RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5804
(113 letters)
>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA
replication, MCM complex, AAA+ Pro ATP-binding,
DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}
Length = 595
Score = 60.7 bits (148), Expect = 2e-12
Identities = 13/46 (28%), Positives = 18/46 (39%)
Query: 31 VKRKFKEFLRQFHEGNFNYKYRDSLKRNYNLGQYFLEINIEDLTSF 76
+ F EFL F N KY + + + L I D+ SF
Sbjct: 4 YRDVFIEFLTTFKGNNNQNKYIERINELVAYRKKSLIIEFSDVLSF 49
>2vl6_A SSO MCM N-TER, minichromosome maintenance protein MCM; helicase,
hydrolase, zinc-finger, ATP-binding, DNA-BIND ssDNA
binding; 2.8A {Sulfolobus solfataricus}
Length = 268
Score = 57.7 bits (140), Expect = 2e-11
Identities = 13/48 (27%), Positives = 18/48 (37%)
Query: 29 QSVKRKFKEFLRQFHEGNFNYKYRDSLKRNYNLGQYFLEINIEDLTSF 76
+ F EFL F N KY + + + L I D+ SF
Sbjct: 8 IDYRDVFIEFLTTFKGNNNQNKYIERINELVAYRKKSLIIEFSDVLSF 55
>1ltl_A DNA replication initiator (CDC21/CDC54); HET: DNA; 3.00A
{Methanothermobacterthermautotrophicus} SCOP: b.40.4.11
Length = 279
Score = 40.8 bits (96), Expect = 2e-05
Identities = 10/52 (19%), Positives = 23/52 (44%), Gaps = 5/52 (9%)
Query: 25 QVNLQSVKRKFKEFLRQFHEGNFNYKYRDSLKRNYNLGQYFLEINIEDLTSF 76
V+ KF+EF ++ + +++++ N +E++ DL F
Sbjct: 8 TVDKSKTLTKFEEFFSLQ---DYKDRVFEAIEKYPN--VRSIEVDYLDLEMF 54
>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 = 31.9 bits (72), Expect = 0.031
Identities = 25/127 (19%), Positives = 44/127 (34%), Gaps = 33/127 (25%)
Query: 4 FDDAGIFFSDNFGAEDQQSGIQVNLQSVKRKFKEF-------LRQFHEGNFNY---KYRD 53
++ A F D +G S + + + + F +R+ NY +
Sbjct: 1646 WNRADNHFKDTYG----FSILDIVINNPVNLTIHFGGEKGKRIRE------NYSAMIFET 1695
Query: 54 SLKRNYNLGQYFLEINIEDLTSF-FINNIDSLKRNYNLGQY-----FL-EINI-EDLTSW 105
+ + F EIN E TS+ F + L + Q+ L E EDL S
Sbjct: 1696 IVDGKLKTEKIFKEIN-EHSTSYTFRSEKGLL----SATQFTQPALTLMEKAAFEDLKSK 1750
Query: 106 RIFKINS 112
+ ++
Sbjct: 1751 GLIPADA 1757
>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 = 29.8 bits (66), Expect = 0.19
Identities = 17/113 (15%), Positives = 36/113 (31%), Gaps = 28/113 (24%)
Query: 4 FDDAGIFFSDNFGAEDQQSGIQVNLQSVKRKFKEFLRQFHEGNFNYKYR-DSLKRNYNLG 62
D IF+ N + + LQ + + + + N K R S++
Sbjct: 180 MDF-KIFWL-NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ------ 231
Query: 63 QYFLEINIEDLTSFFINNIDSLKRNYNLGQYFLEI--NIEDLTSWRIFKINSK 113
+L + + Y L + N+++ +W F ++ K
Sbjct: 232 --------AELRRLLKS------KPYENC---LLVLLNVQNAKAWNAFNLSCK 267
Score = 27.9 bits (61), Expect = 0.72
Identities = 7/60 (11%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 54 SLKRNYNLGQYFLEINIEDLTSFFINNIDSLKRNYNLGQYFLEINIEDLTSWRIFKINSK 113
S++ + +N + LT+ ++++ L+ + + L+ +F ++
