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 19:07:47 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 T0399
--> 206 residues, sequence name: T0399
Database: T:\CBSU\blastdb\20080108\nr
-> 3 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 | 7 | 3 | 0 | 0 | 0 | 0 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 1.64 | 15.63 | 15.86 | 14.24 |
2 | 1.64 | 0.00 | 15.63 | 15.77 | 14.40 |
3 | 15.63 | 15.63 | 0.00 | 23.62 | 25.42 |
4 | 15.86 | 15.77 | 23.62 | 0.00 | 21.84 |
5 | 14.24 | 14.40 | 25.42 | 21.84 | 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 | 100.00 | 14.49 | 9.49 | 14.49 |
2 | 100.00 | 100.00 | 14.49 | 9.49 | 13.04 |
3 | 14.49 | 14.49 | 100.00 | 12.50 | 8.81 |
4 | 9.49 | 9.49 | 12.50 | 100.00 | 10.34 |
5 | 14.49 | 13.04 | 8.81 | 10.34 | 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 | 24.64 | 27.74 | 23.91 |
2 | 100.00 | 100.00 | 24.64 | 28.47 | 20.29 |
3 | 24.64 | 24.64 | 100.00 | 21.88 | 15.03 |
4 | 27.74 | 28.47 | 21.88 | 100.00 | 13.30 |
5 | 23.91 | 20.29 | 15.03 | 13.30 | 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: 13.41% helical, 33.54% extended, 53.05% loops/other (query: 18.45% 25.73% 55.83%)
SCOP classification: [Alpha and beta proteins (a+b)]/[beta-lactamase-inhibitor protein, BLIP]
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.
1JTG_B d.98.1.1 71.2.2.2 NONE -53.482 0 1 67.48% 14.39% OPTM -276.030 -315.340 0.857 0.417 0.642 0.812 0.957 18.480 -42.3 1.500 41.500 4.5 2.880 29.500 -100.0 1.510 10.150 26.6 -0.780 -2.640 -31.5 3.580 15.240 43.6 -0.430 -3.980 -24.5 5.050 13.410 7.8 7.760 7.710 -48.3 -30.000 20.000 -69.0 -30.000 16.000 -106.0 0.700 18.000 51.0 0.290 4.000 -38.0 -2.250 1.000 19.0 5.160 27.000 -87.0 5.000 -2.7 1.464 -52.1 -27.000 212.0 5.000 -2.7 -0.201 0.0 0.27 0.74
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------HHHHHHHH------------- EEEEEEEEE---EEEEEEE---- EEEEEE--EEEE------HHHHHHH
Query: 67 FSGGTSIEQLKQWFGDPNKSEQRNAGN-ITLDSYTWVKDGAVINAQLYKNS----TVARSISNFSFSREAKIGKEDYDEL 141
Sbjct: 12 IQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQV 91
-----HHHHHHHH----EE--------EEEEEEEE--EEEEEEEEE--------EEEEEEE-----------HHHHHH--
H----HHHHHHH-------EEE------ EEEEEEE---------- EEEEEE----EEE------
Query: 142 KIGESYKKVVEKLGEPDVLSQSMSSDKE-------EMQTVWSSGIKTKSSSA--TIELYFENGLLKNKTQKDL 205
Sbjct: 92 TVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDL 164
----HHHHHHHH----EEEEEEE----------EEEEEEE-------------EEEEEEE--EEEEEEEE---
139 residues (67.48%) 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: 13.41% helical, 33.54% extended, 53.05% loops/other (query: 18.45% 25.73% 55.83%)
SCOP classification: [Alpha and beta proteins (a+b)]/[beta-lactamase-inhibitor protein, BLIP]
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.98.1.1.1_B d.98.1.1 71.2.2.2 NONE -53.547 0 1 67.48% 14.39% OPTM -327.847 -308.740 0.958 0.424 0.595 0.764 0.893 18.380 -42.8 1.450 44.500 5.0 2.860 30.000 -99.0 0.670 8.230 24.2 0.600 -0.910 -40.4 2.200 13.120 42.6 -0.680 -5.900 -28.9 5.420 18.480 3.3 8.660 8.990 -48.2 -30.000 20.000 -69.0 -30.000 16.000 -106.0 0.700 17.000 57.0 0.400 3.000 -38.0 -1.490 8.000 13.0 5.380 29.000 -88.0 5.000 -2.7 1.173 -31.8 0.000 -9.3e+061 5.000 -2.7 -0.201 0.0 0.27 0.74
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------HHHHHHHH------------- EEEEEEEEE---EEEEEEE---- EEEEEE--EEEE------HHHHHHH
Query: 67 FSGGTSIEQLKQWFGDPNKSEQRNAGN-ITLDSYTWVKDGAVINAQLYKNS----TVARSISNFSFSREAKIGKEDYDEL 141
Sbjct: 12 IQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQV 91
-----HHHHHHHH----EE--------EEEEEEEE--EEEEEEEEE--------EEEEEEE-----------HHHHHH--
H----HHHHHHH-------EEE------ EEEEEEE---------- EEEEEE----EEE------
Query: 142 KIGESYKKVVEKLGEPDVLSQSMSSDKE-------EMQTVWSSGIKTKSSSA--TIELYFENGLLKNKTQKDL 205
Sbjct: 92 TVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDL 164
----HHHHHHHH----EEEEEEE----------EEEEEEE-------------EEEEEEE--EEEEEEEE---
139 residues (67.48%) 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: 17.02% helical, 41.49% extended, 41.49% loops/other (query: 18.45% 25.73% 55.83%)
SCOP classification: [Alpha and beta proteins (a+b)]/[DNA clamp]
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.
