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 21:29:45 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 T0463
--> 219 residues, sequence name: T0463
Database: T:\CBSU\blastdb\20080108\nr
-> 51 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 | 32 | 113 | 50 | 1 | 0 | 0 | 2 | 3 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 7.69 | 8.65 | 9.32 | 11.19 |
2 | 7.69 | 0.00 | 8.46 | 9.76 | 11.90 |
3 | 8.65 | 8.46 | 0.00 | 11.21 | 12.72 |
4 | 9.32 | 9.76 | 11.21 | 0.00 | 4.74 |
5 | 11.19 | 11.90 | 12.72 | 4.74 | 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 | 52.09 | 28.21 | 52.70 | 53.02 |
2 | 52.09 | 100.00 | 27.74 | 25.68 | 25.50 |
3 | 28.21 | 27.74 | 100.00 | 28.38 | 28.19 |
4 | 52.70 | 25.68 | 28.38 | 100.00 | 74.32 |
5 | 53.02 | 25.50 | 28.19 | 74.32 | 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 | 79.53 | 76.28 | 84.46 | 83.22 |
2 | 79.53 | 100.00 | 76.13 | 81.76 | 79.19 |
3 | 76.28 | 76.13 | 100.00 | 79.73 | 79.19 |
4 | 84.46 | 81.76 | 79.73 | 100.00 | 100.00 |
5 | 83.22 | 79.19 | 79.19 | 100.00 | 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: 30.39% helical, 21.08% extended, 48.53% loops/other (query: 32.42% 20.09% 47.49%)
SCOP classification: [Alpha and beta proteins (a/b)]/[NAD(P)-binding Rossmann-fold domains]
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.
1HDO_A c.2.1.2 238.120.120.84 NONE -56.327 0 1 92.69% 22.48% OPTM -892.785 -491.090 6.027 0.596 0.829 0.911 0.968 44.790 -69.2 7.610 186.500 -177.5 10.390 92.500 -190.0 4.900 28.200 -42.4 2.070 6.210 -75.5 8.440 51.850 -39.0 4.390 17.490 -65.2 19.210 76.860 -90.5 23.380 47.190 -98.3 -30.000 60.000 -163.0 -30.000 59.000 -165.0 17.380 421.000 -332.0 37.310 282.000 -334.0 8.920 102.000 -148.0 10.190 71.000 -157.0 5.000 -29.4 -1.529 -24.6 -31.000 268.0 5.000 -29.5 -0.071 -8.1 0.69 0.94
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----EEEEE---HHHHHHHHHHHHH---EEEEEEE------------ EEEEEE---HHHHHHHHH---EEEEEE-----
Query: 2 EKVKKIVLIGASGFVGSALLNEALNRGFEVTAVVRHPEKIKIENEHL-KVKKADVSSLDEVCEVCKGADAVISAFNPGWN 80
Sbjct: 1 MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRND 80
----EEEEE----HHHHHHHHHHHH---EEEEEE--------------EEEE-----HHHHHHHH----EEEE-------
-HHHHHHHHHHHHHHHHHHHH----EEEEEE------------------------HHHHHHHHHHHHHHHH-----EEEE
Query: 81 NPDIYDETIKVYLTIIDGVKKAGVNRFLMVGGAGSLFIAPGLRLMDSGEVPENILPGVKALGEFYLNFLMKEKEIDWVFF 160
Sbjct: 81 LSPTT-VMSEGARNIVAAMKAHGVDKVVACTSA--------FLLWDPTKVPPRL--QAVTDDHIRMHKVLRESGLKYVAV 149
----- HHHHHHHHHHHHHHHH---EEEEE--- ------------- HHHHHHHHHHHHHHHH---EEEEE
E--EE------------------------- EEEHHHHHHHHHHHHH-------EEEE--
Query: 161 SPAADMRPGVRTGRYRLGKDDMIVDIVGNS-HISVEDYAAAMIDELEHPKHHQERFTIGY 219
Sbjct: 150 MPPHIGDQPL-TGAYTVTLD-----GRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSH 203
---EEE---- ----EEE-- ------EEEHHHHHHHHHH----------EEEEE-
203 residues (92.69%) 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: 41.83% helical, 18.73% extended, 39.44% loops/other (query: 32.42% 20.09% 47.49%)
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.
