RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3942
(160 letters)
>1f0y_A HCDH, L-3-hydroxyacyl-COA dehydrogenase; abortive ternary complex,
oxidoreductase; HET: CAA NAD; 1.80A {Homo sapiens} SCOP:
a.100.1.3 c.2.1.6 PDB: 3rqs_A 1lsj_A* 1il0_A* 1lso_A*
1m76_A* 1m75_A* 1f14_A 1f12_A 1f17_A* 3had_A* 2hdh_A*
3hdh_A*
Length = 302
Score = 227 bits (582), Expect = 4e-76
Identities = 75/173 (43%), Positives = 110/173 (63%), Gaps = 15/173 (8%)
Query: 1 VAAQAGNQ-----------EEGEKLIDSTLSRI--KGSSKEE--GEKLIDLTLSRIKGSS 45
VAA G+ + +K I+ +L ++ K ++ G++ ++ TLS I S+
Sbjct: 33 VAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSTIATST 92
Query: 46 KVEDSVSQSDLVIEAIVENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKD 105
V +DLV+EAIVEN+ +K++LF +DK A I ASNTSSL IT IA+ T R+D
Sbjct: 93 DAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQD 152
Query: 106 KFVGLHFFNPVPMMKLLEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
+F GLHFFNPVP+MKL+EVI+T TS T+ ++ ++ K++GK + CKDTPGF
Sbjct: 153 RFAGLHFFNPVPVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGF 205
>3mog_A Probable 3-hydroxybutyryl-COA dehydrogenase; structural genomics,
PSI, protein structure initiative, NYSG oxidoreductase;
2.20A {Escherichia coli}
Length = 483
Score = 216 bits (551), Expect = 3e-69
Identities = 56/171 (32%), Positives = 85/171 (49%), Gaps = 17/171 (9%)
Query: 1 VAAQAGNQ-----------EEGEKLIDSTLSRI--KGSSKEEGEKLIDLTLSRIKGSSKV 47
VAA G+Q I + L+ +G E + TL R+ + +
Sbjct: 23 VAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKLTAE-TC--ERTLKRLIPVTDI 79
Query: 48 EDSVSQSDLVIEAIVENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKF 107
++ +DLVIEA E +++K LF + ++ P +L +NTSS+SIT IA+ ++
Sbjct: 80 HA-LAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTSSISITAIAAEIKNPERV 138
Query: 108 VGLHFFNPVPMMKLLEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
GLHFFNP P+MKL+EV+ T+ + E S GK + C TPGF
Sbjct: 139 AGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPVRCHSTPGF 189
Score = 100 bits (251), Expect = 1e-25
Identities = 16/102 (15%), Positives = 30/102 (29%), Gaps = 6/102 (5%)
Query: 57 VIEAIVENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFVGLHFFNPV 116
V V + K+ D + +L T + +A R +
Sbjct: 293 VGLEAVSDSFSPMKVEKKSDGVTEIDDVLLIETQGETAQALAIRLARPVVVIDKMA---- 348
Query: 117 PMMKLLEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
K++ + D+ + + GKT + D PG
Sbjct: 349 --GKVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGM 388
>1zej_A HBD-9, 3-hydroxyacyl-COA dehydrogenase; structural genomics, joint
center for structural genomics, J protein structure
initiative, PSI; HET: PE8; 2.00A {Archaeoglobus
fulgidus}
Length = 293
Score = 192 bits (489), Expect = 4e-62
Identities = 41/157 (26%), Positives = 82/157 (52%), Gaps = 12/157 (7%)
Query: 1 VAAQAGNQEEGEKLIDSTLSRIKGSSKEEGEKLI-DLTLSRIKGSSKVEDSVSQSDLVIE 59
+A + + L + + E + I + LS+I+ ++ +E V D+V+E
Sbjct: 29 IAIASK--------HEVVLQDVSEKALEAAREQIPEELLSKIEFTTTLEK-VKDCDIVME 79
Query: 60 AIVENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFVGLHFFNPVPMM 119
