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:Sat Aug 16 08:54:37 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 T0460
--> 111 residues, sequence name: T0460
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 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 9.70 | 12.91 | 10.84 | 11.31 |
2 | 9.70 | 0.00 | 7.55 | 11.77 | 11.77 |
3 | 12.91 | 7.55 | 0.00 | 12.04 | 16.66 |
4 | 10.84 | 11.77 | 12.04 | 0.00 | 14.11 |
5 | 11.31 | 11.77 | 16.66 | 14.11 | 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 | 37.50 | 26.09 | 28.57 | 29.76 |
2 | 37.50 | 100.00 | 48.00 | 46.15 | 34.43 |
3 | 26.09 | 48.00 | 100.00 | 18.06 | 26.39 |
4 | 28.57 | 46.15 | 18.06 | 100.00 | 16.44 |
5 | 29.76 | 34.43 | 26.39 | 16.44 | 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 | 65.00 | 40.58 | 42.86 | 46.43 |
2 | 65.00 | 100.00 | 68.00 | 69.23 | 60.66 |
3 | 40.58 | 68.00 | 100.00 | 37.50 | 38.89 |
4 | 42.86 | 69.23 | 37.50 | 100.00 | 47.95 |
5 | 46.43 | 60.66 | 38.89 | 47.95 | 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: 27.71% helical, 14.46% extended, 57.83% loops/other (query: 33.33% 20.72% 45.95%)
SCOP classification: [Alpha and beta proteins (a/b)]/[Thioredoxin fold]
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.47.1.5.22_A c.47.1.5 18.13.13.6 GUESS -27.793 0 1 70.27% 13.10% OPTM -108.255 -209.910 0.499 0.495 0.487 0.891 0.891 5.100 -20.5 -0.710 -5.000 23.5 -1.440 -13.500 -49.0 0.160 3.690 79.9 -0.330 -0.680 -25.4 0.470 2.730 86.7 0.000 -1.650 -21.4 2.750 -1.030 37.2 6.370 2.690 -28.3 -30.000 6.000 -45.0 -30.000 6.000 -63.0 -0.590 -23.000 49.0 0.210 1.000 -42.0 2.450 19.000 5.0 1.190 7.000 -35.0 5.000 1.3 -1.645 -49.4 -11.000 143.0 5.000 1.3 5.000 -0.1 0.27 0.76
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
E--HHHHHHHHHHH-----EEEEE---E------------E----EEEEEEEEEEE----EEEE-HHHHHHHHHH-----
Query: 25 HLKPEVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMKYTNVKKVKIKKVYFETLDNVRVVTDYSEFQKILKKRGTKL 104
Sbjct: 8 HPASIATRRVLIALHEKNLDFELVHVELKDGEHKKEPFLSRNPFGQV----PAFEDGD--LKLFESRAITQYIAHRYENQ 81
---HHHHHHHHHHHH-----EEEE----------------------- EEEE--E EEE-HHHHHHHHHHH-----
----
Query: 105 EHHH 108
Sbjct: 82 GTNL 85
---L
78 residues (70.27%) 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: 40.70% helical, 17.44% extended, 41.86% loops/other (query: 33.33% 20.72% 45.95%)
SCOP classification: [Alpha and beta proteins (a+b)]/[IF3-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.
1UG8_A d.68.7.1 85.3.2.2 GUESS -28.127 0 1 55.86% 19.35% OPTM -93.703 -101.220 0.296 0.446 0.463 0.511 0.661 8.460 -21.5 -0.680 -46.500 -5.5 -0.020 -4.000 -72.0 -1.240 -1.180 7.4 0.180 0.350 -16.3 -0.280 -1.900 14.7 1.650 3.820 -17.1 3.800 9.500 -5.1 5.760 5.860 -26.0 -30.000 24.000 -39.0 -30.000 10.000 -49.0 0.280 -13.000 3.0 -0.770 -7.000 -41.0 0.340 -3.000 48.0 0.260 5.000 -23.0 5.000 -1.2 3.264 -43.1 22.000 186.0 5.000 -1.2 -0.620 -1.9 0.45 0.79
alignment source: OPTM
HHHHHHHHHHH-HHHHH-----E-- HHHHHHHHHHH-----EEEEE--- E------------
Query: 3 SEVIKEFLEDIGEDYIELENEIHLK--------PEVFYEVWKYVGEPELKTYVIEDE---------IVEPGEYDPPEMK 64
Sbjct: 10 KKFIDQVIEKI-EDFLQSEEKRSLELDPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERSGPSSG 87
HHHHHHHHHHH HHHH-----EEE------HHHHHHHHHHHHH----EEEEEE-------EEEEEE------------G
62 residues (55.86%) 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: 23.76% helical, 29.70% extended, 46.53% loops/other (query: 33.33% 20.72% 45.95%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Acyl-CoA N-acyltransferases (Nat)]
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.
