RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11221
(202 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 = 104 bits (262), Expect = 2e-26
Identities = 23/52 (44%), Positives = 31/52 (59%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNL 80
E +L K+ KRF LEG + LIP +K++I + G VV+GM HRG L
Sbjct: 213 LERYLGAKFPGAKRFSLEGGDALIPMLKEMIRHAGNSGTREVVLGMAHRGRL 264
>2yic_A 2-oxoglutarate decarboxylase; lyase; HET: TPP; 1.96A {Mycobacterium
smegmatis} PDB: 2xta_A* 2y0p_A* 2xt9_A* 2yid_A*
Length = 868
Score = 103 bits (260), Expect = 4e-26
Identities = 28/52 (53%), Positives = 35/52 (67%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNL 80
FE FL K+ +KRF LEG E +IP M VID+ E G++ VV+ MPHRG L
Sbjct: 133 FETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRL 184
>2xt6_A 2-oxoglutarate decarboxylase; lyase, KDH, KGD; HET: TPP; 2.74A
{Mycobacterium smegmatis}
Length = 1113
Score = 103 bits (259), Expect = 6e-26
Identities = 28/52 (53%), Positives = 35/52 (67%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNL 80
FE FL K+ +KRF LEG E +IP M VID+ E G++ VV+ MPHRG L
Sbjct: 378 FETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRL 429
>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 = 40.0 bits (93), Expect = 3e-04
Identities = 37/231 (16%), Positives = 74/231 (32%), Gaps = 82/231 (35%)
Query: 5 VISNSSEIVSPLLLRSSATFSNSEFE--AFLAKKWSSEKRF--GLEG-----CEILIPAM 55
+S +V+ + + + ++ F A F G+ L P++
Sbjct: 270 ATGHSQGLVTAVAIAETDSWE--SFFVSVRKAITVL----FFIGVRCYEAYPNTSLPPSI 323
Query: 56 KQVIDKSTELGVES---VVMGMPHRGNLISETTGQGLQKVPRLFSQN-PQN--------N 103
+ ++ E GV S + + + +Q + + P N
Sbjct: 324 LEDSLENNE-GVPSPMLSISNLTQ----------EQVQDYVNKTNSHLPAGKQVEISLVN 372
Query: 104 GDIRHFVFFSSTPTFLHTFDW----IKAS----QTQ---GDRGPHLTLNCWPRAMFLSTP 152
G ++ V S P L+ + KA Q++ +R + FL
Sbjct: 373 GA-KNLVV-SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNR------FL--- 421
Query: 153 VCILHETFRPIFTPIIFFFFALSHVQMGSAFDI---DL---SISFRVIALR 197
P+ +P F SH+ + A D+ DL ++SF ++
Sbjct: 422 ---------PVASP--FH----SHL-LVPASDLINKDLVKNNVSFNAKDIQ 456
>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 = 31.7 bits (71), Expect = 0.16
Identities = 11/73 (15%), Positives = 23/73 (31%), Gaps = 18/73 (24%)
Query: 2 RIFVISNSSEIVSPL---------LLRSSATFSNSEFEAFLAKKWSSEKRFGL--EGCEI 50
+I + + ++ L L S T + E ++ L K+ + L E
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL-KYLDCRPQDLPREVLTT 325
Query: 51 ------LIPAMKQ 57
+I +
Sbjct: 326 NPRRLSIIAESIR 338
Score = 29.1 bits (64), Expect = 1.1
Identities = 16/139 (11%), Positives = 38/139 (27%), Gaps = 48/139 (34%)
Query: 7 SNSSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELG 66
+ + +++ +S L +K E + + +K ++ L
Sbjct: 397 FDVIKSDVMVVVNKLHKYS-------LVEKQPKESTISIPSIYLE---LKVKLENEYAL- 445
Query: 67 VESVVMGMPHRGNLISETTGQGLQKVPRLFSQN----PQNNGDI-----RH--------- 108
HR +++ +P+ F + P + H
Sbjct: 446 ---------HR-SIVDH------YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPER 489
Query: 109 FVFFSSTPTFLHTFDWIKA 127
F FL F +++
Sbjct: 490 MTLFRM--VFL-DFRFLEQ 505
>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain,
homodimer, exosome, cell-death-related DNAS hydrolase;
3.92A {Caenorhabditis elegans}
Length = 222
Score = 29.3 bits (66), Expect = 0.64
Identities = 8/67 (11%), Positives = 18/67 (26%), Gaps = 10/67 (14%)
Query: 5 VISNSSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDK--S 62
V S + + + + EA + + K V+ + S
Sbjct: 159 VCKGSDGHPEVCAMDAIGHWDFIQLEAAWSL--------AQPSASAIFDFYKTVMKRKLS 210
Query: 63 TELGVES 69
+ +E
Sbjct: 211 VDEQLEH 217
>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate
bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa}
SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A
Length = 239
Score = 28.2 bits (63), Expect = 1.9
Identities = 8/58 (13%), Positives = 19/58 (32%), Gaps = 8/58 (13%)
Query: 4 FVISNSSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDK 61
V++++ + A F +E A L +G + L + + +
Sbjct: 190 VVMTDAGGFIEVQGTAEGAPFRPAELNAMLE--------LAQQGMQELFELQRAALAE 239
>1vhk_A Hypothetical protein YQEU; structural genomics, unknown function;
2.60A {Bacillus subtilis} SCOP: b.122.1.2 c.116.1.5
Length = 268
Score = 26.8 bits (60), Expect = 5.0
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 55 MKQVIDKSTELGVESVV 71
++ +I K TELG + +
Sbjct: 95 LEWIIQKGTELGAHAFI 111
>1yfs_A Alanyl-tRNA synthetase; alpha-beta fold, helix-loop-helix motif,
amino acid binding, ligase; 2.08A {Aquifex aeolicus}
SCOP: a.203.1.1 d.104.1.1 PDB: 1yfr_A* 1riq_A 1yft_A
1ygb_A 3htz_A
Length = 465
Score = 26.4 bits (59), Expect = 7.5
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 163 IFTPIIFFFFALSHVQMGSAFDIDLSISFRVIA--LRPTGF 201
I P+I F +S + G F+ D ++ RVIA LR F
Sbjct: 241 IIFPLIQFGEEVSGKKYGEKFETD--VALRVIADHLRAITF 279
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
0.326 0.139 0.425
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: 2,988,927
Number of extensions: 163043
Number of successful extensions: 353
Number of sequences better than 10.0: 1
Number of HSP's gapped: 353
Number of HSP's successfully gapped: 14
Length of query: 202
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 113
Effective length of database: 4,216,824
Effective search space: 476501112
Effective search space used: 476501112
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: 55 (25.6 bits)