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF------DRLS---VFPPSAH 386
Score = 25.6 bits (55), Expect = 5.3
Identities = 24/109 (22%), Positives = 38/109 (34%), Gaps = 27/109 (24%)
Query: 11 FSDNFGAEDQQSGIQVNLQSVKRKFKEFLRQFHEGNFNYKYRDSLKRNYNLGQYFL--EI 68
++D SG ++ K +E +++F E L+ NY FL I
Sbjct: 51 IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV--------LRINYK----FLMSPI 98
Query: 69 NIED-----LTSFFINNIDSLKRNYNLGQYFLEINIEDLTSWRIFKINS 112
E +T +I D L YN Q F + N+ R+
Sbjct: 99 KTEQRQPSMMTRMYIEQRDRL---YNDNQVFAKYNV-----SRLQPYLK 139
Score = 25.2 bits (54), Expect = 6.3
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 9/45 (20%)
Query: 42 FHEGNFNYKYRDSLKRNYNLGQYFLEINIEDLTSFFINNIDSLKR 86
F G Y+Y+D L F + +++ + D K
Sbjct: 9 FETGEHQYQYKDIL-------SVFEDAFVDNFDCKDVQ--DMPKS 44
>3t5o_A Complement component C6; macpf, MAC, membrane attack complex,
innate IMMU system, blood, membrane, cytolysin, immune
SYST; HET: NAG FUL FUC BGC MAN; 2.87A {Homo sapiens}
PDB: 4a5w_B* 4e0s_B*
Length = 913
Score = 29.8 bits (66), Expect = 0.19
Identities = 9/62 (14%), Positives = 24/62 (38%), Gaps = 3/62 (4%)
Query: 33 RKFKEFLRQFHEGNFNYKYRDSLKRNYNLGQYFLEINIEDLTSFFINNIDSLKRNYNLGQ 92
FK+ ++ H+ + + + + + + + L+ F+ ++ L YN
Sbjct: 276 SAFKQAIQASHK--KDSSFI-RIHKVMKVLNFTTKAKDLHLSDVFLKALNHLPLEYNSAL 332
Query: 93 YF 94
Y
Sbjct: 333 YS 334
>3ojy_A Complement component C8 alpha chain; macpf, lipocalin, immune
system; HET: TPO BMA; 2.51A {Homo sapiens}
Length = 554
Score = 29.2 bits (64), Expect = 0.25
Identities = 15/92 (16%), Positives = 26/92 (28%), Gaps = 13/92 (14%)
Query: 3 GFDDAGIFFSDNFGAEDQQSGIQVNLQSVKRKFKEFLRQFHEGNFNYKYRDSLKRNYNLG 62
G AG G S F L +++E F + +
Sbjct: 223 GIGPAGSPLLVGVGVS----------HSQDTSFLNELNKYNEKKFIFT---RIFTKVQTA 269
Query: 63 QYFLEINIEDLTSFFINNIDSLKRNYNLGQYF 94
+ + + L + ++ L YN G Y
Sbjct: 270 HFKMRKDDIMLDEGMLQSLMELPDQYNYGMYA 301
>3myb_A Enoyl-COA hydratase; ssgcid, struct genomics, seattle structural
genomics center for infectious lyase; 1.55A
{Mycobacterium smegmatis}
Length = 286
Score = 29.1 bits (66), Expect = 0.26
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 4/37 (10%)
Query: 2 EGFDDAGIFFSDNFGAEDQQSGIQVNLQSVKRK--FK 36
+ DAG + N G+ L+ KR+ +
Sbjct: 245 SAYADAGTTMACNMMDPSALEGVSAFLE--KRRPEWH 279
>2vx2_A Enoyl-COA hydratase domain-containing protein 3; isomerase, fatty
acid metabolism, transit peptide, lipid Met crontonase,
mitochondrion, CAsp; 2.3A {Homo sapiens}
Length = 287
Score = 27.6 bits (62), Expect = 0.81
Identities = 11/33 (33%), Positives = 12/33 (36%), Gaps = 2/33 (6%)
Query: 2 EGFDDAGIFFSDNFGAEDQQSGIQVNLQSVKRK 34
+ DN D Q GI LQ KRK
Sbjct: 252 TAYYLTSQAMVDNLALRDGQEGITAFLQ--KRK 282
>3ff1_A Glucose-6-phosphate isomerase; alpha beta, rossmann fold,
