RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5915
(89 letters)
>3k6m_A Succinyl-COA:3-ketoacid-coenzyme A transferase 1, mitochondrial;
SCOT, COA transferase, dynamic domain, glycerol,
mitochondri transferase; 1.50A {Sus scrofa} PDB: 1m3e_A*
1o9l_A 1ooy_A 2nrc_A 2nrb_A 3oxo_A* 1ooz_A 1ope_A 3dlx_A
Length = 481
Score = 73.3 bits (180), Expect = 4e-17
Identities = 30/47 (63%), Positives = 37/47 (78%)
Query: 43 CVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFAVSPDLKPMGQVET 89
VF+VD+++GLTLIE+ EG+ V +I STGCDFAVSP L PM QV T
Sbjct: 435 AVFDVDRKKGLTLIELWEGLTVDDIKKSTGCDFAVSPKLIPMQQVTT 481
>2ahu_A Putative enzyme YDIF; COA transferase, glutamyl thioester,
structural genomi montreal-kingston bacterial structural
genomics initiative; 1.90A {Escherichia coli} SCOP:
c.124.1.3 c.124.1.2 PDB: 2ahv_A* 2ahw_A*
Length = 531
Score = 62.0 bits (151), Expect = 4e-13
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 43 CVFEVDKERGLTLIEIAEGVEV-PEIIVSTGCDFAVSPDLKPMGQ 86
VF + ++ GL LIEIA GV++ +I+ +SP+LK M +
Sbjct: 471 AVFTLKED-GLHLIEIAPGVDLQKDILDKMDFTPVISPELKLMDE 514
>1poi_B Glutaconate coenzyme A-transferase; COA, glutamate, protein
fermentation; 2.50A {Acidaminococcus fermentans} SCOP:
c.124.1.3
Length = 260
Score = 51.5 bits (123), Expect = 2e-09
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 3/71 (4%)
Query: 15 SAYKADALPTKPTRLGLTALS--SDVLSRDCVFEVDKERG-LTLIEIAEGVEVPEIIVST 71
++ P RLGL V++ + + D++ + L +++ +T
Sbjct: 164 TSPGWIDGPGGRERLGLPGDVGPQLVVTDKGILKFDEKTKRMYLAAYYPTSSPEDVLENT 223
Query: 72 GCDFAVSPDLK 82
G D VS ++
Sbjct: 224 GFDLDVSKAVE 234
>3rrl_B Succinyl-COA:3-ketoacid-coenzyme A transferase SU;
MCSG,PSI-biology, structural genomics, midwest center
for ST genomics; 2.29A {Helicobacter pylori} PDB: 3cdk_B
Length = 207
Score = 48.9 bits (117), Expect = 1e-08
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 43 CVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFAVS 78
VFE + L+E+ EGV + ++ T +F V
Sbjct: 172 AVFEFSNN-AMKLVELQEGVSLDQVKEKTEAEFEVR 206
>1hr6_A Alpha-MPP, mitochondrial processing peptidase alpha subunit; hxxeh
zinc-binding motif, hydrolase; HET: EPE; 2.50A
{Saccharomyces cerevisiae} SCOP: d.185.1.1 d.185.1.1
PDB: 1hr7_A 1hr8_A* 1hr9_A*
Length = 475
Score = 28.8 bits (65), Expect = 0.19
Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 8/40 (20%)
Query: 37 DVLSRDCVF-------EVDKERGLTLIEIAEGVEVPEIIV 69
++S + V E+ +++ EI E PE+++
Sbjct: 103 QLMS-ETVRFPKITEQELQEQKLSAEYEIDEVWMKPELVL 141
>1pp9_B Ubiquinol-cytochrome C reductase complex core Pro mitochondrial;
cytochrome BC1, membrane protein, heme protein, rieske
iron protein, cytochrome B, complex III; HET: BHG HEM
HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: d.185.1.1
d.185.1.1 PDB: 1bgy_B* 1be3_B* 1l0n_B* 1ntk_B* 1ntm_B*
1ntz_B* 1nu1_B* 1l0l_B* 1ppj_B* 1sqq_B* 1sqv_B* 1sqx_B*
2a06_B* 2fyu_B* 2ybb_B* 1sqb_B* 1sqp_B* 1qcr_B* 2bcc_B*
3bcc_B* ...