2C29_D not_found 50.50.50.4 NONE -56.769 0 1 98.17% 26.05% OPTM -890.881 -742.590 3.289 0.639 0.870 0.644 0.962 43.800 -65.4 2.730 90.500 161.0 10.700 115.500 -192.5 0.050 -6.880 566.2 0.280 0.650 -48.5 0.230 -4.140 581.7 5.670 17.000 -44.1 3.210 3.500 305.3 10.410 8.390 -62.1 -30.000 8.000 -78.0 -30.000 19.000 -148.0 3.790 135.000 239.0 20.380 116.000 -167.0 1.190 4.000 29.0 6.840 37.000 -172.0 5.000 -45.0 -1.610 -23.2 0.000 -9.3e+061 5.000 -45.0 0.041 -10.0 0.41 0.78
alignment source: OPTM
-EEEEE---HHHHHHHHHHHHH---EEEEEEE--- ---------EEEEEE---HHHHHHHHH---EEEEEE
Query: 5 KKIVLIGASGFVGSALLNEALNRGFEVTAVVRHPE---------KIKIENEHLKVKKADVSSLDEVCEVCKGADAVISAF 75
Sbjct: 6 ETVCVTGASGFIGSWLVMRLLERGYTVRATVRDPTNVKKVKHLLDLPKAETHLTLWKADLADEGSFDEAIKGCTGVFHVA 85
-EEEE-----HHHHHHHHHHHH---EEEEEE-----HHHHHHHH----HHHHEEEEE---------HHHH----EEEE--
-- ---- HHHHHHHHHHHHHHHHHHHH- ---EEEEEE--------- ----------- ---- HH
Query: 76 NP-GWNN----PDIYDETIKVYLTIIDGVKKA-GVNRFLMVGGAGSLFIAP-GLRLMDSGEVP-------ENIL----PG 137
Sbjct: 86 TPMDFESKDPENEVIKPTIEGMLGIMKSCAAAKTVRRLVFTSSAGTVNIQEHQLPVYDESCWSDMEFCRAKKMTAWMYFV 165
---------HHHH-HHHHHHHHHHHHHHHHHH----EEEEE--------------EE-------HHHHHHH----HHHHH
HHHHHHHHHHHHHH-----EEEEE--EE----------- --------------EEEHHHHHHHHHHHHH--
Query: 138 VKALGEFYLNFLMKEKEIDWVFFSPAADMRPGVRTGRYR---------LGKDDMIVDIVGNSHISVEDYAAAMIDELEHP 208
Sbjct: 166 SKTLAEQAAWKYAKENNIDFITIIPTLVVGPFIMSSMPPSLITALSPITGNEAHYSIIRQGQFVHLDDLCNAHIYLFENP 245
HHHHHHHHHHHHHHHH---EEEEEE-EEE---------HHHHHH-HHHH-----HHHH-EEEEEEHHHHHHHHHHHHH--
-----EEEE--
Query: 209 KHHQERFTIGY 219
Sbjct: 246 KA-EGRYICSS 255
-- -EEEEE--
215 residues (98.17%) 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: 31.19% helical, 22.94% extended, 45.87% loops/other (query: 32.42% 20.09% 47.49%)
SCOP classification: [Alpha and beta proteins (a/b)]/[NAD(P)-binding Rossmann-fold domains]
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.
1Y81_A c.2.1.8 238.120.120.3 NONE -56.810 0 1 49.32% 21.79% OPTM -521.604 -405.300 0.564 0.568 0.330 0.662 0.893 8.420 -28.0 2.450 38.000 158.0 3.960 45.500 -122.0 0.090 2.190 320.0 -0.850 -2.310 -28.5 1.680 9.210 321.1 0.550 4.280 -24.9 5.860 3.340 180.2 6.490 6.250 -39.2 -30.000 -4.000 4.0 -30.000 -6.000 -72.0 2.250 28.500 157.0 4.700 47.000 -86.0 -2.090 6.000 178.0 -1.930 -14.000 -42.0 5.000 -5.4 -6.489 -23.6 14.000 210.0 5.000 -5.7 0.079 -4.7 0.34 0.92
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--EEEEE--- HHHHHHHHHHHHH---EEEEEEE------------EEEEEE---HHHHHHHHH---EEEEEE-----
Query: 4 VKKIVLIGAS---GFVGSALLNEALNRGFEVTAVVRHPEKIKIENEHLKVKKADVSSLDEVCEVCKGADAVISAFNPGWN 80
Sbjct: 6 FRKIALVGASKNPAKYGNIILKDLLSKGFEVLPVNPNYDEIEG-------LKCYRS----VRELPKDVDVIVFVVP---- 70
--EEEEE--------HHHHHHHHHHH---EEEEE-----EE-- EE---- ---------EEEE---
-HHHHHHHHHHHHHHHHHHHH----EEEEEE------------------------HHHHHHHHHHHHHHHH-----EEE
Query: 81 NPDIYDETIKVYLTIIDGVKKAGVNRFLMVGGAGSLFIAPGLRLMDSGEVPENILPGVKALGEFYLNFLMKEKEIDWVF 159
Sbjct: 71 --------PKVGLQVAKEAVEAGFKKLWFQPGAES---------------------------EEIRRFLEKAG-VEYSF 113
HHHHHHHHHHHHH----EEEE------ HHHHHHHHHH- -EEE-
108 residues (49.32%) 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: 46.56% helical, 19.85% extended, 33.59% loops/other (query: 32.42% 20.09% 47.49%)
SCOP classification: [Alpha and beta proteins (a/b)]/[NAD(P)-binding Rossmann-fold domains]
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.
