RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2667
(261 letters)
>2c8m_A Lipoate-protein ligase A; lipoylation; HET: LPA; 1.89A
{Thermoplasma acidophilum} SCOP: d.104.1.3 PDB: 2art_A*
2aru_A* 2c7i_A 2ars_A* 3r07_A
Length = 262
Score = 196 bits (501), Expect = 1e-62
Identities = 43/209 (20%), Positives = 84/209 (40%), Gaps = 37/209 (17%)
Query: 53 KSVFISQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLY 112
+ + + N +LA ++ +Y++F + + ++ +R++ V+IG Q +E +L +
Sbjct: 4 RLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMK 63
Query: 113 DEGIEIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNNLEIISRTLE---REWNIQTEI 169
GI +ARR +GGG VYHD G+LN + + + + ++ + R +
Sbjct: 64 KNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARP 123
Query: 170 NTREDIVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGT 229
D+ +N + DI+ K KI G
Sbjct: 124 GELNDVS---------------------------------IPVNKKTDIMAGEK-KIMGA 149
Query: 230 AAKLGRPSSYHHCTLLVNVNKSRLSQSLH 258
A + + + H +LV+ + LS L
Sbjct: 150 AGAMRKGAKLWHAAMLVHTDLDMLSAVLK 178
>2e5a_A Lipoyltransferase 1; lipoyl-AMP, ligase; HET: LAQ; 2.10A {Bos
taurus} PDB: 3a7u_A
Length = 347
Score = 180 bits (459), Expect = 2e-55
Identities = 78/206 (37%), Positives = 119/206 (57%), Gaps = 42/206 (20%)
Query: 55 VFISQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLYDE 114
+ S S++++ NLA+EDW++ + + V+ LWRN+P VVIGRHQNPWQE NL ++ +E
Sbjct: 7 ILQSISNDVYHNLAVEDWIHDHMNLEGKPVLFLWRNSPTVVIGRHQNPWQECNLNLMREE 66
Query: 115 GIEIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNNLEIISRTLEREWNIQTEINTRED 174
G+++ARR SGGGTVYHD GN+N+TFFT +++Y+R NL+++ R L+
Sbjct: 67 GVKLARRRSGGGTVYHDMGNINLTFFTTKKKYDRMENLKLVVRALK-------------- 112
Query: 175 IVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKLG 234
++ + R D++ DG++KISGTA+K+G
Sbjct: 113 ----------------------------AVHPHLDVQATKRFDLLLDGQFKISGTASKIG 144
Query: 235 RPSSYHHCTLLVNVNKSRLSQSLHHH 260
R ++YHHCTLL + + LS L
Sbjct: 145 RNAAYHHCTLLCGTDGTFLSSLLKSP 170
>1vqz_A Lipoate-protein ligase, putative; class II AARS and biotin
synthetases fold, SUFE/NIFU fold, S genomics; HET: MSE;
1.99A {Streptococcus pneumoniae} SCOP: d.224.1.3
d.104.1.3
Length = 341
Score = 180 bits (458), Expect = 2e-55
Identities = 55/206 (26%), Positives = 87/206 (42%), Gaps = 43/206 (20%)
Query: 55 VFISQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLYDE 114
I+ S++ N+ALE++ +K+ + LLW N P +++GRHQN +E N + +
Sbjct: 15 YIINHSNDTAFNIALEEYAFKHLL-DEDQIFLLWINKPSIIVGRHQNTIEEINRDYVREN 73
Query: 115 GIEIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNNLEIISRTLEREWNIQTEINTRED 174
GIE+ RR SGGG VYHD NLN T + + +
Sbjct: 74 GIEVVRRISGGGAVYHDLNNLNYTIISKEDENKAFD------------------------ 109
Query: 175 IVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKLG 234
++++ + TL + ++ E R D+ DGK K G A
Sbjct: 110 ----------------FKSFSTPVINTL-AQLGVKAEFTGRNDLEIDGK-KFCGNAQAYI 151
