RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3865
(107 letters)
>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein;
HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A*
1e32_A* 1s3s_A* 2pjh_B
Length = 489
Score = 103 bits (259), Expect = 1e-27
Identities = 67/93 (72%), Positives = 78/93 (83%)
Query: 15 RGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVR 74
KMDEL LFRGDTVLL+GK+R+E+VCIVLSDDTC DEKIRMNRV+RNNLRVR
Sbjct: 36 NSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVR 95
Query: 75 LSDVVSLVPCPGIVYGKRIHVLPIDDSVQGLTG 107
L DV+S+ PCP + YGKRIHVLPIDD+V+G+TG
Sbjct: 96 LGDVISIQPCPDVKYGKRIHVLPIDDTVEGITG 128
>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix,
transport protein ATPase ubiquitin ubiquitin,
phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A
3qc8_A
Length = 187
Score = 96.3 bits (239), Expect = 1e-26
Identities = 67/93 (72%), Positives = 78/93 (83%)
Query: 15 RGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVR 74
KMDEL LFRGDTVLL+GK+R+E+VCIVLSDDTC DEKIRMNRV+RNNLRVR
Sbjct: 36 NSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVR 95
Query: 75 LSDVVSLVPCPGIVYGKRIHVLPIDDSVQGLTG 107
L DV+S+ PCP + YGKRIHVLPIDD+V+G+TG
Sbjct: 96 LGDVISIQPCPDVKYGKRIHVLPIDDTVEGITG 128
>1ypw_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48; HET: ADP ANP; 3.50A {Mus musculus} PDB: 1oz4_A*
1yq0_A* 1yqi_A* 1r7r_A* 3cf2_A* 3cf1_A* 3cf3_A*
Length = 806
Score = 99.9 bits (249), Expect = 4e-26
Identities = 67/85 (78%), Positives = 78/85 (91%)
Query: 23 AKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLV 82
KMDEL LFRGDTVLL+GK+R+E+VCIVLSDDTC DEKIRMNRV+RNNLRVRL DV+S+
Sbjct: 44 PKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQ 103
Query: 83 PCPGIVYGKRIHVLPIDDSVQGLTG 107
PCP + YGKRIHVLPIDD+V+G+TG
Sbjct: 104 PCPDVKYGKRIHVLPIDDTVEGITG 128
>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding,
transport protein; HET: MLY; 2.00A {Homo sapiens} PDB:
2pjh_B
Length = 211
Score = 95.1 bits (236), Expect = 6e-26
Identities = 66/85 (77%), Positives = 77/85 (90%)
Query: 23 AKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLV 82
KMDEL LFRGDTVLL+G +R+E+VCIVLSDDTC DEKIRMNRV+RNNLRVRL DV+S+
Sbjct: 47 PKMDELQLFRGDTVLLKGXKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQ 106
Query: 83 PCPGIVYGKRIHVLPIDDSVQGLTG 107
PCP + YGKRIHVLPIDD+V+G+TG
Sbjct: 107 PCPDVKYGKRIHVLPIDDTVEGITG 131
>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate
recognition DOM hydrolase; NMR {Thermoplasma
acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A
Length = 185
Score = 80.0 bits (197), Expect = 2e-20
Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 1/92 (1%)
Query: 15 RGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVR 74
+ R + + L+ GD V + R+ + +R++ VMRNN
Sbjct: 21 MSRVRLDESSRRLLDAEIGDVVEIEKVRKTVGRVYRARPEDENKGIVRIDSVMRNNCGAS 80
Query: 75 LSDVVSLVPCPGIVYGKRIHVLPIDDSVQGLT 106
+ D V + K++ + PI Q L
Sbjct: 81 IGDKVKVRKVR-TEIAKKVTLAPIIRKDQRLK 111
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 27.3 bits (60), Expect = 1.0
Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 5/38 (13%)
Query: 62 RMNRVMRNNLRVRLSDVVSLVPCPGIVY-----GKRIH 94
R + ++ + D+V P ++ GKRI
Sbjct: 1648 RADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR 1685
Score = 26.9 bits (59), Expect = 1.4
Identities = 14/85 (16%), Positives = 26/85 (30%), Gaps = 17/85 (20%)
Query: 10 DTVLL---RGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66
V + RG + + DEL + + R V S + + + + RV
Sbjct: 1781 SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGR----VAASFSQEAL--QYV-VERV 1833
Query: 67 MRNNLRVRLSDVVSLV--PCPGIVY 89
+ +V +V Y
Sbjct: 1834 GKRT-----GWLVEIVNYNVENQQY 1853
>1vhv_A Diphthine synthase; structural genomics, transferase; HET: MSE;
1.75A {Archaeoglobus fulgidus} SCOP: c.90.1.1
Length = 268
Score = 25.7 bits (56), Expect = 2.9
Identities = 2/26 (7%), Positives = 11/26 (42%)
Query: 37 LLRGKRRKESVCIVLSDDTCPDEKIR 62
+ + K+ + ++ +E ++
Sbjct: 190 IAEDAQMKDLYAVGIARAGSGEEVVK 215
>1g0d_A Protein-glutamine gamma-glutamyltransferase; tissue
transglutaminase,acyltransferase; 2.50A {Pagrus major}
SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4
Length = 695
Score = 25.4 bits (55), Expect = 4.6
Identities = 10/55 (18%), Positives = 18/55 (32%)
Query: 43 RKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLP 97
+ + + E + N L V L V + G++ +IHV
Sbjct: 583 STPELLVQVPGKAVVWEPLTAYVSFTNPLPVPLKGGVFTLEGAGLLSATQIHVNG 637
>2fl7_A Regulatory protein SIR3; ORC, silencing, chromatin,
transcription; 1.85A {Saccharomyces cerevisiae} PDB:
2fvu_A 3tu4_K*
Length = 232
Score = 24.3 bits (52), Expect = 8.7
Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 15 RGKRRKESAKM------DELNLFRGDTVLLRGKRRKE-SVCIV 50
R R++ + D L+ +G++V+ + SV ++
Sbjct: 32 RRSRKRGGENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLI 74
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.324 0.142 0.413
Gapped
Lambda K H
0.267 0.0539 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,621,625
Number of extensions: 86570
Number of successful extensions: 146
Number of sequences better than 10.0: 1
Number of HSP's gapped: 145
Number of HSP's successfully gapped: 16
Length of query: 107
Length of database: 6,701,793
Length adjustment: 72
Effective length of query: 35
Effective length of database: 4,691,481
Effective search space: 164201835
Effective search space used: 164201835
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.9 bits)