1LSS_A c.2.1.9 238.120.120.2 NONE -57.023 0 1 60.27% 14.86% OPTM -578.115 -324.850 1.067 0.673 0.387 0.794 0.886 8.930 -27.1 3.580 67.000 61.0 -0.230 -9.500 -79.5 0.750 15.460 68.3 0.270 -2.730 -37.5 0.540 12.770 104.9 1.040 4.870 -29.4 3.170 4.700 71.1 5.820 0.180 -39.2 -30.000 1.000 -32.0 -30.000 12.000 -85.0 3.770 94.000 63.0 6.460 56.000 -101.0 -1.350 8.000 140.0 1.760 7.000 -57.0 5.000 -3.7 -1.460 -15.0 26.000 229.0 5.000 -3.7 0.447 0.2 0.23 0.71
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-EEEEE---HHHHHHHHHHHHH---EEEEEEE------------ EEEEEE---HHHHHHH HH---EEEEEE------
Query: 5 KKIVLIGASGFVGSALLNEALNRGFEVTAVVRHPEKIKIENEHL--KVKKADVSSLDEVCEV-CKGADAVISAFNPGWNN 81
Sbjct: 1 MYIIIAGI-GRVGYTLAKSLSEKGHDIVLIDIDKDICKKASAEIDALVINGDCTKIKTLEDAGIEDADMYIAVTGK---- 75
-EEEEE-- -HHHHHHHHHHHH---EEEEEE--HHHHHHHHHH---EEEE-----HHHHHH-------EEEE----
HHHHHHHHHHHHHHHHHHHH----EEEEEE------------------------HHHHHHHHHHHHHHHH-
Query: 82 PDIYDETIKVYLTIIDGVKKAGVNRFLMVGGAGSLFIAPGLRLMDSGEVPENILPGVKALGEFYLNFLMKE 152
Sbjct: 76 -------EEVNLMSSLLAKSYGINKTIARISE-----IEYKDVFERLGVDVVVSP--ELIAANYIEKLIER 132
HHHHHHHHHHHHH-----EEEE--- --HHHHHHH----EEE-H HHHHHHHHHHHH--
132 residues (60.27%) 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: 45.11% helical, 18.80% extended, 36.09% loops/other (query: 32.42% 20.09% 47.49%)
SCOP classification: [Alpha and beta proteins (a/b)]/[NAD(P)-binding Rossmann-fold domains]
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.
1LSU_A c.2.1.9 238.120.120.2 NONE -57.041 0 1 61.19% 17.45% OPTM -600.430 -260.870 1.324 0.622 0.408 0.844 0.935 8.200 -27.7 3.340 58.500 36.5 1.480 8.000 -101.5 -0.290 3.030 54.6 -0.140 0.440 -28.6 1.510 9.720 81.1 2.540 7.570 -26.5 9.190 11.580 43.1 9.310 12.800 -48.5 -30.000 -4.000 -30.0 -30.000 17.000 -88.0 3.390 63.000 57.0 5.840 40.000 -101.0 -0.200 18.000 136.0 2.380 11.000 -55.0 5.000 -7.1 0.310 -16.8 -19.000 216.0 5.000 -7.5 0.000 -1.5 0.23 0.72
alignment source: OPTM
-EEEEE---HHHHHHHHHHHHH---EEEEEEE------------ EEEEEE---HHHHHHH HH---EEEEEE------H
Query: 5 KKIVLIGASGFVGSALLNEALNRGFEVTAVVRHPEKIKIENEHL-KVKKADVSSLDEVCEV-CKGADAVISAFNPGWNNP 82
Sbjct: 7 KQFAVIGL-GRFGGSIVKELHRMGHEVLAVDINEEKVNAYASYATHAVIANATEENELLSLGIRNFEYVIVAIGAN---- 81
--EEEE-- -HHHHHHHHHHHH----EEEEE--HHHHHH------EEEE-----HHHHH--------EEEE-----
HHHHHHHHHHHHHHHHHHH----EEEEEE------------------------HHHHHHHHHHHHHHHH--
Query: 83 DIYDETIKVYLTIIDGVKKAGVNRFLMVGGAGSLFIAPGLRLMDSGEVPENILPGVKALGEFYLNFLMKEK 153
Sbjct: 82 ------IQASTLTTLLLKELDIPNIWVKAQ--NYYHHKVLEKIGA----DRIIHPEKDMGVKIAQSLSDEN 140
HHHHHHHHHHHH-----EEEEE-- -HHHHHHHHHH-- -EEE-HHHHHHHHHHHHHHH--
134 residues (61.19%) of query sequence aligned
DONE: Sun Aug 17 04:00:41 2008 EST