RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7121
(79 letters)
>3rj1_G Mediator of RNA polymerase II transcription subun; RNA polymeras
II, POL II, head module, head, regulator, helical
bundle; 4.30A {Saccharomyces cerevisiae}
Length = 295
Score = 86.4 bits (212), Expect = 2e-22
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 8/74 (10%)
Query: 12 QEPILNMTGLEYIVLHVQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVVYQA 63
+E ++ + G EY++ V+EP +VIRKQ R + + P+ DYYII +YQ+
Sbjct: 104 EEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQS 163
Query: 64 PDLASVISSRLVGT 77
P + ++ SRL+ T
Sbjct: 164 PTIFKIVQSRLMST 177
>2a8x_A Dihydrolipoyl dehydrogenase, E3 component of alpha; lipoamide
dehydrogenase, pyruvate dehydrogenase, alpha keto acid
dehydrogenase; HET: FAD; 2.40A {Mycobacterium
tuberculosis} PDB: 3ii4_A*
Length = 464
Score = 27.9 bits (63), Expect = 0.27
Identities = 4/21 (19%), Positives = 11/21 (52%)
Query: 49 PIADYYIIAGVVYQAPDLASV 69
+ D+ ++ + P++AS
Sbjct: 338 TLGDHRMLPRATFCQPNVASF 358
>2xvl_A Alpha-xylosidase, putative, XYL31A; hydrolase, glycosyl hydrolase
family 31, (beta/alpha)8 barre; HET: PXN; 2.30A
{Cellvibrio japonicus} PDB: 2xvg_A* 2xvk_A*
Length = 1020
Score = 26.8 bits (59), Expect = 0.70
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 7/42 (16%)
Query: 38 KQHRHSMEQTTPIADYYIIAGVVYQAPDLASVIS--SRLVGT 77
+ +T DYY +AG +IS +L G
Sbjct: 390 QHELSLASETGKAIDYYFVAG-----DTKDDIISGYRQLTGK 426
>1xdi_A RV3303C-LPDA; reductase, FAD, NAD, NADP, unkno function; HET: FAD;
2.81A {Mycobacterium tuberculosis} SCOP: c.3.1.5
d.87.1.1
Length = 499
Score = 26.4 bits (59), Expect = 0.90
Identities = 8/25 (32%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 45 EQTTPIADYYIIAGVVYQAPDLASV 69
E +PI +A V+ P++A+V
Sbjct: 342 EGVSPI-RLRTVAATVFTRPEIAAV 365
>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural
genomics, protein structure initiative, PSI; 2.90A
{Pseudomonas aeruginosa} SCOP: c.1.31.1
Length = 265
Score = 26.0 bits (58), Expect = 1.3
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 10/36 (27%)
Query: 44 MEQTTPIADYYIIAGVVYQAPDLASVISSRL-VGTG 78
M Q + ++IAG Y SRL VGTG
Sbjct: 1 MSQASSTDTPFVIAGRTY---------GSRLLVGTG 27
>1dxl_A Dihydrolipoamide dehydrogenase; oxidoreductase, multienzyme complex
protein, pyruvate dehydrogenase complex, glycine
decarboxylase complex; HET: FAD; 3.15A {Pisum sativum}
SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 470
Score = 25.9 bits (58), Expect = 1.5
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 52 DYYIIAGVVYQAPDLASV 69
DY + GVVY P++ASV
Sbjct: 347 DYDKVPGVVYTNPEVASV 364
>3ic9_A Dihydrolipoamide dehydrogenase; APC62701, colwellia psychrer 34H,
structural genomics, PSI-2; HET: FAD; 2.15A {Colwellia
psychrerythraea}
Length = 492
Score = 25.6 bits (57), Expect = 1.5
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 52 DYYIIAGVVYQAPDLASV 69
VV+ P +ASV
Sbjct: 345 QRRAPLSVVFTEPQVASV 362
>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate
kinase); nucleoside monophosphate kinase, NMP kinase;
HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP:
c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*
Length = 194
Score = 25.6 bits (57), Expect = 1.6
Identities = 7/28 (25%), Positives = 11/28 (39%)
