RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4458
(303 letters)
>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
signaling protein; NMR {Mus musculus} SCOP: a.4.5.47
Length = 84
Score = 104 bits (260), Expect = 2e-28
Identities = 21/72 (29%), Positives = 36/72 (50%)
Query: 197 KMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG 256
+L V+EHN+ +K Y IT + + LL +P + E+ S M+ + ID+ G
Sbjct: 10 SILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDG 69
Query: 257 IINFARNKDPGE 268
I++F + G
Sbjct: 70 IVHFETREASGP 81
>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha
solenoid, regulatory PART LID, hydrolase, protein
binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A
Length = 394
Score = 104 bits (261), Expect = 6e-26
Identities = 41/297 (13%), Positives = 105/297 (35%), Gaps = 11/297 (3%)
Query: 1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINT 60
+ D TEA + +L E +K V + L + + A + + + T
Sbjct: 108 LYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSART 167
Query: 61 KFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQN 120
+ L ++ E + ++ ++
Sbjct: 168 TANAIYCPPKVQGALDLQSGILHA-ADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYM 226
Query: 121 VVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELF 180
++ +ML D+ ++ ++ +I K + + L + + Y++EL
Sbjct: 227 LLCKIMLGQSDDVNQLVSGKLAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELA 286
Query: 181 KTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSS 240
+ + Q L ++E N+ + + Y+R+ + + + + LP+ + E+ LS
Sbjct: 287 EDVIV-------QAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQ 339
Query: 241 MVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMI 297
M++ K + +D+ G++ + ++ + K+V+ L K + +
Sbjct: 340 MILDKKFSGILDQGEGVLIVFEETPVDKTYERVLETIQSMGKVVDT---LYQKAKKL 393
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 58.7 bits (141), Expect = 8e-10
Identities = 45/322 (13%), Positives = 105/322 (32%), Gaps = 70/322 (21%)
Query: 11 AANIIQELQVET-------YGSMEKKEKVTLILEQM-RLCL-AKKDYIRTQIISKKINTK 61
A ++ +V+ + +++ +LE + +L ++ T N K
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNW--TSRSDHSSNIK 224
Query: 62 F-FDDEKDDVQEL-KLKYYR--LMIELD-----QHEGSYLATCKHYRAILTTPCIQ-SDP 111
+ +++ L K K Y L++ L + ++ +CK +LTT Q +D
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLLV-LLNVQNAKAWNAFNLSCK---ILLTTRFKQVTDF 280
Query: 112 VQRHAVLQNVVLYLMLAPYDNEQS-DLTHRVLE---DKLLNEI----PLYKGLLQWFTNP 163
+ A ++ L ++ L + L+ L E+ P ++
Sbjct: 281 LS-AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD 339
Query: 164 ELIKWSGLRQLYEEEL---FKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITL 220
L W + + ++L ++S+ E +K F L V + I
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS--VFPPS--------AHIPT 389
Query: 221 QRMCDL-LGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNE 279
+ + + + ++ + + K P E + S+
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLV---------------EKQP----KESTISIPS 430
Query: 280 LMKLVNNTTHLINKEQMIHQRV 301
+ + L N+ + H+ +
Sbjct: 431 I--YLELKVKLENEYAL-HRSI 449
>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 = 50.0 bits (119), Expect = 5e-07
Identities = 58/322 (18%), Positives = 98/322 (30%), Gaps = 114/322 (35%)
Query: 22 TYGSMEKKEKVTLIL--------EQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQEL 73
++GS+E L++ Q++ K T+ + DDE EL
Sbjct: 12 SHGSLE----HVLLVPTASFFIASQLQEQFNKILPEPTEGFAA-------DDEPTTPAEL 60
Query: 74 KLKY---------------YR--LMIELDQHEGSYLATCK-HYRAILTTPCIQSDPVQRH 115
K+ + L + L + E YL H A + V+
Sbjct: 61 VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTK 120
Query: 116 AVLQNVVLY-----LMLAPYDN-EQSDLTHRVLEDKLLNEIPLYK---GLLQ-----WFT 161
+++N Y + P+D S L V E L G Q +F
Sbjct: 121 ELIKN---YITARIMAKRPFDKKSNSALFRAVGE----GNAQLVAIFGG--QGNTDDYF- 170
Query: 162 NPELIKWSGLRQLYE------EELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYY 215
E LR LY+ +L K S + L ++ + K +
Sbjct: 171 -EE------LRDLYQTYHVLVGDLIKFS------------AETLS-ELIRTTLDA-EKVF 209
Query: 216 TRITLQRMCDLLG-LPIEET---EEFLSSMVVS-KTITAKIDRPAGIINFAR-------- 262
