RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8747
(214 letters)
>2jgd_A 2-oxoglutarate dehydrogenase E1 component; flavoprotein,
oxidoreductase, thiamine diphosphate, thiamine
pyrophosphate, adenosine monophosphate; HET: AMP; 2.6A
{Escherichia coli} PDB: 2jgd_B*
Length = 933
Score = 291 bits (747), Expect = 2e-93
Identities = 78/185 (42%), Positives = 113/185 (61%), Gaps = 5/185 (2%)
Query: 31 TTPANLFHILRRQIALPFRKPLVLMTPKSLLRHPEAKSSFDDMIEGTEFLRVIPDDSISE 90
+TPA ++H+LRRQ R+PLV+M+PKSLLRHP A SS +++ GT FL I + E
Sbjct: 752 STPAQVYHMLRRQALRGMRRPLVVMSPKSLLRHPLAVSSLEELANGT-FLPAIGEI--DE 808
Query: 91 RKADSVEKLVFCSGKVYYDLIKARNDNNLGDKIAVVRVEQISPFPFDLVKKECLRYPNAK 150
V+++V CSGKVYYDL++ R NN D +A+VR+EQ+ PFP +++ ++ + K
Sbjct: 809 LDPKGVKRVVMCSGKVYYDLLEQRRKNNQHD-VAIVRIEQLYPFPHKAMQEVLQQFAHVK 867
Query: 151 -VQWVQEEHKNQGAWTYVQPRFNTTVNGQRKMTYVGRPTAASPATGSKMQHVKELENLLA 209
W QEE NQGAW Q F + + Y GRP +ASPA G H K+ ++L+
Sbjct: 868 DFVWCQEEPLNQGAWYCSQHHFREVIPFGASLRYAGRPASASPAVGHMSVHQKQQQDLVN 927
Query: 210 DFMTL 214
D + +
Sbjct: 928 DALNV 932
>2yic_A 2-oxoglutarate decarboxylase; lyase; HET: TPP; 1.96A {Mycobacterium
smegmatis} PDB: 2xta_A* 2y0p_A* 2xt9_A* 2yid_A*
Length = 868
Score = 285 bits (733), Expect = 9e-92
Identities = 62/184 (33%), Positives = 97/184 (52%), Gaps = 6/184 (3%)
Query: 31 TTPANLFHILRRQIALPFRKPLVLMTPKSLLRHPEAKSSFDDMIEGTEFLRVIPDDSISE 90
+TPAN FH+LRR ++PL++ TPKS+LR+ A S D E F V+ + ++
Sbjct: 684 STPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESK-FRSVLEEPMYTD 742
Query: 91 R--KADSVEKLVFCSGKVYYDLIKARNDNNLGDKIAVVRVEQISPFPFDLVKKECLRYPN 148
+ V +L+ SGK+YY+L + N D +A+VR+EQ++P P + + RYPN
Sbjct: 743 GEGDRNKVTRLLLTSGKIYYELAARKAKENRED-VAIVRIEQLAPLPRRRLAETLDRYPN 801
Query: 149 AK-VQWVQEEHKNQGAWTYVQPRFNTTV-NGQRKMTYVGRPTAASPATGSKMQHVKELEN 206
K WVQEE NQGAW + + + + R ++P++GS H E +
Sbjct: 802 VKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQE 861
Query: 207 LLAD 210
+L
Sbjct: 862 ILDT 865
>2xt6_A 2-oxoglutarate decarboxylase; lyase, KDH, KGD; HET: TPP; 2.74A
{Mycobacterium smegmatis}
Length = 1113
Score = 284 bits (730), Expect = 5e-90
Identities = 62/184 (33%), Positives = 97/184 (52%), Gaps = 6/184 (3%)
Query: 31 TTPANLFHILRRQIALPFRKPLVLMTPKSLLRHPEAKSSFDDMIEGTEFLRVIPDDSISE 90
+TPAN FH+LRR ++PL++ TPKS+LR+ A S D E F V+ + ++
Sbjct: 929 STPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESK-FRSVLEEPMYTD 987
Query: 91 R--KADSVEKLVFCSGKVYYDLIKARNDNNLGDKIAVVRVEQISPFPFDLVKKECLRYPN 148
+ V +L+ SGK+YY+L + N D +A+VR+EQ++P P + + RYPN
Sbjct: 988 GEGDRNKVTRLLLTSGKIYYELAARKAKENRED-VAIVRIEQLAPLPRRRLAETLDRYPN 1046
Query: 149 AK-VQWVQEEHKNQGAWTYVQPRFNTTV-NGQRKMTYVGRPTAASPATGSKMQHVKELEN 206
K WVQEE NQGAW + + + + R ++P++GS H E +
Sbjct: 1047 VKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQE 1106
Query: 207 LLAD 210
+L
Sbjct: 1107 ILDT 1110
>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 = 38.5 bits (89), Expect = 0.001
Identities = 43/236 (18%), Positives = 74/236 (31%), Gaps = 86/236 (36%)
Query: 7 HRYPTMTLR---DGAQRDK--FPPVSVGTTT-----PANLFHILRR----QIALPFRKPL 52
Y M DG + + F ++ +T+ L L Q AL
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGL---LSATQFTQPAL------ 1736
Query: 53 VLMTPKSLLRHPEAKSSFDDMIEGTEFLRVIPDD------SISE-----RKAD--SVE-- 97
LM K++F+D+ + L IP D S+ E AD S+E
