RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18031
(136 letters)
>1pp9_F Ubiquinol-cytochrome C reductase complex 14 kDa P; cytochrome BC1,
membrane protein, heme protein, rieske iron protein,
cytochrome B, complex III; HET: BHG HEM HEC SMA UQ CDL
PEE; 2.10A {Bos taurus} SCOP: f.27.1.1 PDB: 1bgy_F*
1be3_F* 1l0n_F* 1ntk_F* 1ntm_F* 1ntz_F* 1nu1_F* 1l0l_F*
1ppj_F* 1sqb_F* 1sqq_F* 1sqv_F* 1sqx_F* 2a06_F* 2fyu_F*
2ybb_F* 1sqp_F* 1qcr_F* 1bcc_F* 2bcc_F* ...
Length = 110
Score = 130 bits (328), Expect = 1e-40
Identities = 47/95 (49%), Positives = 70/95 (73%)
Query: 40 ALQKWAWEYSGFRKYGLYYDDLANETPVVEEALRRLPEKLKNERHFRQLRAVQLNIQKSI 99
++KW + +GF K GL DD +E V+EA+RRLPE L ++R FR RA+ L++++ I
Sbjct: 15 GIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAIRRLPENLYDDRVFRIKRALDLSMRQQI 74
Query: 100 LPKDQWTKYEDETRYLKPYIEQVEKEFKEKEEWGK 134
LPK+QWTKYE++ YL+PY+++V +E KE+EEW K
Sbjct: 75 LPKEQWTKYEEDKSYLEPYLKEVIRERKEREEWAK 109
>3cx5_G Cytochrome B-C1 complex subunit 7; complex III, electron transfer
complex, cytochrome BC1 complex,
mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ
HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces
cerevisiae} SCOP: f.27.1.1 PDB: 1kyo_G* 3cxh_G* 2ibz_F*
1ezv_F* 1kb9_G* 1p84_G*
Length = 126
Score = 126 bits (318), Expect = 7e-39
Identities = 35/97 (36%), Positives = 56/97 (57%), Gaps = 1/97 (1%)
Query: 40 ALQKWAWEYSGFRKYGLYYDDLANE-TPVVEEALRRLPEKLKNERHFRQLRAVQLNIQKS 98
+ +G++K GL +DDL E P+++ ALRRLPE R +R +RA Q +
Sbjct: 26 PVANQFINLAGYKKLGLKFDDLIAEENPIMQTALRRLPEDESYARAYRIIRAHQTELTHH 85
Query: 99 ILPKDQWTKYEDETRYLKPYIEQVEKEFKEKEEWGKL 135
+LP+++W K +++ YL PYI + E KEK+E +
Sbjct: 86 LLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELDNI 122
>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 = 35.0 bits (80), Expect = 0.004
Identities = 14/102 (13%), Positives = 33/102 (32%), Gaps = 37/102 (36%)
Query: 68 VEEALRR----LPEK------LKN-ERHF------RQLRAVQLNIQKSILP--KDQW-TK 107
V++ + + LP L N ++ + L + L ++K+ P DQ
Sbjct: 349 VQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIP 408
Query: 108 YEDE----------------TRYLKPYIEQVEKEFKEKE-EW 132
+ + + L P + + K+ + +
Sbjct: 409 FSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSF 450
Score = 25.4 bits (55), Expect = 9.7
Identities = 19/80 (23%), Positives = 27/80 (33%), Gaps = 9/80 (11%)
Query: 60 DLANETPVVEEALRRLPEKLKNERHFRQLRAVQLN-IQKSILPKDQWTKYEDETRYLKPY 118
DL + ++ R K+ F L V N + +I + K E Y
Sbjct: 1634 DLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRE-NYSAMI 1692
Query: 119 IE-------QVEKEFKEKEE 131
E + EK FKE E
Sbjct: 1693 FETIVDGKLKTEKIFKEINE 1712
>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 = 32.9 bits (74), Expect = 0.022
Identities = 13/84 (15%), Positives = 31/84 (36%), Gaps = 11/84 (13%)
Query: 58 YDDLANETPVVEEALRRLPEKLKNERHFRQLRAVQLNIQKSILPKDQW------TKYEDE 111