Length = 439
Score = 28.0 bits (63), Expect = 0.39
Identities = 7/40 (17%), Positives = 14/40 (35%), Gaps = 8/40 (20%)
Query: 37 DVLSRDCVF-------EVDKERGLTLIEIAEGVEVPEIIV 69
+ L + EV + I+ A ++ P+ V
Sbjct: 121 EFLL-NVTTAPEFRRWEVAALQPQLRIDKAVALQNPQAHV 159
>1pp9_A Ubiquinol-cytochrome C reductase complex core Pro mitochondrial;
cytochrome BC1, membrane protein, heme protein, rieske
iron protein, cytochrome B, complex III; HET: BHG HEM
HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: d.185.1.1
d.185.1.1 PDB: 1bgy_A* 1be3_A* 1l0n_A* 1ntk_A* 1ntm_A*
1ntz_A* 1nu1_A* 1l0l_A* 1ppj_A* 1sqq_A* 1sqv_A* 1sqx_A*
2a06_A* 2fyu_A* 2ybb_A* 1sqb_A* 1sqp_A* 1qcr_A* 1bcc_A*
2bcc_A* ...
Length = 446
Score = 26.8 bits (60), Expect = 1.0
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 37 DVLSRDCVF-------EVDKERGLTLIEIAEGVEVPEIIV 69
++L+ D V +++KER + L E+ E +V
Sbjct: 111 ELLA-DIVQNCSLEDSQIEKERDVILQELQENDTSMRDVV 149
>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 = 26.1 bits (56), Expect = 1.3
Identities = 5/33 (15%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 1 REQIRPGRESNPRPSAYKADALPTKPTRLGLTA 33
++ ++ +++ + Y D+ P L + A
Sbjct: 19 KQALKK-LQASLKL--YADDSAPA----LAIKA 44
>1hr6_B Beta-MPP, mitochondrial processing peptidase beta subunit; hxxeh
zinc-binding motif, hydrolase; HET: EPE; 2.50A
{Saccharomyces cerevisiae} SCOP: d.185.1.1 d.185.1.1
PDB: 1hr7_B 1hr8_B* 1hr9_B*
Length = 443
Score = 26.0 bits (58), Expect = 1.6
Identities = 9/40 (22%), Positives = 20/40 (50%), Gaps = 8/40 (20%)
Query: 37 DVLSRDCVF-------EVDKERGLTLIEIAEGVEVPEIIV 69
D+LS D + +++ER + + E E ++ + +V
Sbjct: 105 DILS-DILTKSVLDNSAIERERDVIIRESEEVDKMYDEVV 143
>1vrm_A Hypothetical protein TM1553; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI; HET: UNL; 1.58A {Thermotoga maritima} SCOP:
d.96.2.1
Length = 325
Score = 26.0 bits (58), Expect = 1.7
Identities = 11/70 (15%), Positives = 17/70 (24%), Gaps = 18/70 (25%)
Query: 14 PSAYKADALPTKPTRLGLTALSSDVLSRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGC 73
A ADAL T + + ++ + +IV G
Sbjct: 270 EDATTADALSTAGFVMAG------------------KDWRKVVLDFPNMGAHLLIVLEGG 311
Query: 74 DFAVSPDLKP 83
S K
Sbjct: 312 AIERSETFKL 321
>3hv8_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase;
HET: C2E; 1.45A {Pseudomonas aeruginosa PAO1} PDB:
3hv9_A
Length = 268
Score = 25.5 bits (57), Expect = 2.2
Identities = 4/22 (18%), Positives = 7/22 (31%), Gaps = 3/22 (13%)
Query: 58 IAEGVEVPEII---VSTGCDFA 76
I VE ++ G +
Sbjct: 226 IVPFVESASVLATLWQAGATYI 247
>3kzp_A LMO0111 protein, putative diguanylate cyclase/phosphodiesterase;
EAL-domain, structural genomics, PSI-2; 2.00A {Listeria
monocytogenes}
Length = 235
Score = 25.5 bits (57), Expect = 2.6
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 3/29 (10%)
Query: 51 RGLTLIEIAEGVEVPE---IIVSTGCDFA 76
+ L + EG+E E ++ S G
Sbjct: 196 QKNKLDFVVEGIETKETMTLLESHGVSIF 224
>3hdi_A Processing protease; CAGE structure, M16B peptidase,
metallopeptidase, peptidasome, protease, hydrolase;
2.70A {Bacillus halodurans c-125}
Length = 421
Score = 25.6 bits (57), Expect = 2.7
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 37 DVLSRDCVF-------EVDKERGLTLIEIAEGVEVPEIIV 69
D LS D F E++KER + EI + P+ IV