Query: 35 VIRKQHRHSMEQTTPIADYYIIAGVVYQ 62
I+K+ QT + D+Y V
Sbjct: 144 SIKKRFNTFNVQTKLVIDHYNKFDKVKI 171
>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces
cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*
Length = 203
Score = 25.6 bits (57), Expect = 1.6
Identities = 6/28 (21%), Positives = 13/28 (46%)
Query: 35 VIRKQHRHSMEQTTPIADYYIIAGVVYQ 62
I+K+ E + P+ +Y+ V +
Sbjct: 154 SIKKRFNTFKETSMPVIEYFETKSKVVR 181
>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region,
conformational changes, transferase; 2.10A {Homo
sapiens} SCOP: c.37.1.1
Length = 196
Score = 25.6 bits (57), Expect = 1.6
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 35 VIRKQHRHSMEQTTPIADYYIIAGVVYQ 62
+ K+ + ++ T PI D Y G V +
Sbjct: 147 SLEKRIQTYLQSTKPIIDLYEEMGKVKK 174
>2yqu_A 2-oxoglutarate dehydrogenase E3 component; lipoamide dehydrogenase,
2-oxoglutarate dehydrogenase comple pyruvate
dehydrogenase complex; HET: FAD; 1.70A {Thermus
thermophilus} PDB: 2eq7_A*
Length = 455
Score = 25.5 bits (57), Expect = 1.8
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 52 DYYIIAGVVYQAPDLASV 69
DY I VVY P++A+V
Sbjct: 332 DYQAIPSVVYTHPEIAAV 349
>2qae_A Lipoamide, dihydrolipoyl dehydrogenase; FAD-cystine-oxidoreductase,
homodimer; HET: FAD; 1.90A {Trypanosoma cruzi}
Length = 468
Score = 25.5 bits (57), Expect = 1.9
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 52 DYYIIAGVVYQAPDLASV 69
+Y +I V+Y P++ASV
Sbjct: 345 NYGVIPAVIYTMPEVASV 362
>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide
biosynthesis, nucleotide-BIND transferase, structural
genomics; 2.10A {Burkholderia pseudomallei 1710B}
Length = 230
Score = 25.3 bits (56), Expect = 2.0
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 45 EQTTPIADYYIIAGVVYQAPDLASVISSRLVGTGS 79
QT P+ YY L + ++ G G+
Sbjct: 181 AQTKPLITYYGDWARRGAENGLKAPAYRKISGLGA 215
>1lvl_A Dihydrolipoamide dehydrogenase; oxidoreductase; HET: FAD NAD; 2.45A
{Pseudomonas putida} SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 458
Score = 25.5 bits (57), Expect = 2.0
Identities = 5/18 (27%), Positives = 9/18 (50%)
Query: 52 DYYIIAGVVYQAPDLASV 69
+ IA V + P++ V
Sbjct: 335 EPAAIAAVCFTDPEVVVV 352
>1ebd_A E3BD, dihydrolipoamide dehydrogenase; redox-active center,
glycolysis, oxidoreductase; HET: FAD; 2.60A {Geobacillus
stearothermophilus} SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 455
Score = 25.5 bits (57), Expect = 2.0
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 52 DYYIIAGVVYQAPDLASV 69
DY I VV+ P+ ASV
Sbjct: 338 DYVAIPAVVFSDPECASV 355
>3urh_A Dihydrolipoyl dehydrogenase; PSI-biology, structural genomics,
protein structure initiati YORK structural genomics
research consortium; HET: FAD; 1.90A {Sinorhizobium
meliloti}
Length = 491
Score = 25.2 bits (56), Expect = 2.1
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 52 DYYIIAGVVYQAPDLASV 69
+Y +I GVVY P++ASV
Sbjct: 368 NYDVIPGVVYTQPEVASV 385
>1v59_A Dihydrolipoamide dehydrogenase; 2-oxoacid dehydroganese complex,
pyruvate dehydrogenase complex; HET: FAD NAD; 2.20A
{Saccharomyces cerevisiae} SCOP: c.3.1.5 c.3.1.5
d.87.1.1 PDB: 1jeh_A*
Length = 478
Score = 25.2 bits (56), Expect = 2.4
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 52 DYYIIAGVVYQAPDLASV 69