T+ ++L L +++L S+ +S I G+I A
Sbjct: 210 TQG-----LNILEWLENPSNTPDKDYLLSIPISCPLI--------GVIQLAHYVVTAKLL 256
Query: 263 NKDPGEILNEWSASLNELMKLV 284
PGE+ + + LV
Sbjct: 257 GFTPGELRSYLKGATGHSQGLV 278
>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export,
transcription; 2.12A {Homo sapiens}
Length = 203
Score = 31.8 bits (72), Expect = 0.20
Identities = 21/198 (10%), Positives = 61/198 (30%), Gaps = 31/198 (15%)
Query: 76 KYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQS 135
KYY + + + ++ L+ + + +++YL+
Sbjct: 17 KYYVGRKAMFDSD--FKQAEEY----LSF-AFEHCHRSSQKNKRMILIYLLPVKM----- 64
Query: 136 DLTHRVLEDKLLNEIPL--YKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQ 193
L + +LL + L + + + + L+ +E + +F
Sbjct: 65 -LLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFL------- 116
Query: 194 KCFKMLKHRVVEHNIRVMAKYY--TRITLQRMCDLLGL------PIEETEEFLSSMVVSK 245
+ LK + + + +++L L I+E + L++++
Sbjct: 117 -ILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMG 175
Query: 246 TITAKIDRPAGIINFARN 263
+ I + ++
Sbjct: 176 HVKGYISHQHQKLVVSKQ 193
>1z8o_A 6-deoxyerythronolide B hydroxylase; heme, CYP, erythromycin,
oxidoreductase; HET: HEM DEB; 1.70A {Saccharopolyspora
erythraea} SCOP: a.104.1.1 PDB: 1z8p_A* 1z8q_A* 1jio_A*
1jip_A* 1eup_A* 1egy_A* 1jin_A* 1oxa_A*
Length = 404
Score = 28.0 bits (63), Expect = 4.2
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 11/57 (19%)
Query: 223 MCDLLGLPIEETEEF--LSSMVVSKTITAKIDRPAGIINF---------ARNKDPGE 268
+C+LLG+ + EF SS ++ R R +PG+
Sbjct: 153 ICELLGVDEKYRGEFGRWSSEILVMDPERAEQRGQAAREVVNFILDLVERRRTEPGD 209
>1ued_A P450 OXYC, P450 monooxygenase; cytochrome P450 vancomycin
biosynthesis, oxidoreductase; HET: HEM PG4; 1.90A
{Amycolatopsis orientalis} SCOP: a.104.1.1
Length = 406
Score = 27.6 bits (62), Expect = 6.2
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 12/57 (21%)
Query: 223 MCDLLGLPIEETEEF--LSSMVVSKTITAKIDRPAGIINF---------ARNKDPGE 268
+C+LLG+P ++ EF + K R A F + DP +
Sbjct: 161 LCELLGIPRDDQREFVRRIRRNADLSRGLK-ARAADSAAFNRYLDNLLARQRADPDD 216
>2q9q_C DNA replication complex GINS protein PSF1; elongated spindle, helix
bundle, replication; HET: DNA; 2.36A {Homo sapiens}
Length = 196
Score = 26.8 bits (59), Expect = 6.6
Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 1/49 (2%)
Query: 171 LRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKY-YTRI 218
++ LYE+ + +H + N R Y Y R+
Sbjct: 36 MKALYEQNQSDVNEAKSGGRSDLIPTIKFRHCSLLRNRRCTVAYLYDRL 84
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA,
DNA-binding, phosphorylation, POL I, POLI, rpoli,
nuclear protein; 3.10A {Saccharomyces cerevisiae}
Length = 214
Score = 27.0 bits (59), Expect = 8.0
Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 2/77 (2%)
Query: 96 KHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPY--DNEQSDLTHRVLEDKLLNEIPLY 153
K ++ +T P + + V + LY+ LAP +N + + L ++
Sbjct: 18 KKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQGVMKQHLNPLVMKYNNKV 77
Query: 154 KGLLQWFTNPELIKWSG 170
G++ + +++
Sbjct: 78 GGVVLGYEGLKILDADP 94
>1w4s_A Polybromo, polybromo 1 protein; BAH, bromo-associated homology
domain, chromatin remodelling, PBAF, SWI/SNF-B, RSC,
nuclear protein; 1.55A {Gallus gallus}
Length = 174
Score = 26.4 bits (58), Expect = 9.8
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 158 QWFTNPELIKWSGLRQLYEEELFKTSVFN 186
WF P R+ E+E+FK+ +N
Sbjct: 65 CWFYRPNETFHLATRKFLEKEVFKSDYYN 93
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
0.319 0.134 0.381
Gapped
Lambda K H
0.267 0.0473 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,537,513
Number of extensions: 266046
Number of successful extensions: 701
Number of sequences better than 10.0: 1
Number of HSP's gapped: 696
Number of HSP's successfully gapped: 23
Length of query: 303
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 210
Effective length of database: 4,105,140
Effective search space: 862079400
Effective search space used: 862079400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.4 bits)