Sbjct: 100 DTLS-DMFFHSTFQKEELEKERKVVFEEIKMVDDTPDDIV 138
>2bas_A YKUI protein; EAL domain, structural genom protein structure
initiative, midwest center for structural genomics,
MCSG, signaling protein; 2.61A {Bacillus subtilis} SCOP:
c.1.33.1 d.110.6.2 PDB: 2w27_A*
Length = 431
Score = 25.4 bits (56), Expect = 3.0
Identities = 5/28 (17%), Positives = 8/28 (28%), Gaps = 5/28 (17%)
Query: 52 GLTLIEIAEGVEVPE---IIVSTGCDFA 76
G L+ E +E G +
Sbjct: 227 GAALL--YEDIEANFQLQYAWRNGGRYF 252
>3hvb_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase;
2.99A {Pseudomonas aeruginosa PAO1}
Length = 437
Score = 25.1 bits (56), Expect = 3.7
Identities = 4/29 (13%), Positives = 8/29 (27%), Gaps = 3/29 (10%)
Query: 51 RGLTLIEIAEGVEVPEII---VSTGCDFA 76
+ I VE ++ G +
Sbjct: 388 HEQQKLSIVPFVESASVLATLWQAGATYI 416
>2eqx_A Kelch repeat and BTB domain-containing protein 4; BACK domain,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 105
Score = 24.2 bits (53), Expect = 4.7
Identities = 3/14 (21%), Positives = 4/14 (28%)
Query: 34 LSSDVLSRDCVFEV 47
+S V E
Sbjct: 61 ISDGVPCSQNPTEA 74
>3pjx_A Cyclic dimeric GMP binding protein; ggdef-EAL tandem domain,
C-DI-GMP receptor, lyase; 2.00A {Pseudomonas
fluorescens} PDB: 3pjw_A 3pju_A* 3pjt_A* 3pfm_A
Length = 430
Score = 24.7 bits (55), Expect = 4.7
Identities = 8/29 (27%), Positives = 10/29 (34%), Gaps = 3/29 (10%)
Query: 51 RGLTLIEIAEGVEVPE---IIVSTGCDFA 76
+ L IAE VE +I G
Sbjct: 390 HSIDLPLIAERVETEGELSVIREMGLYGV 418
>3aln_A Dual specificity mitogen-activated protein kinase; protein AMP-PNP
complex, transferase; HET: ANP; 2.30A {Homo sapiens}
PDB: 3alo_A*
Length = 327
Score = 24.2 bits (53), Expect = 7.4
Identities = 6/10 (60%), Positives = 8/10 (80%)
Query: 52 GLTLIEIAEG 61
G+TL E+A G
Sbjct: 216 GITLYELATG 225
>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI,
protei structure initiative, midwest center for
structural genomic; HET: SO4; 1.65A {Escherichia coli}
SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A
2iu7_A 2iv1_A 2iuo_A 2ivg_A
Length = 156
Score = 24.2 bits (52), Expect = 7.4
Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 9/50 (18%)
Query: 24 TKPTRLGLTALSSDVLSRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGC 73
+ RL L + ++ L+ EIA+G + E V+
Sbjct: 7 NRNIRLDLADA---------ILLSKAKKDLSFAEIADGTGLAEAFVTAAL 47
>3fme_A Dual specificity mitogen-activated protein kinase; active mutant,
structural genomics consortium, SCG, binding,
nucleotide-binding, phosphoprotein; HET: STU; 2.26A
{Homo sapiens} PDB: 3enm_A
Length = 290
Score = 24.1 bits (53), Expect = 8.3
Identities = 5/10 (50%), Positives = 8/10 (80%)
Query: 52 GLTLIEIAEG 61
G+T+IE+A
Sbjct: 200 GITMIELAIL 209
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
0.314 0.134 0.382
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,325,067
Number of extensions: 68252
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 152
Number of HSP's successfully gapped: 29
Length of query: 89
Length of database: 6,701,793
Length adjustment: 57
Effective length of query: 32
Effective length of database: 5,110,296
Effective search space: 163529472
Effective search space used: 163529472
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 (21.9 bits)
S2: 51 (23.3 bits)