gluconeogenesis, glycolysis, structural genomics; HET:
G6Q; 1.65A {Staphylococcus aureus subsp} PDB: 3ifs_A*
Length = 446
Score = 27.3 bits (61), Expect = 1.2
Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 15/111 (13%)
Query: 2 EGFDDAGIFFSDNFGAEDQQSGIQVNLQSVKRKFKEFLR---QFHEGNFNYKYRDSLKRN 58
EG D GI+ S D S Q + + F+ ++ ++ D N
Sbjct: 290 EGKDFKGIYPSSANYTTDLHSLGQYVQEGRRFLFETVVKVNHPKYDITIEKDSDDLDGLN 349
Query: 59 YNLGQYFLEINIE----DLTSFFINNIDSL-----KRN-YNLGQ--YFLEI 97
Y G+ E+N + L + + ++ + + G YF E+
Sbjct: 350 YLAGKTIDEVNTKAFEGTLLAHTDGGVPNMVVNIPQLDEETFGYVVYFFEL 400
>1v9n_A Malate dehydrogenase; riken structural genomics/proteomics initiati
structural genomics, oxidoreductase; HET: NDP; 2.10A
{Pyrococcus horikoshii}
Length = 360
Score = 26.2 bits (58), Expect = 2.6
Identities = 8/42 (19%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 45 GNFNYKYRDSLKRNYNLGQYFLEINIEDLTSF--FINNIDSL 84
G ++ +++ ++ N+ +F+ I+IE F I +
Sbjct: 262 GTWSKYVKNTSEKGSNVCHFFMVIDIEHFIPLEEFKEKISQM 303
>1b0z_A Protein (phosphoglucose isomerase); autocrinefactor, neuroleukin,
crystallography motility; 2.30A {Geobacillus
stearothermophilus} SCOP: c.80.1.2 PDB: 1c7q_A* 1c7r_A*
2pgi_A
Length = 445
Score = 26.1 bits (58), Expect = 2.7
Identities = 22/111 (19%), Positives = 37/111 (33%), Gaps = 15/111 (13%)
Query: 2 EGFDDAGIFFSDNFGAEDQQSGIQVNLQSVKRKFKEFLR---QFHEGNFNYKYRDSLKRN 58
EG D G+F + D S Q + + + L E + N
Sbjct: 287 EGKDQKGLFPASVDFTTDLHSMGQYVQEGRRNLIETVLHVKKPQIELTIQEDPENIDGLN 346
Query: 59 YNLGQYFLEINIE----DLTSFFINNIDSL-----KRN-YNLGQ--YFLEI 97
+ G+ E+N + L + + +L + N Y G+ YF E
Sbjct: 347 FLAGKTLDEVNKKAFQGTLLAHVDGGVPNLIVELDEMNEYTFGEMVYFFEK 397
>1nxu_A Hypothetical oxidoreductase YIAK; hypothetical protein, structural
genomics, PSI, protein structure initiative; 1.80A
{Escherichia coli} SCOP: c.122.1.1 PDB: 1s20_A*
Length = 333
Score = 26.1 bits (58), Expect = 2.8
Identities = 6/42 (14%), Positives = 13/42 (30%), Gaps = 2/42 (4%)
Query: 45 GNFNYKYRDSLKRNYNLGQYFLEINIEDLTSF--FINNIDSL 84
G + Y + Q F+ I ++ L + +
Sbjct: 243 GASVAEVTQDNSDEYGISQIFIAIEVDKLIDGPTRDAKLQRI 284
>1vqz_A Lipoate-protein ligase, putative; class II AARS and biotin
synthetases fold, SUFE/NIFU fold, S genomics; HET: MSE;
1.99A {Streptococcus pneumoniae} SCOP: d.224.1.3
d.104.1.3
Length = 341
Score = 25.8 bits (57), Expect = 3.0
Identities = 6/50 (12%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 62 GQYFLEINIEDLTSFFIN---NIDSLK---RNYNLGQYFLEINIEDLTSW 105
G +F ++ + + + + ++ +YF I+ E++
Sbjct: 289 GDFFGIEDVAAVEDVLRGVKYEREDVLKALKTIDITRYFAGISREEIAEA 338
>3hp0_A Putative polyketide biosynthesis enoyl-COA hydratase homolog PKSH;
polyketide synthase, enoyl COA hydratase,isomerase;
