RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9433
(105 letters)
>1zoy_C Large cytochrome binding protein, FAD-binding protein; succinate,
ubiquinone oxidoreductase, mitochondrial respiratory
complex II; HET: FAD HEM EPH UQ1; 2.40A {Sus scrofa}
PDB: 1zp0_C* 3abv_C* 3ae1_C* 3ae2_C* 3ae3_C* 3ae4_C*
3ae5_C* 3ae6_C* 3ae7_C* 3ae8_C* 3ae9_C* 3aea_C* 3aeb_C*
3aec_C* 3aed_C* 3aee_C* 3aef_C* 3aeg_C* 3sfd_C* 3sfe_C*
Length = 140
Score = 81.1 bits (200), Expect = 3e-21
Identities = 40/107 (37%), Positives = 63/107 (58%), Gaps = 2/107 (1%)
Query: 1 ITSVLSITHRGTGVALT--AYALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFILAF 58
+ +SI HRGTG+AL+ GL+ + L + S + V +L L ++ KF + F
Sbjct: 34 LPMAMSICHRGTGIALSAGVSLFGLSALLLPGNFESHLELVKSLCLGPTLIYTAKFGIVF 93
Query: 59 PVSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVLTLL 105
P+ YHT NGIRHLIWD G+ LTI ++ +G +L +L+++ L +
Sbjct: 94 PLMYHTWNGIRHLIWDLGKGLTIPQLTQSGVVVLILTVLSSVGLAAM 140
>2h88_C Succinate dehydrogenase cytochrome B, large subun; complex II,
membrane protein, heme protein, iron sulfur PROT
cytochrome B, oxidoreductase; HET: FAD BHG HEM UNL;
1.74A {Gallus gallus} PDB: 2h89_C* 1yq3_C* 1yq4_C*
2fbw_C* 2wqy_C*
Length = 140
Score = 78.9 bits (194), Expect = 2e-20
Identities = 41/104 (39%), Positives = 62/104 (59%), Gaps = 2/104 (1%)
Query: 1 ITSVLSITHRGTGVALTA--YALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFILAF 58
+ +SITHRGTGVAL+ LA + L V+ V +L+LS ++ + KF L F
Sbjct: 34 LPMAMSITHRGTGVALSLGVSLFSLAALLLPEQFPHYVAVVKSLSLSPALIYSAKFALVF 93
Query: 59 PVSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVL 102
P+SYHT NGIRHL+WD G+ + +V +G +L +L++ +
Sbjct: 94 PLSYHTWNGIRHLVWDMGKGFKLSQVEQSGVVVLILTLLSSAAI 137
>3vr8_C Cytochrome B-large subunit; membrane protein, reductase,
mitochondria MEMB oxidoreductase; HET: FAD HEM RQX EPH;
2.81A {Ascaris suum} PDB: 3vrb_C*
Length = 188
Score = 74.5 bits (182), Expect = 3e-18
Identities = 36/106 (33%), Positives = 56/106 (52%), Gaps = 2/106 (1%)
Query: 1 ITSVLSITHRGTGVALTA--YALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFILAF 58
+T ++S HR TG A+ G+ L D + V F+ L + IL KFI+AF
Sbjct: 67 MTWMVSGLHRVTGCAMAGTLLIGGVGFSVLPLDFTTFVEFIRGLGIPWVILDTFKFIIAF 126
Query: 59 PVSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVLTL 104
P+++HT NGIR + +D + I +Y Y +LG A L +L + +
Sbjct: 127 PIAFHTLNGIRFIGFDMAKGTDIPSIYRGAYLVLGLAALISLAVVV 172
>2wdq_C Succinate dehydrogenase cytochrome B556 subunit; succinate
dehydrogenase activity, cell inner membrane, trica acid
cycle; HET: FAD HEM CBE; 2.40A {Escherichia coli} PDB:
1nen_C* 2acz_C* 1nek_C* 2wdr_C* 2wdv_C* 2wp9_C* 2ws3_C*
2wu5_C* 2wu2_C*
Length = 129
Score = 72.8 bits (179), Expect = 3e-18
Identities = 25/107 (23%), Positives = 48/107 (44%), Gaps = 3/107 (2%)
Query: 1 ITSVLSITHRGTGVALTAYALGLAGVGLTTDINSVVSFVDALNL-SAPILLAGKFILAFP 59