A+ E+++ K ++ V+++ +A L SNTS +S+ +IA + +F+G+H+ NP +M
Sbjct: 80 AVFEDLNTKVEVLREVERLT--NAPLCSNTSVISVDDIAERLDSPSRFLGVHWMNPPHVM 137
Query: 120 KLLEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTP 156
L+E++ + T T V + + +GK +VCK
Sbjct: 138 PLVEIVISRFTDSKTVAFVEGFLRELGKEVVVCKGQS 174
>3k6j_A Protein F01G10.3, confirmed by transcript evidenc; rossmann fold,
oxidoreductase; 2.20A {Caenorhabditis elegans}
Length = 460
Score = 182 bits (463), Expect = 2e-56
Identities = 46/170 (27%), Positives = 84/170 (49%), Gaps = 18/170 (10%)
Query: 1 VAAQAG--------NQEEG----EKLIDSTLSRIKGSSKEEGEKLIDLTLSRIKGSSKVE 48
AG N++ E + S K + + EK+ + +K +S
Sbjct: 72 CFGLAGIETFLVVRNEQRCKQELEVMYAREKSF-KRLNDKRIEKI----NANLKITSDFH 126
Query: 49 DSVSQSDLVIEAIVENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFV 108
+S DL++E+++E+M +K +LF +++ I ++ I +NTSSL + EI+SV V
Sbjct: 127 K-LSNCDLIVESVIEDMKLKKELFANLENICKSTCIFGTNTSSLDLNEISSVLRDPSNLV 185
Query: 109 GLHFFNPVPMMKLLEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
G+HFFNP +++L+E+I + TS + +SI K ++ + F
Sbjct: 186 GIHFFNPANVIRLVEIIYGSHTSSQAIATAFQACESIKKLPVLVGNCKSF 235
>1wdk_A Fatty oxidation complex alpha subunit; alpha2BETA2 heterotetrameric
complex, lyase, oxidoreductase/transferase complex,
lyase; HET: ACO NAD N8E; 2.50A {Pseudomonas fragi} SCOP:
a.100.1.3 a.100.1.3 c.2.1.6 c.14.1.3 PDB: 1wdl_A*
1wdm_A* 2d3t_A*
Length = 715
Score = 183 bits (466), Expect = 4e-55
Identities = 56/157 (35%), Positives = 82/157 (52%), Gaps = 7/157 (4%)
Query: 2 AAQAGNQEEGEKLIDSTLSRIKGSSKEEGEKLIDLTLSRIKGSSKVEDSVSQSDLVIEAI 61
+ G E KL+ + + + + ++ L+ I+ + D DLV+EA+
Sbjct: 349 GIEQG-LAEAAKLLVGRVDK-GRMTPAKMAEV----LNGIRPTLSYGD-FGNVDLVVEAV 401
Query: 62 VENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFVGLHFFNPVPMMKL 121
VEN +K + V+ AILASNTS++SI+ +A R + FVG+HFFNPV MM L
Sbjct: 402 VENPKVKQAVLAEVENHVREDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPL 461
Query: 122 LEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
+EVIR +SD + K +GK IV D PGF
Sbjct: 462 VEVIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGF 498
>1zcj_A Peroxisomal bifunctional enzyme; peroxisomal multifunctional enzyme
type 1, L-bifunction enzyme, MFE-1, fatty acid beta
oxidation; 1.90A {Rattus norvegicus}
Length = 463
Score = 178 bits (454), Expect = 4e-55
Identities = 48/157 (30%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 2 AAQAGNQEEGEKLIDSTLSRIKGSSKEEGEKLIDLTLSRIKGSSKVEDSVSQSDLVIEAI 61
A ++ ++ SR + + +++ SS ++ +S DLV+EA+
Sbjct: 72 QLDAA-KKIITFTLEKEASRAHQNGQAS-------AKPKLRFSSSTKE-LSTVDLVVEAV 122
Query: 62 VENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFVGLHFFNPVPMMKL 121
E+M++K K+F + + A L +NTS+L++ +IAS T+R +G HFF+P +M+L
Sbjct: 123 FEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRL 182
Query: 122 LEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
LEVI + +S T V K IGK +V + GF
Sbjct: 183 LEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGF 219
>2wtb_A MFP2, fatty acid multifunctional protein (ATMFP2); oxidoreductase,
peroxisomes, beta-oxidation, fatty acid oxidation; 2.50A
