RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1283
(123 letters)
>1nvp_B Transcription initiation factor IIA alpha chain; transcription
regulation, DNA, complex, transcription/DNA complex;
2.10A {Homo sapiens} SCOP: a.32.1.1
Length = 57
Score = 71.4 bits (175), Expect = 4e-18
Identities = 25/49 (51%), Positives = 34/49 (69%)
Query: 6 QSLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGV 54
+ KLY++VI DVIN+V++ F ++GVDEQVL ELK +WE KL
Sbjct: 6 TNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRA 54
>1nh2_B Transcription initiation factor IIA large chain;
transcription/DNA; HET: 5IU; 1.90A {Saccharomyces
cerevisiae} SCOP: a.32.1.1 PDB: 1ytf_B*
Length = 53
Score = 70.3 bits (172), Expect = 1e-17
Identities = 19/49 (38%), Positives = 32/49 (65%)
Query: 6 QSLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGV 54
+ ++Y+ ++ V+N V+E F+ G+DEQ LQ+LK+IW+ KL V
Sbjct: 2 NAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKV 50
>1rm1_C Transcription initiation factor IIA large chain; yeast TFIIA, TBP
protein, ATA-box DNA, transcription/DNA complex; 2.50A
{Saccharomyces cerevisiae}
Length = 286
Score = 73.8 bits (179), Expect = 4e-17
Identities = 20/53 (37%), Positives = 33/53 (62%)
Query: 6 QSLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLS 58
+ ++Y+ ++ V+N V+E F+ G+DEQ LQ+LK+IW+ KL V S
Sbjct: 3 NAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTFS 55
>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 = 35.4 bits (81), Expect = 0.002
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 13/84 (15%)
Query: 4 TPQSLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELK---------HIWEAKLFGIGV 54
TP L K + ++ ++ + Q + V L E + H AKL
Sbjct: 56 TPAELVGK-FLGYVSSLVEP-SKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEND 113
Query: 55 GKLSKRKEWMSKCY-RSSNISGRP 77
L K KE + K Y + ++ RP
Sbjct: 114 TTLVKTKELI-KNYITARIMAKRP 136
Score = 28.1 bits (62), Expect = 0.97
Identities = 18/97 (18%), Positives = 32/97 (32%), Gaps = 25/97 (25%)
Query: 11 KLYQAVIADVINNVKEAFQEEGVDEQVLQEL-KHIWEA-KLFGIGVGKLSKRKEWMSKCY 68
+ Y ++ D+I + L EL + +A K+F G+ L W+
Sbjct: 178 QTYHVLVGDLIKFS----------AETLSELIRTTLDAEKVFTQGLNILE----WL---- 219
Query: 69 RSSNISGRPSLSGNLKARLVYQP--CLTQPVELLSIC 103
N S P L + + P + Q +
Sbjct: 220 --ENPSNTPDKD-YLLSIPISCPLIGVIQLAHYVVTA 253
Score = 25.8 bits (56), Expect = 5.9
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 18/49 (36%)
Query: 5 PQSLTMKLYQAVIADVINNVKEA-----F--QEEGVDEQVLQELKHIWE 46
S L++AV A F Q G + +EL+ +++
Sbjct: 141 SNS---ALFRAVGE------GNAQLVAIFGGQ--GNTDDYFEELRDLYQ 178
>3ka2_A [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydrolase-hydrolase
inhibitor complex; HET: YCM 2NC; 1.40A {Synthetic} PDB:
3fsm_A* 3gi0_A* 2o40_A* 3hzc_A* 3hlo_A* 3iaw_A* 3nxe_A*
3nxn_A* 1hvc_A* 1g6l_A 2whh_A* 1lv1_A* 3dox_A 3kt5_A
3kt2_A 3n3i_A*
Length = 203
Score = 28.7 bits (64), Expect = 0.43
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 24 VKEAFQEEGVDEQVLQE--LKHIWEAKLFGIGVGKLSKRKEW 63
+KEA + G D+ V++E L W+ KL G G+G K +++
Sbjct: 123 LKEALLDTGADDTVIEELNLPGXWKPKLIG-GIGGFIKVRQY 163
Score = 28.4 bits (63), Expect = 0.45
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 24 VKEAFQEEGVDEQVLQE--LKHIWEAKLFGIGVGKLSKRKEW 63
+KEA + G D+ V++E L W+ KL G G+ K +++
Sbjct: 19 LKEALLDTGADDTVIEELNLPGXWKPKLIG-GIAGFIKVRQY 59
>2hs1_A HIV-1 protease; ultra-high resolution active site surface binding
site, HYDR; HET: 017; 0.84A {Human immunodeficiency
virus 1} PDB: 3nu4_A* 3tl9_A* 3tkw_A* 3tkg_A* 3ndu_A*
3ndt_A* 3k4v_A* 3a2o_A* 1fgc_C* 2a1e_A* 2aod_A* 2aoi_A*
2aoj_A* 2hb3_A* 2ien_A* 1sdt_A* 2z4o_A* 2zye_A* 2nmw_A*
3b7v_A* ...