1UD9_A d.131.1.2 71.14.14.10 NONE -999.000 0 1 85.92% 9.84% OPTM -316.488 -167.620 0.492 0.281 0.297 0.461 0.555 2.010 -31.1 0.180 19.000 -8.5 -0.900 -17.500 -85.0 0.670 5.880 42.9 -0.130 -3.400 -26.7 1.560 17.070 61.6 -0.540 -1.260 -15.8 0.900 4.370 25.8 6.720 3.040 -47.8 -30.000 16.000 -87.0 -30.000 -6.000 -97.0 -0.150 7.000 66.0 0.720 20.000 -67.0 -1.210 6.000 12.0 0.330 2.000 -46.0 5.000 0.7 -0.092 -26.6 -54.000 167.0 5.000 0.8 -0.602 -0.1 0.29 0.66
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHH---------------------------HHHHH----EEEEEE--------- HHHHHHHH--
Query: 12 VFLTVTFCFLMLGCQSKEDKKGGTKPSNEAALTKTENLDFRLSFNKIKVTTDQNHFSGGTS---------IEQLKQWFGD 82
Sbjct: 11 LKAIIQALLKLV-----DEALFDIKPEGIQLVAIDKA-----HISLIKIELPKEMFKEYDVPEEFKFGFNTQYMSKLLKA 80
HHHHHHHHHH-- EEEEEEE--EEEEEEE---- -EEEEEEEE-----EEE----EEEEEEHHHHHHHH---
-----------EEEEEEEEE---EEEEEEE----EEEEEE--EEEE---- --HHHHHHHH----HHHHHHH
Query: 83 PNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISNFSFSREAK---------IGKEDYDELKIGESYKKVVEK 153
Sbjct: 81 AKRKEE-------IIIDADSPE--VVKLTLSGALNRVFNVNNIEVLPPEVPLEFDIKATINASGLKNA-----IGEIAEV 146
-----E EEEEEE--E EEEEE-----EEEEEE--------------EEEEEEHHHHHHHH HHHHHH-
-------EEE------EEEEEEE----------EEEEEE----EEE-----
Query: 154 LGEPDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYFENGLLKNKTQKD 204
Sbjct: 147 AD------TLLISGNEEKVVVKGEG----ENKVEVEFSKDTGSLADIEFNK 187
-E EEEEE---EEEEEE--- ----EEEE-----EEEEEE---
177 residues (85.92%) 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: 4.17% helical, 48.81% extended, 47.02% loops/other (query: 18.45% 25.73% 55.83%)
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.