2.32A {Bacillus subtilis}
Length = 267
Score = 26.0 bits (58), Expect = 3.2
Identities = 7/35 (20%), Positives = 10/35 (28%), Gaps = 2/35 (5%)
Query: 2 EGFDDAGIFFSDNFGAEDQQSGIQVNLQSVKRKFK 36
A D F Q GI ++ +F
Sbjct: 223 RAKATALTANQDMFSDPQNQMGIIRYVE--TGQFP 255
>2rd7_A Complement component C8 alpha chain; membrane attack system,
cleavage on PAIR of basic residues, complement alternate
pathway, complement pathway; 2.15A {Homo sapiens} PDB:
2qqh_A
Length = 367
Score = 25.8 bits (55), Expect = 3.4
Identities = 14/89 (15%), Positives = 27/89 (30%)
Query: 6 DAGIFFSDNFGAEDQQSGIQVNLQSVKRKFKEFLRQFHEGNFNYKYRDSLKRNYNLGQYF 65
D F G S + V + + FL + ++ N + +
Sbjct: 118 DKSDSFGVTIGIGPAGSPLLVGVGVSHSQDTSFLNELNKYNEKKFIFTRIFTKVQTAHFK 177
Query: 66 LEINIEDLTSFFINNIDSLKRNYNLGQYF 94
+ + L + ++ L YN G Y
Sbjct: 178 MRKDDIMLDEGMLQSLMELPDQYNYGMYA 206
>1i1q_B Anthranilate synthase component II; tryptophan biosynthesis, lyase;
HET: TRP; 1.90A {Salmonella typhimurium} SCOP: c.23.16.1
PDB: 1i7q_B 1i7s_B*
Length = 192
Score = 25.5 bits (57), Expect = 4.5
Identities = 6/25 (24%), Positives = 9/25 (36%), Gaps = 2/25 (8%)
Query: 76 FFINNIDSLKRNYNLGQYFLEINIE 100
++NIDS +NL
Sbjct: 4 LLLDNIDSF--TWNLADQLRTNGHN 26
>1ab8_A Adenylyl cyclase; lyase, complex (transferase-inhibitor); HET:
FOK; 2.20A {Rattus norvegicus} SCOP: d.58.29.1 PDB:
1azs_B* 1cjk_B* 1cjt_B* 1cju_B* 1cjv_B* 1cs4_B* 1tl7_B*
1u0h_B* 2gvd_B* 2gvz_B* 3c14_B* 3c15_B* 3c16_B* 3e8a_B*
3g82_B* 3maa_B* 1cul_B*
Length = 220
Score = 24.9 bits (55), Expect = 6.1
Identities = 3/16 (18%), Positives = 8/16 (50%), Gaps = 2/16 (12%)
Query: 2 EGFDDAGIFFSD--NF 15
+ +D + F+ +F
Sbjct: 10 QSYDCVCVMFASIPDF 25
>1qdl_B Protein (anthranilate synthase (TRPG-SUBUNIT)); tryptophan
biosynthesis, glutamine amidotransferase, allosteric
interaction, lyase; 2.50A {Sulfolobus solfataricus}
SCOP: c.23.16.1
Length = 195
Score = 24.3 bits (54), Expect = 9.2
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 78 INNIDSLKRNYNLGQYFLEINIE 100
I+N DS YN+ Q E+
Sbjct: 7 IDNYDSF--VYNIAQIVGELGSY 27
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
0.322 0.141 0.411
Gapped
Lambda K H
0.267 0.0466 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,724,776
Number of extensions: 91412
Number of successful extensions: 250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 246
Number of HSP's successfully gapped: 44
Length of query: 113
Length of database: 6,701,793
Length adjustment: 77
Effective length of query: 36
Effective length of database: 4,551,876
Effective search space: 163867536
Effective search space used: 163867536
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 (21.9 bits)
S2: 51 (24.1 bits)