDTKMMYVQDSNCSMDNSDFCDLSKEEIEYIQTNARKL 137
Sbjct: 96 RQSFIITLGC---NSVLIQFA------------TPHDFCSFYNILKTC 128
--EEEEEE-- EEEEEE-- -HHHHHHHHHHHHHH
105 residues (75.00%) 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: 6.29% helical, 54.09% extended, 39.62% loops/other (query: 14.29% 42.86% 42.86%)
SCOP classification: [All beta proteins]/[Concanavalin A-like lectins/glucanases]
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.
1KQR_A b.29.1.14 182.2.2.1 NONE -36.056 0 1 97.14% 15.44% OPTM -402.718 -320.060 1.395 0.549 0.720 0.775 0.902 5.300 -33.1 1.870 59.500 -16.5 2.110 31.500 -79.0 1.310 2.620 13.0 1.090 3.010 -35.0 2.140 9.290 26.5 2.320 4.770 -28.1 6.870 17.830 -19.5 7.530 7.050 -50.8 -30.000 28.000 -89.0 -30.000 11.000 -97.0 1.450 36.000 61.0 0.190 1.000 -38.0 1.730 4.000 -37.0 3.080 0.000 -66.0 5.000 -0.2 4.477 -42.1 15.000 148.0 5.000 -0.2 0.826 -0.8 0.71 0.62
alignment source: OPTM
------- EEE-----EEEEEE--- EEEEEEE--------HHHEEEE-----EEEEEE-- -EEEEEE---
Query: 1 SNAMKPD-----IYENNREGILCVYKNEK--WLVCIKNWKPDNDIEGIAHLEIHHSTDEQFILSAG----KAILITAEKE 69
Sbjct: 71 PTTFNPPVDYWMLLAPTAAGVVVEGTNNTDRWLATILVEPNVTSET--RSYTLFGTQEQITIANASQTQWKFIDVVKTTQ 148
EEE-----EEEEE-----EEEEEEE-----EEEEEEE---EEEEEE EEEE--EEEEEEEEE-----EEEEEEEE----
--EEEEEEEEE---E EEEE---EEEEE------EEEEEE----- -----EEE--HHHHHHHHHHHHH
Query: 70 NDKFNIELTLMEKGK---VYNVPAECWFYSITQKDTKMMYVQDSNCS----MDNSDFCDLSKEEIEYIQTNARK 136
Sbjct: 149 NGSYSQYGPLQSTPKLYAVMKHNGKIYTYNGETPNVTTKYYSTTNYDSVNMTAFCDFYIIPREEESTCTEYINN 222
---EEEEEEEE----EEEEEE--EEEEEEEE----EEEEEE-------EEEE---EEEEE---HHHHHHHHHH-
136 residues (97.14%) of query sequence aligned
DONE: Mon Aug 11 14:19:55 2008 EST