D + RL L + +Q VQ +++ + ++ T+
Sbjct: 51 IDHIIMS-KDAVSGTLRLFWTLLS----KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQP 105
Query: 112 TRYLKPYIEQVEKEFKEKEEWGKL 135
+ + YIEQ ++ + + + + K
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKY 129
Score = 32.1 bits (72), Expect = 0.042
Identities = 22/132 (16%), Positives = 45/132 (34%), Gaps = 32/132 (24%)
Query: 4 LNKRLVRTYEVLTHTSADVHDFESSKTHL---IFVYISGALQKW--AWEYSGFRKYGLYY 58
L++ +V Y + + D D +L + +I L+ + FR ++
Sbjct: 445 LHRSIVDHYNI--PKTFDSDDL--IPPYLDQYFYSHIGHHLKNIEHPERMTLFRM--VFL 498
Query: 59 DDLANETPVVEEALRRLPEKLKNERHFRQLRAVQLNI-------QKSILPKDQWTKYEDE 111
D R L +K++++ LN + I D KYE
Sbjct: 499 D------------FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDND--PKYERL 544
Query: 112 TRYLKPYIEQVE 123
+ ++ ++E
Sbjct: 545 VNAILDFLPKIE 556
>1oxw_A Patatin; alpha/beta class fold with approximately three layers;
2.20A {Solanum cardiophyllum} SCOP: c.19.1.3
Length = 373
Score = 26.4 bits (57), Expect = 3.7
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 69 EEALRRLPEKLKNERHFRQLRA 90
EEAL+R + L + + R +A
Sbjct: 350 EEALKRFAKLLSDRKKLRANKA 371
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.9 bits (56), Expect = 4.5
Identities = 9/63 (14%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 69 EEALRRLPEKLKNERHFRQLRAVQLNIQKSILPKDQWTKYEDETRYLKPYIEQVEKEFKE 128
EE +RL E + + + +K + ++ + ++ K +K F +
Sbjct: 92 EEQRKRLQELDAASK--VMEQEWREKAKKDL--EEWNQRQSEQVEKNKINNRIADKAFYQ 147
Query: 129 KEE 131
+ +
Sbjct: 148 QPD 150
Score = 25.1 bits (54), Expect = 8.1
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 17/68 (25%)
Query: 69 EEALRRLPEKLKNERHFRQLRAVQLNIQKSILPKDQWTKYEDETRYLKPYIEQVEKEFKE 128
+ L + PE ++ R ++ R +Q+ D +K ++ E EK K+
Sbjct: 77 ADRLTQEPESIRKWREEQRKR-----LQE----LDAASKVMEQ--------EWREKAKKD 119
Query: 129 KEEWGKLY 136
EEW +
Sbjct: 120 LEEWNQRQ 127
>3rfo_A Methionyl-tRNA formyltransferase; structural genomics, center for
structural genomics of infec diseases, csgid, alpha-beta
structure, cytosol; HET: PGE; 2.40A {Bacillus anthracis}
Length = 317
Score = 25.5 bits (57), Expect = 6.9
Identities = 11/68 (16%), Positives = 25/68 (36%), Gaps = 30/68 (44%)
Query: 65 TPVVEEALR-----RLPEKLKNERHFRQLRAVQ-------------------------LN 94
TPV EA + P +++ + + ++ A++ +N
Sbjct: 50 TPVKVEAEKHGIPVLQPLRIREKDEYEKVLALEPDLIVTAAFGQIVPNEILEAPKYGCIN 109
Query: 95 IQKSILPK 102
+ S+LP+
Sbjct: 110 VHASLLPE 117
>3rq1_A Aminotransferase class I and II; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG,
alpha-beta structure, cytosol; HET: AKG GOL; 2.20A
{Veillonella parvula}
Length = 418
Score = 25.3 bits (56), Expect = 7.1
Identities = 6/31 (19%), Positives = 10/31 (32%), Gaps = 4/31 (12%)
Query: 55 GLYYDDLANETPV---VEEALRRLPEKLKNE 82
G +D+ N V+E L +
Sbjct: 46 GAIHDEEGN-LVFLKTVKEEYLSLSDSEHVG 75