{Arabidopsis thaliana}
Length = 725
Score = 182 bits (463), Expect = 1e-54
Identities = 56/157 (35%), Positives = 88/157 (56%), Gaps = 7/157 (4%)
Query: 2 AAQAGNQEEGEKLIDSTLSRIKGSSKEEGEKLIDLTLSRIKGSSKVEDSVSQSDLVIEAI 61
+AG + + S + + S+E+ EK +S +KGS E D+VIEA+
Sbjct: 347 FLEAG-IGRVKANLQSRVRK-GSMSQEKFEKT----MSLLKGSLDYES-FRDVDMVIEAV 399
Query: 62 VENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFVGLHFFNPVPMMKL 121
+EN+ +K ++F ++K P ILASNTS++ + +I T +D+ VG HFF+P +M L
Sbjct: 400 IENISLKQQIFADLEKYCPQHCILASNTSTIDLNKIGERTKSQDRIVGAHFFSPAHIMPL 459
Query: 122 LEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
LE++RTN TS + + GK I KT +V + GF
Sbjct: 460 LEIVRTNHTSAQVIVDLLDVGKKIKKTPVVVGNCTGF 496
>2dpo_A L-gulonate 3-dehydrogenase; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
1.70A {Oryctolagus cuniculus} PDB: 2ep9_A* 3ado_A 3a97_A
3adp_A* 3f3s_A*
Length = 319
Score = 172 bits (438), Expect = 4e-54
Identities = 36/170 (21%), Positives = 75/170 (44%), Gaps = 12/170 (7%)
Query: 1 VAAQAGNQ-----------EEGEKLIDSTLSRIKGSSKEEGEKLIDLTLSRIKGSSKVED 49
+ A G + + I + ++ S +G + LS I + + +
Sbjct: 24 LFASGGFRVKLYDIEPRQITGALENIRKEMKSLQQSGSLKGSLSAEEQLSLISSCTNLAE 83
Query: 50 SVSQSDLVIEAIVENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFVG 109
+V + E + EN+D+K K+F +D I +L+S++S L +++ + + +
Sbjct: 84 AVEGVVHIQECVPENLDLKRKIFAQLDSIVDDRVVLSSSSSCLLPSKLFTGLAHVKQCIV 143
Query: 110 LHFFNPVPMMKLLEVIRTNDTSDATYNAVTEWGKSIGKTTIVC-KDTPGF 158
H NP + L+E++ +TS AT + + IG++ + K+ GF
Sbjct: 144 AHPVNPPYYIPLVELVPHPETSPATVDRTHALMRKIGQSPVRVLKEIDGF 193
>3zwc_A Peroxisomal bifunctional enzyme; beta oxidation pathway,
oxidoreductase, lipid metabolism, LY isomerase,
peroxisome, fatty acid metabolism; HET: NAD HSC; 2.30A
{Rattus norvegicus} PDB: 3zw9_A* 3zw8_A* 3zwa_A* 3zwb_A*
2x58_A*
Length = 742
Score = 179 bits (457), Expect = 8e-54
Identities = 48/157 (30%), Positives = 81/157 (51%), Gaps = 9/157 (5%)
Query: 2 AAQAGNQEEGEKLIDSTLSRIKGSSKEEGEKLIDLTLSRIKGSSKVEDSVSQSDLVIEAI 61
A ++ ++ SR + +++ SS ++ +S DLV+EA+
Sbjct: 351 QLDAA-KKIITFTLEKEASR--AHQNGQ-----ASAKPKLRFSSSTKE-LSTVDLVVEAV 401
Query: 62 VENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNRKDKFVGLHFFNPVPMMKL 121
E+M++K K+F + + A L +NTS+L++ +IAS T+R +G HFF+P +M+L
Sbjct: 402 FEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRL 461
Query: 122 LEVIRTNDTSDATYNAVTEWGKSIGKTTIVCKDTPGF 158
LEVI + +S T V K IGK +V + GF
Sbjct: 462 LEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGF 498
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 37.6 bits (86), Expect = 5e-04
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 63 ENMDIKHKLFTSVDKIAPASA-ILASNTS 90
E +K KL S+ A SA LA +
Sbjct: 18 EKQALK-KLQASLKLYADDSAPALAIKAT 45
Score = 31.1 bits (69), Expect = 0.082
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 31 EKLIDLTLSRIKGSSKV--EDSVSQSDLVIEAIVE 63
EK L +++ S K+ +DS L I+A +E
Sbjct: 18 EKQ---ALKKLQASLKLYADDSAPA--LAIKATME 47
>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 = 38.1 bits (88), Expect = 7e-04
Identities = 30/160 (18%), Positives = 54/160 (33%), Gaps = 54/160 (33%)
