RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9514
(611 letters)
>1vhn_A Putative flavin oxidoreducatase; structural genomics, unknown
function; HET: FMN; 1.59A {Thermotoga maritima} SCOP:
c.1.4.1
Length = 318
Score = 173 bits (441), Expect = 2e-49
Identities = 71/341 (20%), Positives = 125/341 (36%), Gaps = 113/341 (33%)
Query: 255 IDWQGKLYLSPLTTVGNLPFRRLCKKWGADITCSEMAVATELLKSSPQEWALIKRHESED 314
+ + K+ L+P+ + FR L +WGAD SEM A L +S + L+ E
Sbjct: 1 MSLEVKVGLAPMAGYTDSAFRTLAFEWGADFAFSEMVSAKGFLMNSQKTEELLP-QPHER 59
Query: 315 LFGVQLCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLLQRANLFGVQ 374
VQ+ G+ P L++ ++L E+ ++D+N GCP+ + K+G+G LL+ F
Sbjct: 60 NVAVQIFGSEPNELSEAARILSEK--YKWIDLNAGCPVRKVVKEGAGGALLKDLRHF--- 114
Query: 375 LCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITCMN 434
I++ +
Sbjct: 115 ------------------------------------------------RYIVRELR---- 122
Query: 435 EVSSLPITVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKC 494
+ S +VKTR G K+ + + G + +H RT Q +T +A+W +
Sbjct: 123 KSVSGKFSVKTRLGWEKNE--VEEIYRILVEEGVDEVFIHTRTVVQSFTGRAEWKALSVL 180
Query: 495 AQLCSRDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSPAPLYG 554
+ I P +
Sbjct: 181 EK------RI----------------------------------------------PTFV 188
Query: 555 NGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEIKE 595
+GDI + ED +L++S G+++ RGA+ +PWIF++IK+
Sbjct: 189 SGDIFTPEDAKRALEES-GCDGLLVARGAIGRPWIFKQIKD 228
>3b0p_A TRNA-dihydrouridine synthase; TIM barrel, oxidoreductase; HET: FMN;
1.70A {Thermus thermophilus} PDB: 3b0u_X* 3b0v_C*
Length = 350
Score = 56.9 bits (138), Expect = 8e-09
Identities = 29/109 (26%), Positives = 50/109 (45%), Gaps = 9/109 (8%)
Query: 373 VQLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGS-G--LLQRANILQSV 429
+QL G++P L + ++ E D +++NLGCP E K G G LL ++ +
Sbjct: 62 LQLAGSDPKSLAEAARIGEA-FGYDEINLNLGCPSE---KAQEGGYGACLLLDLARVREI 117
Query: 430 ITCMNEVSSLPITVKTRTGIHKDNN--IIHNFMPKFRDWGASLITLHGR 476
+ M E +P+TVK R G+ + + + G + +H R
Sbjct: 118 LKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHAR 166
Score = 38.0 bits (89), Expect = 0.007
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 555 NGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEIKEKKLFD 600
NG I S E+ LK+ + GVM+GR P++ +E ++++F
Sbjct: 203 NGGIRSLEEALFHLKR---VDGVMLGRAVYEDPFVLEEA-DRRVFG 244
Score = 36.8 bits (86), Expect = 0.015
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 288 SEMAVATELLKSSPQEWALIKRHESEDLFGVQLCGNNPYVLTKCTQLLEEQMAVDFVDVN 347
+EM V +L+ + + L+ E +QL G++P L + ++ E D +++N
Sbjct: 34 TEMTVDQAVLRGNRER--LLAFRPEEHPIALQLAGSDPKSLAEAARIGEA-FGYDEINLN 90
Query: 348 LGCP 351
LGCP
Sbjct: 91 LGCP 94
>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein;
NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A
Length = 77
Score = 50.3 bits (120), Expect = 2e-08
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 88 TCKYGEKCKFVHDKNV--FMKSKPEDISEQCYVFLQHGYCPMGIACRF 133
C+YG KC+F H P+ +E C+ F G CP G C F
Sbjct: 23 RCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHF 70
Score = 29.5 bits (66), Expect = 0.59
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 88 TCKYGEKCKFVHDKN 102