2FGS_A not_found 18.18.18.18 NONE -999.000 0 1 81.55% 10.84% OPTM -259.191 -212.630 0.470 0.375 0.164 0.617 0.734 2.410 -34.1 0.550 18.000 -61.0 -0.480 2.500 -103.0 -1.660 -0.880 21.8 0.100 2.380 -21.8 -1.160 -3.310 36.6 0.190 1.650 -17.3 5.740 12.290 -13.0 6.260 7.450 -47.1 -30.000 12.000 -82.0 -30.000 5.000 -91.0 0.920 6.000 10.0 -0.460 -8.000 -48.0 0.460 40.000 43.0 0.560 -2.000 -60.0 5.000 0.4 0.204 -17.3 0.000 -9.3e+061 5.000 0.4 0.079 0.8 0.73 0.25
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---------EEHHHHHHHHHH---------------------------HHHHH----EEEEEE---------HHHHHHHH
Query: 1 MSMKKTKNWLLVFLTVTFCFLMLGCQSKEDKKGGTKPSNEAALTKTENLDFRLSFNKIKVTTDQNHFSGGTSIEQLKQWF 80
Sbjct: 24 YTLDKAHTDVG---------FKIKHLQISNVKGNFKDYSAVIDFDPAS----AEFKKLDVTIKIASVNTEN--QTRDNHL 88
----------- ------------EE--EEEEEEEE---- EEEEEEEEEE---EE---H HHHHHH-
-------------EEEEEEEEE--- EEEEEEE----EEEEEE--EEEE------HHHHHHHH----HHHHHHH----
Query: 81 GDPNKSEQRNAGNITLDSYTWVKDG---AVINAQLYKNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKVVEKLGEP 157
Sbjct: 89 QQDDFFKAKKYPDMTFTMKKYEKIDNEKGKMTGTLTIAGVSKDIVLDAEIGGVAKGK----------------------- 145
-----------EEEEEEEEEEE----EEEEEEEEEE--EEEEEEEEEEEEEEEE---
---EEE------EEEEEEE---- ------EEEEEE----EEE----
Query: 158 DVLSQSMSSDKEEMQTVWSSGIK-----------TKSSSATIELYFENGLLKNKTQK 203
Sbjct: 146 --------DGKEKIGFSLNGKIKRSDFKFATSTSTITLSDDINLNIE---VEANEKE 191
--EEEEEEEEEEEE-----------------EEEEEEEE EEE---E
168 residues (81.55%) 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: 6.64% helical, 24.64% extended, 68.72% loops/other (query: 18.45% 25.73% 55.83%)
SCOP classification: [All beta proteins]/[Nucleoplasmin-like/VP (viral coat and capsid proteins)]
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.
1BEV_3 b.121.4.1 106.3.3.3 NONE -999.000 0 1 99.03% 10.29% OPTM -169.600 -166.850 0.438 0.315 0.072 0.374 0.432 7.030 -31.6 -0.580 4.000 1.0 1.370 5.000 -102.0 -1.160 -4.010 15.4 -0.590 0.930 -24.6 -2.730 -16.820 42.8 -0.460 -4.450 -16.1 1.000 3.500 -10.5 2.350 7.810 -48.4 -30.000 16.000 -101.0 -30.000 15.000 -117.0 -0.360 -11.000 81.0 -0.780 5.000 -40.0 1.330 26.000 51.0 3.610 16.000 -53.0 5.000 -0.3 -0.356 -38.5 49.000 230.0 5.000 -0.3 1.255 -0.6 0.81 0.74
alignment source: OPTM
---------EEHHHHHHHHHH--------- ------------- -----HHHHH- --- E
Query: 1 MSMKKTKNWLLVFLTVTFCFLMLGCQSKED----KKGGTKPSNEAAL-TKTENLDFRLS-------FNK----------I 58
Sbjct: 2 LPTKPGPGS------------YQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQVESILEANNREGVEGVERYVI 69
--------- --------------------------------HHHH---EE----------------EE
EEEEE--- ------HHHHHHHH-------------EEEEEEEEE---EEEEEEE----EEEEEE--EE
Query: 59 KVTTDQNH------------FSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISNFS 126
Sbjct: 70 PVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKH----------------YTQWSGSVEITCMFTGTFMTTGKVLLAY 133
EE-------EEEEEE------------HHHHHH--E EEEE--EEEEEEE--------EEEEEEE
EE------HHHHHHHH----HHHHHHH-------EEE------EEEEEEE----- -----EEEEEE
Query: 127 FSREAKIGKEDYDELKIGESYKKVVEKLGEPDVLSQSMSSDKEEMQTVWSSGIKT--------------KSSSATIELYF 192
Sbjct: 134 TPPGGDMPR-NREEAMLG--------------THVIWDFGLQSSITLVIPWISASHFRGVSNDDVLNYQYYAAGHVTIWY 198
--------- HHHH---E EEEEE-----EEEEEE--------EE---------------EEEEEE-
----EEE-----
Query: 193 ENGLLKNKTQKD 204
Sbjct: 199 QTNMVIPPGFPN 210
-----------E
204 residues (99.03%) of query sequence aligned
DONE: Sat Aug 09 00:06:41 2008 EST