+Y I V+Y P++A V
Sbjct: 355 NYNNIPSVMYSHPEVAWV 372
>3lad_A Dihydrolipoamide dehydrogenase; oxidoreductase; HET: FAD; 2.20A
{Azotobacter vinelandii} SCOP: c.3.1.5 c.3.1.5 d.87.1.1
PDB: 1lpf_A*
Length = 476
Score = 25.2 bits (56), Expect = 2.5
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 52 DYYIIAGVVYQAPDLASV 69
+Y +I V+Y P++A V
Sbjct: 348 NYDLIPAVIYTHPEIAGV 365
>1mo9_A ORF3; nucleotide binding motifs, nucleotide binding domain, oxidor;
HET: FAD KPC; 1.65A {Xanthobacter autotrophicus} SCOP:
c.3.1.5 c.3.1.5 d.87.1.1 PDB: 1mok_A* 2c3c_A* 2c3d_A*
3q6j_A*
Length = 523
Score = 25.0 bits (55), Expect = 2.6
Identities = 0/18 (0%), Positives = 6/18 (33%)
Query: 52 DYYIIAGVVYQAPDLASV 69
++ +++ +
Sbjct: 383 TPKNYPDFLHTHYEVSFL 400
>1zmd_A Dihydrolipoyl dehydrogenase; lipoamide dehydrogenase, pyruvate
dehydrogenase, alpha- ketoglutarate dehydrogenase; HET:
FAD NAI; 2.08A {Homo sapiens} PDB: 1zmc_A* 2f5z_A*
1zy8_A* 3rnm_A*
Length = 474
Score = 25.2 bits (56), Expect = 2.7
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 52 DYYIIAGVVYQAPDLASV 69
DY + V+Y P++A V
Sbjct: 350 DYNCVPSVIYTHPEVAWV 367
>1ojt_A Surface protein; redox-active center, glycolysis, oxidoreductase,
NAD, flavop FAD, P64K; HET: FAD; 2.75A {Neisseria
meningitidis} SCOP: c.3.1.5 c.3.1.5 d.87.1.1 PDB:
1bhy_A*
Length = 482
Score = 24.8 bits (55), Expect = 3.6
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 52 DYYIIAGVVYQAPDLASV 69
D +I GV Y +P++A V
Sbjct: 354 DARVIPGVAYTSPEVAWV 371
>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis,
nucleotide-binding, transferase, structural genomics;
1.80A {Thermus thermophilus}
Length = 186
Score = 24.4 bits (54), Expect = 4.8
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 35 VIRKQHRHSMEQTTPIADYYIIAGVVYQ 62
+R++ E+T P+ YY GV+ +
Sbjct: 139 TVRRRLEVYREKTEPLVGYYEARGVLKR 166
>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET:
AMP; 2.3A {Homo sapiens}
Length = 199
Score = 24.0 bits (53), Expect = 5.6
Identities = 5/28 (17%), Positives = 11/28 (39%)
Query: 35 VIRKQHRHSMEQTTPIADYYIIAGVVYQ 62
I K+ + P+ YY +++
Sbjct: 149 TIAKRLEAYYRASIPVIAYYETKTQLHK 176
>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP
phosphotransferase, myokinase, structural genomics,
structural genomics consortium, SGC; 1.48A {Homo
sapiens} PDB: 2ak3_A*
Length = 227
Score = 24.1 bits (53), Expect = 5.7
Identities = 8/39 (20%), Positives = 18/39 (46%), Gaps = 9/39 (23%)
Query: 45 EQTTPIADYYIIAGVVYQ---------APDLASVISSRL 74
+QT P+ +YY GV+ P + + + +++
Sbjct: 178 DQTKPVLEYYQKKGVLETFSGTETNKIWPYVYAFLQTKV 216
>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding,
human, structura genomics, structural genomics
consortium, SGC, transferase; HET: GP5; 2.05A {Homo
sapiens} PDB: 2ar7_A* 3ndp_A
Length = 246
Score = 24.1 bits (53), Expect = 5.8
Identities = 7/39 (17%), Positives = 18/39 (46%), Gaps = 9/39 (23%)
Query: 45 EQTTPIADYYIIAGVVYQ---------APDLASVISSRL 74
+ P+ + Y GV++Q P + ++ S+++
Sbjct: 198 DVAKPVIELYKSRGVLHQFSGTETNKIWPYVYTLFSNKI 236
>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination,
ATP-binding, cytoplasm, metal-binding, nucleotide
biosynthesis, nucleotide-binding; HET: AP5; 1.58A
{Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A*