>2p22_D Hypothetical 12.0 kDa protein in ADE3-Ser2 intergenic region;
endosome, trafficking complex, VPS23, VPS28, VPS37,
MVB12; 2.70A {Saccharomyces cerevisiae}
Length = 79
Score = 24.3 bits (52), Expect = 7.7
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 68 VEEALRRLPEKLKNERHFRQLRAVQLNIQKSILPKDQWTK-----YEDETRYLKPYIEQV 122
VEE LRR+P K + F Q + + + LP Q T+ + +E + +
Sbjct: 3 VEELLRRIPLYNKYGKDFPQETVTRFQMPEFKLPALQPTRDLLCPWYEECDNITKVCQLH 62
Query: 123 EKEFKEKEEW 132
+ K+ ++W
Sbjct: 63 DSSNKKFDQW 72
>1fmt_A Methionyl-tRNA FMet formyltransferase; initiator tRNA, translation
initiation; 2.00A {Escherichia coli} SCOP: b.46.1.1
c.65.1.1 PDB: 2fmt_A* 3r8x_A
Length = 314
Score = 25.2 bits (56), Expect = 8.0
Identities = 10/68 (14%), Positives = 21/68 (30%), Gaps = 30/68 (44%)
Query: 65 TPVVEEALR-----RLPEKLKNERHFRQLRAVQ-------------------------LN 94
+PV A P L+ + + + + +Q +N
Sbjct: 49 SPVKVLAEEKGLPVFQPVSLRPQENQQLVAELQADVMVVVAYGLILPKAVLEMPRLGCIN 108
Query: 95 IQKSILPK 102
+ S+LP+
Sbjct: 109 VHGSLLPR 116
>3tqq_A Methionyl-tRNA formyltransferase; protein synthesis; 2.00A
{Coxiella burnetii}
Length = 314
Score = 25.1 bits (56), Expect = 8.3
Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 30/68 (44%)
Query: 65 TPVVEEALR-----RLPEKLKNERHFRQLRAVQ-------------------------LN 94
+PV E A + P L++E +L A+ +N
Sbjct: 48 SPVKEIARQNEIPIIQPFSLRDEVEQEKLIAMNADVMVVVAYGLILPKKALNAFRLGCVN 107
Query: 95 IQKSILPK 102
+ S+LP+
Sbjct: 108 VHASLLPR 115
>2bln_A Protein YFBG; transferase, formyltransferase, L-ARA4N biosynthesis,
methyltransferase; HET: FON U5P; 1.2A {Escherichia coli}
SCOP: b.46.1.1 c.65.1.1 PDB: 1yrw_A
Length = 305
Score = 25.1 bits (56), Expect = 9.2
Identities = 4/49 (8%), Positives = 15/49 (30%), Gaps = 10/49 (20%)
Query: 65 TPVVEEALR-----RLPEKLKNERHFRQLRAVQLNIQKS-----ILPKD 103
V A P+ + + ++ + ++ S ++ +
Sbjct: 43 GSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDE 91
>2fxq_A Single-strand binding protein; strand beta-sheet extended loops,
DNA binding protein; 1.85A {Thermus aquaticus} PDB:
2ihe_A 2cwa_A 2ihf_A
Length = 264
Score = 25.1 bits (55), Expect = 9.9
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 35 VYISGALQKWAWEYSGFRKY 54
+++ G L+ WE G +K
Sbjct: 76 IFVEGRLEYRQWEKDGEKKS 95
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 0.404
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,183,927
Number of extensions: 120806
Number of successful extensions: 338
Number of sequences better than 10.0: 1
Number of HSP's gapped: 334
Number of HSP's successfully gapped: 37
Length of query: 136
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 52
Effective length of database: 4,356,429
Effective search space: 226534308
Effective search space used: 226534308
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: 52 (23.8 bits)