C YG +C F+H+
Sbjct: 61 RCPYGSRCHFIHNPT 75
Score = 26.5 bits (58), Expect = 6.1
Identities = 7/33 (21%), Positives = 13/33 (39%), Gaps = 6/33 (18%)
Query: 101 KNVFMKSKPEDISEQCYVFLQHGYCPMGIACRF 133
+ K++ C + + G C G C+F
Sbjct: 6 TSSRYKTEL------CRTYSESGRCRYGAKCQF 32
>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 = 49.1 bits (116), Expect = 4e-06
Identities = 87/533 (16%), Positives = 154/533 (28%), Gaps = 147/533 (27%)
Query: 6 VAKIKQEFIVEDHVKVLSIECVNE--TDKRKLEELEVEDDGTAKKKFKKNKQVLKGQNKA 63
++ IK E + + IE + D + + V + + + K +Q L A
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV----SRLQPYLKLRQALLELRPA 150
Query: 64 RGPTFVT--------KPEDCYCPFLKDSTL-EQTCK-YGEKCKFVHDKNVF-----MKSK 108
+ V K + + C Y +CK D +F +
Sbjct: 151 KN---VLIDGVLGSGK-----------TWVALDVCLSYKVQCKM--DFKIFWLNLKNCNS 194
Query: 109 PEDISEQ----CYVFLQHGYC-----PMGIACRFGS-----SHL--DENGGN--IVKEDV 150
PE + E Y + + I R S L + N +V +V
Sbjct: 195 PETVLEMLQKLLYQ-IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV 253
Query: 151 --LKEWKN---------TVGNKTV-NMLANEVRQDLR--KHTYNFEKSEKICKENKASKN 196
K W T K V + L+ + H+ E ++ K
Sbjct: 254 QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV---KSLLLKY 310
Query: 197 ENKDTDD----CCKN--QDSKVI--EGREEINT------PNTDDVIKVQEETKSGPVLDT 242
+ D + +I R+ + T N D + + E S VL+
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE--SSLNVLEP 368
Query: 243 DIIK------------IKNSEKK-KIDWQGKLYLSPLTTVGNLPFRRLCKKWGADITCSE 289
+ + W + + V L L +K + T S
Sbjct: 369 AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428
Query: 290 MAVATELLKSSPQEWAL----------IKRHESEDLFGVQLCGNNPYV-------LTKCT 332
++ EL E+AL K +S+DL L Y L
Sbjct: 429 PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ---YFYSHIGHHLKNIE 485
Query: 333 Q----LLEEQMAVD--FVDVNLGCPIEFIYKQGSGSGLLQRANLFGVQLCGNNPYVLTKC 386
L + +D F++ + GS LQ+ + +C N+P
Sbjct: 486 HPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKY---- 541
Query: 387 TQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITCMNEVSSL 439
E++V +D F+ K + ++L+ I M E ++
Sbjct: 542 -----ERLVNAILD--------FLPKIEENLICSKYTDLLR--IALMAEDEAI 579
Score = 46.4 bits (109), Expect = 3e-05
Identities = 28/192 (14%), Positives = 63/192 (32%), Gaps = 56/192 (29%)
Query: 450 HKDNNIIHNFMPKF-RDWGASLITLHGRTREQRYTKQ----ADWDYIEKCAQ-------- 496
++ +I+ F F ++ + Q K + D+I
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDV--------QDMPKSILSKEEIDHIIMSKDAVSGTLRL 67
Query: 497 ---LCSRDNNIIHNFM-----PKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCS 548
L S+ ++ F+ + + S I R YIE+ +L +
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRINY-KFLMSPIKTEQRQPSMMTRM-----YIEQRDRLYN 121
Query: 549 PAPLYGNGDILSYEDYTE------SLKKSPSIS--GVMIGRGALIKPWI------FQEIK 594
++ ++ + Y + L+ + ++ G ++G G K W+ +++
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG-VLGSG---KTWVALDVCLSYKVQ 177
Query: 595 EKKLFDIYAIVW 606
K F I+ W
Sbjct: 178 CKMDFKIF---W 186
Score = 35.6 bits (81), Expect = 0.059
Identities = 59/375 (15%), Positives = 110/375 (29%), Gaps = 103/375 (27%)
Query: 283 ADITCSEMAVATELLKSSPQEWALIKRHESEDLFGVQLCGNNPYVLTKCTQLLEEQMAVD 342
+ C ++ ++ KS ++ + E + + + + L +E+M