1R57_A d.108.1.1 85.4.4.4 GUESS -28.355 0 1 64.86% 25.00% OPTM -60.473 -80.320 0.592 0.480 0.214 0.511 0.671 4.620 -23.2 5.160 85.500 -117.5 4.810 68.000 -128.0 0.830 -2.120 -10.5 0.300 -2.410 -18.7 3.670 7.320 -12.4 0.250 -0.640 -14.9 0.010 -1.770 -8.4 3.300 -1.850 -24.6 -30.000 -23.000 -16.0 -30.000 -6.000 -45.0 3.440 50.000 -62.0 3.090 23.000 -72.0 1.480 2.000 8.0 0.130 3.000 -31.0 5.000 0.5 -3.713 -61.7 -3.000 141.0 5.000 0.5 -3.000 -4.7 -0.09 0.63
alignment source: OPTM
----EEEEE---E------------E----EEEEEEEEEEE-- --EEEE-HHHHHHHHHH
Query: 40 EPELKTYVIEDEIVEPGEYDPPEMKYTNVKKVKIKKVYFETLD--------------------NVRVVTDYSEFQKILKK 99
Sbjct: 8 QGENKFYIGDD---ENNALAEITYRFVDNNEINIDHTGVSDELGGQGVGKKLLKAVVEHARENNLKIIASCSFAKHMLEK 84
E--EEEEE--- --EEEEEEEEE----EEEEEEEEE---------HHHHHHHHHHHHHHH--EEEE--HHHHHHHHH-
--- ---------
Query: 100 RGT------KLEHHHHHH 111
Sbjct: 85 EDSYQDVYLGLEHHHHHH 102
-----------------H
72 residues (64.86%) 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: 27.06% helical, 36.47% extended, 36.47% loops/other (query: 33.33% 20.72% 45.95%)
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.
2JXT_A not_found 72.72.72.26 GUESS -28.760 0 1 65.77% 19.18% OPTM -59.828 -49.460 0.882 0.454 0.389 0.460 0.525 4.510 -17.6 3.580 86.000 -92.0 4.690 51.500 -133.5 1.030 1.620 5.1 1.210 2.140 -19.5 3.260 11.360 5.5 3.160 5.770 -21.8 2.970 6.520 1.6 3.080 -1.700 -21.2 -30.000 -6.000 -14.0 -30.000 -8.000 -36.0 5.130 90.000 -84.0 5.490 55.000 -111.0 3.120 29.000 25.0 0.890 7.000 -32.0 5.000 0.7 1.935 -31.9 0.000 -9.3e+061 5.000 0.7 -3.046 -4.5 0.00 0.56
alignment source: OPTM
-----EEEEE---E------------E--- -EEEEEEEEEEE----EEEE-HHHHHHHH
Query: 39 GEPELKTYVIEDEIVEPGEYDPPEMKYTNV---------------------KKVKIKKVYFETLDNVRVVTDYSEFQKIL 97
Sbjct: 1 MKMKTKIFRVKGKFLMGDKLQPFTKELNAIREEEIYERLYSEFGSKHRVPRSKVKIEEIEEISPEEVQD----PVVKALV 76
-----EEEEEEEEEEE--EEEEEEEEEEE--HHHHHHHHHHHHHHH-------EEEEEEEEE------- HHHHHHH
HH------------
Query: 98 KKRGTKLEHHHHHH 111
Sbjct: 77 QRL----EHHHHHH 86
H-- -------
73 residues (65.77%) 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: 36.64% helical, 19.08% extended, 44.27% loops/other (query: 33.33% 20.72% 45.95%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Ferredoxin-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.
1NXI_A d.58.47.1 85.15.1.1 NONE -999.000 0 1 97.30% 20.37% OPTM -140.601 -159.220 1.359 0.398 0.319 0.448 0.530 5.590 -21.9 4.390 60.000 -112.0 6.300 65.500 -150.0 1.430 -0.130 -6.2 0.760 -0.530 -22.4 4.490 11.230 -7.3 4.080 7.620 -24.1 4.450 8.220 -13.0 5.490 1.310 -29.8 -30.000 4.000 -46.0 -30.000 6.000 -54.0 4.410 42.000 -61.0 7.040 53.000 -105.0 2.600 5.000 -2.0 2.550 -3.000 -45.0 5.000 1.0 2.079 -35.9 -33.000 297.0 5.000 1.0 -3.000 -4.0 0.60 0.90
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHH-HHHHH---- -E--HHHHHHHHHHH-----EEEEE---E------------E----EEE
Query: 4 EVIKEFLEDIGEDYIELENE-----------IHLKPEVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMKYTNVKKVK 72
Sbjct: 15 EIQKEETRDIIQALLEDGSDPDALYEIEHHLFAEDFDKLEKAAVEAFKMGFE--VLEAEETEDEDGN---------KLLC 83
HHHHHHHHHHHHHHHH-------EEEEEEEEE--HHHHHHHHHHHHHH---- ------------- -EEE
EEEEEEEE----EEEE-H HHHHHHHHH-- ----------
Query: 73 IKKVYFETLDNVRVVTDY-------SEFQKILKKRG----------TKLEHHHHHH 111
Sbjct: 84 FDATMQSALD-------AKLIDEQVEKLVNLAEKFDIIYDGWGTYYEGLEHHHHHH 132
EEEEEE---H HHHHHHHHHHHHHHHHH--EEEEEEE------------H
108 residues (97.30%) of query sequence aligned
DONE: Sat Aug 16 12:05:59 2008 EST