Length = 99
Score = 26.6 bits (59), Expect = 1.2
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 24 VKEAFQEEGVDEQVLQE--LKHIWEAKLFGIGVGKLSKRKEW 63
+KEA + G D+ +++E L W+ K+ G G+G K +++
Sbjct: 19 LKEALLDTGADDTIIEEMSLPGRWKPKMIG-GIGGFIKVRQY 59
>2qpq_A Protein BUG27; alpha/beta domain, venus flytrap, transport protein;
HET: CIT; 1.92A {Bordetella pertussis}
Length = 301
Score = 27.2 bits (61), Expect = 1.4
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 2 AGTPQSLTMKLYQAVIADVINN--VKEAFQEEGVD 34
TP ++ KLY IA V+ V++ + G
Sbjct: 236 GATPMAVRQKLYDG-IAKVMQRDDVQKKLADLGYS 269
>1x40_A ARAP2; ASAP-related protein2, GTPase activity, signal
transduction, SAM domain, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: a.60.1.2
Length = 91
Score = 26.4 bits (58), Expect = 1.4
Identities = 8/37 (21%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 25 KEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSKRK 61
F E G +++ I ++ L IG+ R+
Sbjct: 31 LLHFHESGFTT--VKDCAAINDSLLQKIGISPTGHRR 65
>1s1m_A CTP synthase; CTP synthetase, UTP:ammonia ligase (ADP-forming),
cytidine 5 triphosphate synthase, ammonia lyase; 2.30A
{Escherichia coli} SCOP: c.23.16.1 c.37.1.10 PDB:
2ad5_A*
Length = 545
Score = 27.1 bits (61), Expect = 1.6
Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 4/33 (12%)
Query: 14 QAVI----ADVINNVKEAFQEEGVDEQVLQELK 42
+AVI D I + + +G+D+ + +
Sbjct: 233 KAVISLKDVDSIYKIPGLLKSQGLDDYICKRFS 265
>2dvz_A BUGE, putative exported protein; periplamsic binding proteins,
carboxylate binding, glutamate, transport protein; HET:
GLU; 2.30A {Bordetella pertussis}
Length = 314
Score = 26.8 bits (60), Expect = 2.0
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 2 AGTPQSLTMKLYQAVIADVINN--VKEAFQEEGVD 34
GTP + KL A + + V +A ++G
Sbjct: 249 KGTPMDVVNKLRDA-AVVALKDPKVIKALDDQGSA 282
>2f5x_A BUGD; periplasmic binding protein, transport protein; 1.72A
{Bordetella pertussis tohama I}
Length = 312
Score = 26.4 bits (59), Expect = 2.3
Identities = 7/35 (20%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 2 AGTPQSLTMKLYQAVIADVINN--VKEAFQEEGVD 34
GTP+ + KL ++ + + + +E ++ G +
Sbjct: 245 KGTPKPVVDKLVKS-LQAGLADPKFQERMKQLGAE 278
>3nva_A CTP synthase; rossman fold, nucleotide binding, LIG; 2.50A
{Sulfolobus solfataricus}
Length = 535
Score = 26.7 bits (60), Expect = 2.4
Identities = 4/33 (12%), Positives = 12/33 (36%), Gaps = 4/33 (12%)
Query: 14 QAVI----ADVINNVKEAFQEEGVDEQVLQELK 42
++ + V + + + ++L LK
Sbjct: 235 DHIVSSYDVETSYEVPIILESQKLVSKILSRLK 267
>1vco_A CTP synthetase; tetramer, riken structural genomics/proteomics
initiative, RSGI, structural genomics, ligase; HET: GLN;
2.15A {Thermus thermophilus} SCOP: c.23.16.1 c.37.1.10
PDB: 1vcn_A 1vcm_A
Length = 550
Score = 26.7 bits (60), Expect = 2.4
Identities = 6/33 (18%), Positives = 12/33 (36%), Gaps = 4/33 (12%)
Query: 14 QAVI----ADVINNVKEAFQEEGVDEQVLQELK 42
V + + V +E+G+ V + L
Sbjct: 244 GHVFSSPTVEHLYEVPLLLEEQGLGRAVERALG 276
>2f3n_A SH3 and multiple ankyrin repeat domains 3; postsynaptic density,