Sbjct: 31 DNFDCKDV---QDMPKS------ILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81
Query: 343 FVDVNLGCPIEFI-------YKQGSGSGLL---QRANLFGVQLCGNNPYV---------L 383
FV+ L +F+ +Q S + QR L+ N +
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN----DNQVFAKYNVSRLQPY 137
Query: 384 TKCTQLLEEQMVVDFVDVN--LGC-----------------PIEF-IY-----KQGSGSG 418
K Q L E V ++ LG ++F I+ S
Sbjct: 138 LKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPET 197
Query: 419 LLQRANILQSVITCMNEVSSLPITVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTR 478
+L+ L I N S + + IH + + K + + L+ L
Sbjct: 198 VLEMLQKLLYQIDP-NWTSRSDHSSNIKLRIHSIQAELRRLL-KSKPYENCLLVL----L 251
Query: 479 EQRYTKQADWDYIE-KCAQLC-SRDNNIIHNFMPKFRDWGASLITLHGRTREQR--YTKQ 534
+ K W+ C L +R + D+ ++ T H T
Sbjct: 252 NVQNAK--AWNAFNLSCKILLTTRFKQVT--------DFLSAATTTHISLDHHSMTLTPD 301
Query: 535 ADWDYIEKCAQLCSPA--PLYGNGDILSYEDYTESLKKSP-SISGVMIGRGALIKPWI-- 589
+ K C P P E L +P +S +I I+ +
Sbjct: 302 EVKSLLLKYLD-CRPQDLPR-------------EVLTTNPRRLS--II--AESIRDGLAT 343
Query: 590 ---FQEIKEKKLFDI 601
++ + KL I
Sbjct: 344 WDNWKHVNCDKLTTI 358
>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1
Length = 98
Score = 41.6 bits (97), Expect = 5e-05
Identities = 12/53 (22%), Positives = 17/53 (32%), Gaps = 14/53 (26%)
Query: 85 LEQTCKYGEKCKFVHDKNVFMKSKPEDISEQCYVFLQHGYCPMGIACRFGSSH 137
+ C E C ++H C ++ G C G C F SH
Sbjct: 20 ITGFCARAENCPYMHGDFP------------CKLYHTTGNCINGDDCMF--SH 58
Score = 29.3 bits (65), Expect = 0.97
Identities = 8/30 (26%), Positives = 11/30 (36%), Gaps = 6/30 (20%)
Query: 77 CPFLKDST------LEQTCKYGEKCKFVHD 100
CP++ C G+ C F HD
Sbjct: 30 CPYMHGDFPCKLYHTTGNCINGDDCMFSHD 59
>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit;
CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 77
Score = 36.0 bits (83), Expect = 0.003
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 10/58 (17%)
Query: 85 LEQTCKYGEKCKFVHDKNVFMKSKPEDISEQCYVFLQHGYCPMGIACRFGSSHLDENG 142
L CK G++C+F+H+ ++ +CY + + G C C F H+D
Sbjct: 17 LRGLCKKGDQCEFLHEYDM-------TKMPECYFYSKFGECS-NKECPF--LHIDPES 64
>2rhk_C Cleavage and polyadenylation specificity factor subunit 4;
influenza A, nonstructural protein, viral protein: HOST
complex, Zn finger; 1.95A {Homo sapiens}
Length = 72
Score = 35.6 bits (82), Expect = 0.003
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 10/57 (17%)
Query: 85 LEQTCKYGEKCKFVHDKNVFMKSKPEDISEQCYVFLQHGYCPMGIACRFGSSHLDEN 141
L CK G++C+F+H+ ++ E CY + + G C C F H+D
Sbjct: 23 LRGLCKKGDQCEFLHEYDM--TKMSE-----CYFYSKFGECS-NKECPF--LHIDPE 69
>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 = 36.6 bits (84), Expect = 0.027
Identities = 52/303 (17%), Positives = 89/303 (29%), Gaps = 104/303 (34%)
Query: 1 MD---ASGVAK-IKQEFIVEDHVKV---LSI-ECVNETDKRKLEELEVEDDGTAKKKFKK 52
MD S A+ + ++H K SI + V L + G K+ ++
Sbjct: 1633 MDLYKTSKAAQDVWNR--ADNHFKDTYGFSILDIVINNPV----NLTIHFGGEKGKRIRE 1686
Query: 53 NKQVLKGQNKARGPTFVTKPEDCYCPFLKDSTLEQTCKYGEKCKFVHDKNV--------- 103
N + + G K K+ E + Y F +K +
Sbjct: 1687 NYSAMIFETIVDGKLKTEK-------IFKEIN-EHSTSY----TFRSEKGLLSATQFTQP 1734
Query: 104 ---------F--MKSK---PEDISEQCYVFLQH--G-YCPMGIACRFGSSHLD-ENG--- 142
F +KSK P D F H G Y +A + E+