IT++ SI HR +GV A+G+ L T ++S F A + + + + +
Sbjct: 22 ITAIASILHRVSGVIT-FVAVGILLWLLGTSLSSPEGFEQASAIMGSFFVKFIMWGILTA 80
Query: 60 VSYHTANGIRHLIWDTGRALTIKK-VYTTGYAMLGAAILTNLVLTLL 105
++YH GIRH++ D G + + ++ +L+ +L
Sbjct: 81 LAYHVVVGIRHMMMDFGYLEETFEAGKRSAKISFVITVVLSLLAGVL 127
>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 = 32.3 bits (73), Expect = 0.022
Identities = 20/102 (19%), Positives = 31/102 (30%), Gaps = 42/102 (41%)
Query: 4 VLSITHRGTGVALTAYALGLAGVGLTTDINS------------VVSFVDALNLSAP---I 48
V+S G +L L L + ++ F L +++P
Sbjct: 378 VVS----GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF---LPVASPFHSH 430
Query: 49 LL--AGKFI---------------LAFPVSYHTANG--IRHL 71
LL A I + PV Y T +G +R L
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPV-YDTFDGSDLRVL 471
>2yy8_A ATRM56, UPF0106 protein PH0461; DEEP trefoil knot, structural
genomics, NPPSFA; HET: SAM MTA; 2.48A {Pyrococcus
horikoshii}
Length = 201
Score = 27.9 bits (62), Expect = 0.53
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 3 SVLSITHRG-------TGVALTAYALGLAGVGLTTDINSVV 36
VL + HR T VALTA A G G+ + ++ + V
Sbjct: 3 VVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKV 43
>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 = 27.5 bits (60), Expect = 0.91
Identities = 7/51 (13%), Positives = 16/51 (31%), Gaps = 6/51 (11%)
Query: 60 VSYHTANGIRHLIWDTGRALTI------KKVYTTGYAMLGAAILTNLVLTL 104
+ +H N R + + +K+ A + + N + L
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527
>2iaf_A Hypothetical protein SDHL; MCSG, PSI2, MAD, structural genomics,
L-serine dehydratase, structure initiative; 2.05A
{Legionella pneumophila} SCOP: d.81.2.1 PDB: 2iqq_A
Length = 151
Score = 26.6 bits (59), Expect = 1.3
Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 9/76 (11%)
Query: 5 LSITHRGTGVALTAYALGLAGVGL-TTDINSVVSFVDALNLSAPILLAGKFILAFPVSYH 63
L++T +G G A GL T D S++ + + S + LAGK + F +
Sbjct: 44 LALTGKGHGTD-KAILNGLENKAPETVDPASMIPRMHEILDSNLLNLAGKKEIPFHEA-- 100
Query: 64 TANGIRHLIWDTGRAL 79
++ L
Sbjct: 101 -----TDFLFLQKELL 111
>2o3a_A UPF0106 protein AF_0751; structural genomics, unknown function,
PSI-2, protein structure initiative; 2.20A
{Archaeoglobus fulgidus} SCOP: c.116.1.8
Length = 178
Score = 26.3 bits (58), Expect = 1.6
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 3 SVLSITHRG-------TGVALTAYALGLAGVGLTTDINSVVSFVDALN 43
VL + HR T VALTA A G G+ T+ SV V +
Sbjct: 6 YVLRLGHRPERDKRISTHVALTARAFGAKGIYFDTEDKSVFESVRDVV 53
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain,
PIN-tower interface, coupling hydrolysis to DNA
unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Length = 459
Score = 26.1 bits (57), Expect = 2.7
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 22 GLAGVGLTTDINSVVSFVDALNLSAPILLA 51
G AG G TT ++ + + + IL A
Sbjct: 52 GPAGTGATTLTKFIIEALISTGETGIILAA 81
>1nj8_A Proline-tRNA synthetase, proline--tRNA ligase; class-II tRNA