SAM domain, shank, scaffolding protein, structural
protein; 2.10A {Rattus norvegicus} SCOP: a.60.1.2 PDB:
2f44_A
Length = 76
Score = 25.4 bits (56), Expect = 2.4
Identities = 6/37 (16%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 25 KEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSKRK 61
++ F++ ++ L L +GV ++ R+
Sbjct: 23 RDRFEDHEIEGAHLPALTK---EDFVELGVTRVGHRE 56
>2vv5_A MSCS, small-conductance mechanosensitive channel; ION transport,
transmembrane, inner membrane, membrane struc membrane
protein, membrane; 3.45A {Escherichia coli} SCOP:
b.38.1.3 d.58.43.1 f.34.1.1 PDB: 2oau_A
Length = 286
Score = 26.2 bits (58), Expect = 3.4
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 13 YQAVIADVINNVKEAFQEEGVD 34
Q V DV+ +K F G+
Sbjct: 246 LQNVYWDVLERIKREFDAAGIS 267
>1f0x_A DLDH, D-lactate dehydrogenase; oxidoreductase; HET: FAD; 1.90A
{Escherichia coli} SCOP: d.58.32.2 d.145.1.1
Length = 571
Score = 25.4 bits (55), Expect = 6.4
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 53 GVGKLSKRKEW 63
G+GK SKRK W
Sbjct: 557 GIGKTSKRKNW 567
>3mg1_A OCP, orange carotenoid protein; carotenoid binding protein,
echinone, phycobilisome; HET: ECH; 1.65A {Synechocystis
SP} PDB: 3mg2_A* 3mg3_A* 1m98_A*
Length = 323
Score = 25.4 bits (55), Expect = 6.7
Identities = 8/36 (22%), Positives = 13/36 (36%)
Query: 1 MAGTPQSLTMKLYQAVIADVINNVKEAFQEEGVDEQ 36
M T S + ADV+ F + ++Q
Sbjct: 1 MPFTIDSARGIFPNTLAADVVPATIARFSQLNAEDQ 36
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 25.2 bits (55), Expect = 7.2
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 35 EQVLQELKHIWEAKLFGIGVGKLSKRKEWM 64
+ + L+ + E+ + +G + R EWM
Sbjct: 178 SDIRERLEKVPESDVEILGYDPTTSRPEWM 207
>2gle_A Neurabin-1; SAM domain, scaffold, protein protein interaction,
protein binding; NMR {Rattus norvegicus}
Length = 74
Score = 24.2 bits (53), Expect = 7.3
Identities = 7/37 (18%), Positives = 13/37 (35%), Gaps = 3/37 (8%)
Query: 25 KEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSKRK 61
F + + + L +L KL +G+ R
Sbjct: 25 VSEFSAQNISGEQLLQLDG---NKLKALGMTSSQDRA 58
>3b4r_A Putative zinc metalloprotease MJ0392; intramembrane protease, CBS
domain, hydrolase, metal-binding, transmembrane; 3.30A
{Methanocaldococcus jannaschii}
Length = 224
Score = 24.9 bits (54), Expect = 7.6
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 37 VLQELKHIWEAKLFGIGVGKL 57
VL EL H + AK +G+ + K+
Sbjct: 52 VLHELGHSYVAKKYGVKIEKI 72
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
0.318 0.132 0.383
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,822,225
Number of extensions: 95202
Number of successful extensions: 204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 204
Number of HSP's successfully gapped: 27
Length of query: 123
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,412,271
Effective search space: 180903111
Effective search space used: 180903111
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.6 bits)