Sbjct: 1737 TLM----------EKAAFEDLKS--KGL--IPADATFAGHSLGEYAALASLADVMSIESL 1782
Query: 98 -KLVFCSGKVYYDLIKARNDNNLGDKIAVVRVEQISPFPFDLVKKECLRYPNAKVQWVQE 156
++VF G + + + +++ + +Q+V E
Sbjct: 1783 VEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA-----------ASFSQEALQYVVE 1831
Query: 157 EHKNQGAWTYVQPRFNTTVN----GQRKMTYVGRPTAASPATGSKMQHVKELENLL 208
+ W V+ VN Q YV A G ++ + + N+L
Sbjct: 1832 RVGKRTGW-LVEI-----VNYNVENQ---QYV--------AAG-DLRALDTVTNVL 1869
>3ju3_A Probable 2-oxoacid ferredoxin oxidoreductase, ALP; structural
genomics, PSI-2, protein structu initiative; 1.90A
{Thermoplasma acidophilum}
Length = 118
Score = 29.6 bits (67), Expect = 0.34
Identities = 7/32 (21%), Positives = 12/32 (37%)
Query: 120 GDKIAVVRVEQISPFPFDLVKKECLRYPNAKV 151
G ++ ++ SPFP + VK
Sbjct: 39 GISANLLYLKMFSPFPTEFVKNVLSSANLVID 70
>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 = 27.9 bits (61), Expect = 3.3
Identities = 21/116 (18%), Positives = 38/116 (32%), Gaps = 37/116 (31%)
Query: 47 PFRKPL----VLMTPKSLLRHPEAKSSFDDMIEG----TEFLRVIPDDSISERKADSVEK 98
F V PKS+L E D +I + LR+ ++ ++ + V+K
Sbjct: 28 AFVDNFDCKDVQDMPKSILSKEE----IDHIIMSKDAVSGTLRLF--WTLLSKQEEMVQK 81
Query: 99 LVFCSGKVYYDLIKAR-----------------------NDNNLGDKIAVVRVEQI 131
V ++ Y + + NDN + K V R++
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPY 137
>2an1_A Putative kinase; structural genomics, PSI, protein structure
initiative, midwest center for structural genomics,
MCSG, transferase; 2.00A {Salmonella typhimurium}
Length = 292
Score = 27.6 bits (62), Expect = 3.5
Identities = 8/51 (15%), Positives = 18/51 (35%), Gaps = 4/51 (7%)
Query: 62 RHPEAKSSFDDMIEGTEFLRVIPDDSISERKADSVEKLVFCSGKVYYDLIK 112
R + + S D L + + + R+ D L+ Y++ +
Sbjct: 236 RRSDLEISCD----SQIALPIQEGEDVLIRRCDYHLNLIHPKDYSYFNTLS 282
>3lub_A Putative creatinine amidohydrolase; structural genomics, joint
center for structural genomics, JCSG, protein structure
initiative, PSI-2; 2.11A {Bacteroides fragilis}
Length = 254
Score = 27.4 bits (60), Expect = 3.8
Identities = 14/78 (17%), Positives = 23/78 (29%), Gaps = 9/78 (11%)
Query: 137 DLVKKECLRYPNAKVQWVQEEHKNQGAWTYVQPRFNTTVNGQRKMTYVGRPTAASPATGS 196
+LV + + AW TV+ VG P A+ G
Sbjct: 178 ELVNLAEAG-DGESKPFAIASLNEKVAWVPRHWD-KATVDS-----GVGNPKKATAEKGE 230
Query: 197 KM--QHVKELENLLADFM 212
+ V++L L +
Sbjct: 231 RYVKPIVEKLAGLFEEMA 248
>1yd7_A 2-keto acid:ferredoxin oxidoreductase subunit alpha; structural
genomics, southeast collaboratory for structural
genomics, secsg; 2.30A {Pyrococcus furiosus}
Length = 395
Score = 27.1 bits (61), Expect = 5.2
Identities = 8/22 (36%), Positives = 16/22 (72%)
Query: 120 GDKIAVVRVEQISPFPFDLVKK 141
G K ++++E I PF F+L+++
Sbjct: 317 GIKAGLLKIETIWPFDFELIER 338
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 0.399
Gapped
Lambda K H
0.267 0.0495 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,274,410
Number of extensions: 186575
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 258
Number of HSP's successfully gapped: 13
Length of query: 214
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 124
Effective length of database: 4,188,903
Effective search space: 519423972
Effective search space used: 519423972
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 (21.8 bits)
S2: 55 (25.5 bits)