RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7218
(93 letters)
>3eh7_A 4-hydroxybutyrate COA-transferase; citrate lyase, structural
genomics, PSI-2, protein structure initiative; HET: MSE;
2.05A {Porphyromonas gingivalis}
Length = 434
Score = 97.4 bits (243), Expect = 8e-26
Identities = 34/55 (61%), Positives = 37/55 (67%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFERL 87
GA V T R V YVVTE+GIA L GK+LRQRA ALI IA PD RE L K +R
Sbjct: 379 GAAVTTLRNEVDYVVTEYGIAQLKGKSLRQRAEALIAIAHPDFREELTKHLRKRF 433
>3gk7_A 4-hydroxybutyrate COA-transferase; alpha/beta protein; HET: SPD;
1.85A {Clostridium aminobutyricum} PDB: 3qdq_A*
Length = 448
Score = 92.9 bits (231), Expect = 4e-24
Identities = 28/59 (47%), Positives = 37/59 (62%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFERLKVMP 91
GA V T+R YVVTE+GIA + GK+L+ RA ALINIA PD ++ L+ +R
Sbjct: 380 GAAVTTSRNDADYVVTEYGIAEMKGKSLQDRARALINIAHPDFKDELKAEFEKRFNAAF 438
>2oas_A ATOA, 4-hydroxybutyrate coenzyme A transferase; alpha beta protein,
structural genomics, PSI-2, protein STRU initiative;
HET: COA; 2.40A {Shewanella oneidensis}
Length = 436
Score = 92.8 bits (231), Expect = 4e-24
Identities = 38/57 (66%), Positives = 45/57 (78%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFERLKV 89
GAGVVTTRAHVHY+VTE+G A L G++LR+RA ALINIA PD RE L + AFE +
Sbjct: 370 GAGVVTTRAHVHYIVTEYGAANLKGRSLRERAQALINIAHPDFREQLSRDAFEVWGL 426
>3qli_A Coenzyme A transferase; COEN transferase; 1.90A {Yersinia pestis}
PDB: 3qlk_A 3s8d_A
Length = 455
Score = 90.2 bits (224), Expect = 4e-23
Identities = 21/54 (38%), Positives = 30/54 (55%)
Query: 32 LGAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFE 85
+ V T R HY+VTE G L G + +RA +I +A PD R+ L +AA +
Sbjct: 398 IDGPVTTPRIDTHYIVTEFGAVNLKGLSSTERALRIIELAHPDFRDELTQAAKK 451
>3d3u_A 4-hydroxybutyrate COA-transferase; alpha-beta protein, structural
genomics, PSI-2, protein STRU initiative; 2.80A
{Porphyromonas gingivalis}
Length = 439
Score = 89.8 bits (223), Expect = 5e-23
Identities = 32/57 (56%), Positives = 37/57 (64%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFERLKV 89
GA V T R V YVVTE+G+A L G TLRQRA AL IA PD R ALE+ R ++
Sbjct: 376 GACVTTGRNEVDYVVTEYGVARLRGATLRQRAEALTAIAHPDFRPALEEEIRRRFEL 432
>2nvv_A Acetyl-COA hydrolase/transferase family protein; alpha beta
protein, structural genomics, PSI-2, protein STRU
initiative; 2.70A {Porphyromonas gingivalis}
Length = 506
Score = 82.2 bits (203), Expect = 4e-20
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 32 LGAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALI-NIAPPDHREALEKAA 83
+ A + V +++E G+A L GK R+RAH +I PD+R L +
Sbjct: 408 MVAHHDHSEHSVKVIISEWGVADLRGKNPRERAHEIIDKCVHPDYRPLLRQYL 460
>2g39_A Acetyl-COA hydrolase; coenzyme A transferase, structural G PSI,
protein structure initiative, midwest center for struc
genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP:
c.124.1.2 c.124.1.2
Length = 497
Score = 79.5 bits (196), Expect = 3e-19
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 32 LGAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALI-NIAPPDHREALEKAA 83
+ + V T V +VTE G+A L G R+RA +I N P ++ L
Sbjct: 412 MVSHVDHTEHDVDILVTEQGLADLRGLAPRERARVIIENCVHPSYQAPLLDYF 464
>1xr4_A Putative citrate lyase alpha chain/citrate-ACP TR; the midwest
center for structural genomics, MCSG, structural
genomics; 2.37A {Salmonella typhimurium} SCOP: c.124.1.2
c.124.1.2
Length = 509
Score = 61.5 bits (149), Expect = 6e-13
Identities = 12/54 (22%), Positives = 18/54 (33%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFER 86
G V R + + G+A + + L+QRA L P A
Sbjct: 442 GIAVNPARQDLLDNLRAAGVALMTIEQLQQRAEQLTGKPQPIEFTDRVVAVVRY 495
>2hj0_A Putative citrate lyase, ALFA subunit; alpha beta protein.,
structural genomics, PSI-2, protein STR initiative; HET:
CIT; 2.70A {Streptococcus mutans}
Length = 519
Score = 56.1 bits (135), Expect = 5e-11
Identities = 15/51 (29%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAF-LFGKTLRQRAHALINIAPPDHREALEKA 82
V+T V VVTE GIA L + + + E EKA