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPAD-----ATFAGHSLGEYA--ALASLADV--MSIESLVEV 1785
Query: 143 ----GNIVKEDVLKEWKNTVGNKTVNMLANEVRQDLRKHTYNFEKSEKICKENKASKNEN 198
G ++ V ++ +G M+A + +++ E + + +
Sbjct: 1786 VFYRGMTMQVAVPRD---ELGRSNYGMIA--INPGRVAASFSQEALQYVVER-------- 1832
Query: 199 KDTDDCCKNQDSKVIEGREEI---NTPNTDDVIKVQEETKSGPV--LDTDIIKIKNSEKK 253
K V EI N N V +G + LDT + + +
Sbjct: 1833 -----VGKRTGWLV-----EIVNYNVENQQYVA-------AGDLRALDTVTNVLNFIKLQ 1875
Query: 254 KID 256
KID
Sbjct: 1876 KID 1878
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.0 bits (64), Expect = 3.3
Identities = 9/78 (11%), Positives = 25/78 (32%), Gaps = 19/78 (24%)
Query: 148 EDVLKEW----------KNTVGNKTVNMLANEVRQDLRK--HTYNFEKSEKICKENKASK 195
+ +++W + + ++DL + + E+ EK N+ +
Sbjct: 84 PESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQS-EQVEKNKINNRIAD 142
Query: 196 NENKDTDDCCKNQDSKVI 213
+ D+ +I
Sbjct: 143 KAFY------QQPDADII 154
>1jub_A Dihydroorotate dehydrogenase A; homodimer, alpha-beta barrel,
flavoprotein, mutant enzyme, oxidoreductase; HET: FMN;
1.40A {Lactococcus lactis} SCOP: c.1.4.1 PDB: 1ovd_A*
1jue_A* 1dor_A* 2bsl_A* 2bx7_A* 2dor_A* 1jqv_A* 1jrb_A*
1jrc_A* 1jqx_A*
Length = 311
Score = 29.5 bits (67), Expect = 3.5
Identities = 10/81 (12%), Positives = 25/81 (30%), Gaps = 19/81 (23%)
Query: 371 FGVQLCGNNP--YVLTKCTQLLEEQMVVDFVDVNLGCP-----IEFIYKQGSGSGLLQRA 423
+ G + + + ++E ++NL CP + Y
Sbjct: 96 IFFSIAGMSAAENI--AMLKKIQESDFSGITELNLSCPNVPGEPQLAYD----------F 143
Query: 424 NILQSVITCMNEVSSLPITVK 444
+ ++ + + P+ VK
Sbjct: 144 EATEKLLKEVFTFFTKPLGVK 164
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.4 bits (62), Expect = 4.4
Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 8/26 (30%)
Query: 251 EK---KKIDWQGKLYLSPLTTVGNLP 273
EK KK+ KLY + + P
Sbjct: 18 EKQALKKLQASLKLY-AD----DSAP 38
>2lhn_A Nuclear polyadenylated RNA-binding protein NAB2; nuclear protein;
NMR {Saccharomyces cerevisiae S288C}
Length = 80
Score = 27.2 bits (60), Expect = 4.5
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 11/56 (19%)
Query: 86 EQTCKYGEKCK-----FVHDKNVFM-KSKPEDISEQCYVFLQHGYCPMGIACRFGS 135
+ CK+G C + H ++ M + C H P+ CRFG
Sbjct: 9 LEQCKFGTHCTNKRCKYRHARSHIMCREGANCTRIDC--LFGH---PINEDCRFGV 59
>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse,
cytoplastic, hydrolase; 2.00A {Homo sapiens}
Length = 223
Score = 27.8 bits (61), Expect = 9.7
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 6/36 (16%)
Query: 64 RGPTFVTKPEDCYCPFLKDSTLEQTCKYGEKCKFVH 99
R + CP+ + C YG KC+F H
Sbjct: 182 RKKPLTLEHRKQPCPYGR------KCTYGIKCRFFH 211
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 0.135 0.414
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 9,337,909
Number of extensions: 551615
Number of successful extensions: 1037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1018
Number of HSP's successfully gapped: 25
Length of query: 611
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 512
Effective length of database: 3,937,614
Effective search space: 2016058368
Effective search space used: 2016058368
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: 60 (27.4 bits)