2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A*
1s3g_A*
Length = 216
Score = 24.0 bits (53), Expect = 5.9
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 45 EQTTPIADYYIIAGVVYQ 62
+QT P+ D+Y G +
Sbjct: 177 KQTAPLLDFYDEKGYLVN 194
>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase,
transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens}
PDB: 1z83_A* 3adk_A
Length = 196
Score = 23.6 bits (52), Expect = 7.2
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 35 VIRKQHRHSMEQTTPIADYYIIAGVVYQ 62
I+K+ + T P+ +Y G+V +
Sbjct: 146 TIKKRLETYYKATEPVIAFYEKRGIVRK 173
>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding,
nucleotide-binding, transferase; HET: AP5; 2.00A
{Marinibacillus marinus}
Length = 216
Score = 23.7 bits (52), Expect = 7.2
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 45 EQTTPIADYYIIAGVVYQ 62
+QT P+ D+Y GV+
Sbjct: 177 KQTQPLLDFYSQKGVLKD 194
>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase,
transferase (phosphotransferase); HET: AP5; 1.63A
{Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB:
2aky_A* 3aky_A* 1dvr_A*
Length = 220
Score = 23.7 bits (52), Expect = 7.3
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 45 EQTTPIADYYIIAGVVYQ 62
QT PI D+Y G+
Sbjct: 182 AQTEPIVDFYKKTGIWAG 199
>2rgx_A Adenylate kinase; transferase(phosphotransferase), ATP-binding,
nucleo binding, transferase; HET: AP5; 1.90A {Aquifex
aeolicus} PDB: 2rh5_A
Length = 206
Score = 23.3 bits (51), Expect = 9.1
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 45 EQTTPIADYYIIAGVVYQ 62
EQT P+ +YY G++
Sbjct: 167 EQTAPLIEYYKKKGILRI 184
>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase,
phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1
g.41.2.1 PDB: 2ak2_A 2c9y_A*
Length = 233
Score = 23.3 bits (51), Expect = 9.2
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 45 EQTTPIADYYIIAGVVYQ 62
QTTP+ +YY G+
Sbjct: 193 TQTTPLVEYYSKRGIHSA 210
>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein
inhibitors, nucleotide-binding, transferase; HET: AP5;
1.60A {Cryptosporidium parvum iowa II}
Length = 217
Score = 23.6 bits (52), Expect = 9.3
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 45 EQTTPIADYYIIAGVVYQ 62
+QT P+ +Y G++ +
Sbjct: 182 KQTAPLVKFYEDLGILKR 199
>3tlx_A Adenylate kinase 2; structural genomics, structural genomics
consortium, SGC, RO fold, transferase, ATP binding,
phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium
falciparum}
Length = 243
Score = 23.3 bits (51), Expect = 9.5
Identities = 4/18 (22%), Positives = 9/18 (50%)
Query: 45 EQTTPIADYYIIAGVVYQ 62
+T+P+ YY ++
Sbjct: 206 SETSPLISYYKNKNLLIN 223
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
0.322 0.138 0.393
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,201,483
Number of extensions: 58569
Number of successful extensions: 150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 149
Number of HSP's successfully gapped: 40
Length of query: 79
Length of database: 6,701,793
Length adjustment: 48
Effective length of query: 31
Effective length of database: 5,361,585
Effective search space: 166209135
Effective search space used: 166209135
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 (21.9 bits)
S2: 51 (23.3 bits)