Sbjct: 428 VNTVITPGTSVDVVVTEVGIAINPNRPDLIEYFKD-LKVPQLTIEELKEKA 477
>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 = 33.5 bits (76), Expect = 0.006
Identities = 17/103 (16%), Positives = 32/103 (31%), Gaps = 25/103 (24%)
Query: 3 ACRNTAPLCFFPFQVLFQASDS--GRPDRQLLGAGVVTTRAHVHYVVTEHGIAFLFGKTL 60
C P P +L + ++ G P L + + T+ V V + L
Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL--TQEQVQDYVNK------TNSHL 360
Query: 61 RQRAH---ALIN------IA-PPDHREALE--KAAFERLKVMP 91
+L+N ++ PP ++L + K
Sbjct: 361 PAGKQVEISLVNGAKNLVVSGPP---QSLYGLNLTLRKAKAPS 400
Score = 28.5 bits (63), Expect = 0.34
Identities = 21/84 (25%), Positives = 30/84 (35%), Gaps = 20/84 (23%)
Query: 24 SGRPDRQ-LLGAGV------VTTRAHVHYVVTEHGIAFLFGKTLRQRAHALIN------- 69
S PD+ LL + V AH YVVT + F G+ LR
Sbjct: 223 SNTPDKDYLLSIPISCPLIGVIQLAH--YVVTAKLLGFTPGE-LRSYLKGATGHSQGLVT 279
Query: 70 ---IAPPDHREALEKAAFERLKVM 90
IA D E+ + + + V+
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVL 303
Score = 26.2 bits (57), Expect = 2.1
Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 26/86 (30%)
Query: 18 LFQASDSGRPDRQLLGAGVVTTRAHVHY----------VVTE--HGIAFLF----GKTLR 61
L++ S + + V RA H+ +V + F GK +R
Sbjct: 1635 LYKTSKAAQD---------VWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 62 QRAHALINIAPPDHREALEKAAFERL 87
+ A+I D + EK F+ +
Sbjct: 1686 ENYSAMIFETIVDGKLKTEK-IFKEI 1710
>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 = 28.3 bits (62), Expect = 0.40
Identities = 3/15 (20%), Positives = 6/15 (40%)
Query: 3 ACRNTAPLCFFPFQV 17
C + C F++
Sbjct: 170 VCLSYKVQCKMDFKI 184
>2uz8_A Eukaryotic translation elongation factor 1 epsilon-1; protein
biosynthesis, aminoacyl-tRNA synthetase, GST, nuclear
protein, RNA-binding protein; HET: MSE; 2.0A {Homo
sapiens}
Length = 174
Score = 25.5 bits (56), Expect = 2.8
Identities = 5/47 (10%), Positives = 15/47 (31%), Gaps = 7/47 (14%)
Query: 43 VHYVVTEHGIAFLFGKTLRQRAH-------ALINIAPPDHREALEKA 82
++V + +L G T ++A + + + +
Sbjct: 48 AAHLVKQANKEYLLGSTAEEKAMVQQWLEYRVTQVDGHSSKNDIHTL 94
>1srq_A RAP1GAP, GTPase-activating protein 1; mixed alpha-beta, signaling
protein; 2.90A {Homo sapiens} SCOP: e.55.1.1 PDB:
3brw_A*
Length = 341
Score = 24.8 bits (53), Expect = 6.2
Identities = 8/48 (16%), Positives = 12/48 (25%)
Query: 28 DRQLLGAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDH 75
D Q L V V + F+ HA + +
Sbjct: 204 DAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGG 251
>2v82_A 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; lyase, kdpgal;
HET: KDP; 2.1A {Escherichia coli} PDB: 2v81_A*
Length = 212
Score = 24.4 bits (53), Expect = 6.9
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 27 PDRQLLGAGVVTTRAHVHYVVTEHGIAFLF 56
D+ L+GAG V V + G +
Sbjct: 57 GDKALIGAGTVLKPEQVDALA-RMGCQLIV 85
>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613,
structural genomics, PSI, protein structure initiative;
HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69
Length = 146
Score = 24.2 bits (53), Expect = 7.5
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 5/32 (15%)
Query: 29 RQLLGAGVVTTR-----AHVHYVVTEHGIAFL 55
R L+ GV+ +H Y +T+ G A
Sbjct: 59 RNLVEHGVMVAVPAESGSHQEYRLTDKGRALF 90
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 24.1 bits (53), Expect = 9.7
Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 11/49 (22%)
Query: 51 GIAFLFGKTLRQRAHALINIA----------PPDHREALEKAAFERLKV 89
G++ F ++ + I P D E LEK LK+
Sbjct: 461 GVSINF-VHDKKSWEEMNAIQEYFQRPITRVPTDDYEELEKVVKNALKM 508
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
0.329 0.139 0.432
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,472,514
Number of extensions: 80434
Number of successful extensions: 257
Number of sequences better than 10.0: 1
Number of HSP's gapped: 254
Number of HSP's successfully gapped: 27
Length of query: 93
Length of database: 6,701,793
Length adjustment: 60
Effective length of query: 33
Effective length of database: 5,026,533
Effective search space: 165875589
Effective search space used: 165875589
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (23.4 bits)