synthetase; 3.20A {Methanocaldococcus jannaschii} SCOP:
c.51.1.1 d.68.5.1 d.104.1.1
Length = 459
Score = 25.8 bits (57), Expect = 2.9
Identities = 10/79 (12%), Positives = 28/79 (35%), Gaps = 13/79 (16%)
Query: 29 TTDINSVVSFVDALNLSAPILLAGKFILAFPVSYHTANGIRHLIWDTGRALTIKKVYTTG 88
T +++ + ++ L F F + + T G + + T ++ +
Sbjct: 206 TMAFDTIFPDGRTMQIATVHNLGQNFSKTFEIIFETPTGDKDYAYQTCYGISDR------ 259
Query: 89 YAMLGAAILTN-----LVL 102
++ + I + L+L
Sbjct: 260 --VIASIIAIHGDEKGLIL 276
>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter,
transport protein; HET: ANP; 2.90A {Thermotoga maritima}
Length = 587
Score = 25.6 bits (57), Expect = 3.9
Identities = 9/37 (24%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 28 LTTDINSVVSFVDA---LNLSAPILLAGKFILAFPVS 61
LT D+ + + V + + AP+L G ++A ++
Sbjct: 126 LTNDVTQLQNLVMMLLRIVVRAPLLFVGGIVMAVSIN 162
>2f9s_A Thiol-disulfide oxidoreductase RESA; thioredoxin-like protein; HET:
MSE; 1.40A {Bacillus subtilis} SCOP: c.47.1.10 PDB:
1st9_A 1su9_A 2h1d_A 2h1b_A 2h1a_A 2h19_A 2h1g_A 3c71_A
3c73_A
Length = 151
Score = 25.3 bits (56), Expect = 3.9
Identities = 6/45 (13%), Positives = 19/45 (42%), Gaps = 7/45 (15%)
Query: 25 GVGLTTDINSVVSFVDALNLSAPILL------AGKF-ILAFPVSY 62
V + +V +F+ + ++ P++L + + P ++
Sbjct: 64 AVNVGESKIAVHNFMKSYGVNFPVVLDTDRQVLDAYDVSPLPTTF 108
>3lq6_A Capsid protein; protruding (P) domain, viral protein; 2.00A {Murine
norovirus 1} PDB: 3lqe_A
Length = 320
Score = 25.3 bits (55), Expect = 4.1
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 35 VVSFVDALNLSAPILLAGKFILAFPVSYHTANG----IRHLIWDTGRALTIKKVYTTGY 89
+ DA + L +F+ F + T +R+ TG+ L K+Y GY
Sbjct: 217 QIDTADAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNTLTGQLLFECKLYNEGY 275
>3k6h_A Nitroreductase family protein; APC5990, agrobacterium tumefaciens
ST structural genomics, PSI-2, protein structure
initiative; HET: FMN; 3.05A {Agrobacterium tumefaciens
str}
Length = 197
Score = 24.5 bits (53), Expect = 8.5
Identities = 11/44 (25%), Positives = 18/44 (40%)
Query: 16 LTAYALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFILAFP 59
A A G A LT + +F+ + +SA +AG +
Sbjct: 132 FAANASGFAANWLTEWLAFDPAFLAEIGVSAEEKVAGYIHIGST 175
>3or5_A Thiol:disulfide interchange protein, thioredoxin protein; PSI-II,
structural genomics, protein structure initiative; 1.66A
{Chlorobaculum tepidum}
Length = 165
Score = 24.3 bits (53), Expect = 9.4
Identities = 4/29 (13%), Positives = 15/29 (51%)
Query: 25 GVGLTTDINSVVSFVDALNLSAPILLAGK 53
G+ + + +V +++ + P+++A
Sbjct: 72 GIAVNEQLPNVKNYMKTQGIIYPVMMATP 100
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
0.324 0.138 0.395
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: 1,535,206
Number of extensions: 83082
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 26
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.0 bits)