Query: 9 EEGEKLIDSTLSRIKGSSKEEGEKLIDLTLSRIKGSSKVEDSVSQSDLVIEAIVENMDIK 68
E E + LS I ++E+ + ++ T S + +V +S LV N
Sbjct: 329 ENNEGVPSPMLS-ISNLTQEQVQDYVNKTNSHLPAGKQV--EIS---LV------N---- 372
Query: 69 HKLFTSVDKIAPASAILASNTSSL-------------SITEIASV--TNRKDKFVGLHFF 113
+ +++ SL S + + + + RK KF + F
Sbjct: 373 ----------GAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFS--NRF 420
Query: 114 NPV--P-----MMKLLEVIRTNDTSDATYNAVTEWGKSIG 146
PV P ++ ++I D N V+ K I
Sbjct: 421 LPVASPFHSHLLVPASDLIN----KDLVKNNVSFNAKDIQ 456
>3ctv_A HBD-10, 3-hydroxyacyl-COA dehydrogenase; structural genomics,
APC7539, PSI-2, protein structure initiative; 2.46A
{Archaeoglobus fulgidus dsm 4304}
Length = 110
Score = 28.0 bits (63), Expect = 0.63
Identities = 3/17 (17%), Positives = 5/17 (29%), Gaps = 1/17 (5%)
Query: 142 GKSIGKTTIVCKDTPGF 158
G S G+ +
Sbjct: 1 GHSKGRP-QIDSSKATD 16
>3irs_A Uncharacterized protein BB4693; structural genomics, PSI-2, protein
structure initiative, TI protein; HET: GOL; 1.76A
{Bordetella bronchiseptica} PDB: 3k4w_A
Length = 291
Score = 27.9 bits (62), Expect = 1.3
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 48 EDSVSQSDLVIEAIVENMDIKHKLFTSVDKIAPASAILASNTSSLSITEIASVTNR-KDK 106
E + S + +E + E M +++ +S S+S ++A+V DK
Sbjct: 39 EPAPSAEEKSLELMFEEMAAAG-----IEQ-GVCVGRNSSVLGSVSNADVAAVAKAYPDK 92
Query: 107 FVGLHFFNPVPMMKLLEVIR 126
F + + + ++
Sbjct: 93 FHPVGSIEAATRKEAMAQMQ 112
>1v2z_A Circadian clock protein KAIA homolog; all alpha, riken structural
genomics/proteomics initiative, structural genomics;
1.80A {Thermosynechococcus elongatus} SCOP: a.186.1.1
PDB: 1q6a_A 1q6b_A 1suy_A 1sv1_A
Length = 111
Score = 25.2 bits (55), Expect = 6.1
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 98 ASVTNRKDKFVGLHFFNPVPMMKLLEV 124
A V R D+FV FF + + ++LE+
Sbjct: 37 AKVNERIDEFVSKAFFADISVSQVLEI 63
>1r5q_A KAI A, circadian oscillation regulator; four-helix-bundle, gene
regulation; 2.00A {Nostoc SP} SCOP: a.186.1.1
Length = 102
Score = 25.2 bits (55), Expect = 6.8
Identities = 6/27 (22%), Positives = 16/27 (59%)
Query: 98 ASVTNRKDKFVGLHFFNPVPMMKLLEV 124
++ + DKF+ F +P+ +++E+
Sbjct: 30 KALKEKIDKFINAVFCANIPVPEIIEI 56
>1r8j_A KAIA; circadian clock protein; 2.03A {Synechococcus elongatus pcc
7942} SCOP: a.186.1.1 c.23.1.5 PDB: 1m2e_A 1m2f_A
Length = 289
Score = 25.7 bits (56), Expect = 6.9
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 98 ASVTNRKDKFVGLHFFNPVPMMKLLEV 124
+++ D FV + FF VP+ K++E+
Sbjct: 215 SNLNQSIDNFVNMAFFADVPVTKVVEI 241
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
0.310 0.127 0.338
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,176,505
Number of extensions: 118520
Number of successful extensions: 244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 241
Number of HSP's successfully gapped: 21
Length of query: 160
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 74
Effective length of database: 4,300,587
Effective search space: 318243438
Effective search space used: 318243438
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.2 bits)