Query: 235 RPSSYHHCTLLVNVNKSRLSQSLHHH 260
HH LL +V+ S L+ +L
Sbjct: 152 NGRIMHHGCLLFDVDLSVLANALKVS 177
>3a7r_A Lipoate-protein ligase A; adenylate-forming enzyme, lipoic acid,
ATP-binding, cytoplasm, nucleotide-binding, transferase,
lipoyl; HET: LAQ; 2.05A {Escherichia coli} PDB: 1x2h_A*
3a7a_A* 1x2g_A*
Length = 337
Score = 178 bits (454), Expect = 8e-55
Identities = 59/206 (28%), Positives = 94/206 (45%), Gaps = 42/206 (20%)
Query: 55 VFISQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLYDE 114
+ IS S + + NLA+E+ +++ V+ LWRN VVIGR QNPW+E N + ++
Sbjct: 5 LLISDSYDPWFNLAVEECIFRQMPA-TQRVLFLWRNADTVVIGRAQNPWKECNTRRMEED 63
Query: 115 GIEIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNNLEIISRTLEREWNIQTEINTRED 174
+ +ARR+SGGG V+HD GN TF + Y++ + I+ L + E + R D
Sbjct: 64 NVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNAL-NALGVSAEASGRND 122
Query: 175 IVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKLG 234
+V +G K+SG+A +
Sbjct: 123 LVVKTV----------------------------------------EGDRKVSGSAYRET 142
Query: 235 RPSSYHHCTLLVNVNKSRLSQSLHHH 260
+ +HH TLL+N + SRL+ L+
Sbjct: 143 KDRGFHHGTLLLNADLSRLANYLNPD 168
>2p5i_A BH3822 protein; PFAM03099, structural genomics, PSI-2, protein
structure initiative, NEW YORK structural genomix
research consortium; 2.21A {Bacillus halodurans c-125}
SCOP: d.104.1.3
Length = 288
Score = 118 bits (296), Expect = 5e-32
Identities = 36/209 (17%), Positives = 68/209 (32%), Gaps = 45/209 (21%)
Query: 58 SQSSNIFTNLALEDWLYKNFDF-TNHHVMLLWRNNPCVVIGRHQN--PWQETNLGVLYDE 114
+ + A +D L + + + W ++ VV+G + P + + L
Sbjct: 24 GPTFQALQSFAYDDTLCTSIGKSQSPPTLRAWVHHNTVVLGIQDSRLPQIKAGIEALKGF 83
Query: 115 GIEIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNN-----LEIISRTLEREWNIQTEI 169
++ RNSGG V DSG LN++ E+ ++ E+I ++ Q E
Sbjct: 84 QHDVIVRNSGGLAVVLDSGILNLSLVLKEEKGFSIDDGYELMYELICSMF-QDHREQIEA 142
Query: 170 NTREDIVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGT 229
G Y D+ DGK K +G
Sbjct: 143 REIVGSYCPGSY-----------------------------------DLSIDGK-KFAGI 166
Query: 230 AAKLGRPSSYHHCTLLVNVNKSRLSQSLH 258
+ + R L V+ + + ++ +
Sbjct: 167 SQRRIRGGVAVQIYLCVSGSGAERAKMIR 195
>2p0l_A Lipoate-protein ligase A; PFAM, lopoate-protein ligase A, 10425H,
structural genomics, structure initiative, PSI-2; 2.04A
{Streptococcus agalactiae} SCOP: d.104.1.3
Length = 288
Score = 117 bits (295), Expect = 7e-32
Identities = 32/212 (15%), Positives = 61/212 (28%), Gaps = 47/212 (22%)
Query: 56 FISQSSNIFTNLALEDWLYKNF-DFTNHHVMLLWRNNPCVVIGRHQN--PWQETNLGVLY 112
+++ + + + + ++ +W V++G P E +
Sbjct: 19 YVTDAQDAEKPFIWTEVFLREINRSNQEIILHIWPMTKTVILGMLDRELPHLELAKKEII 78
Query: 113 DEGIEIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNN-------LEIISRTLEREWNI 165
G E RN GG V D G LN + P + + ++ I ++
Sbjct: 79 SRGYEPVVRNFGGLAVVADEGILNFSLVIPDVFERKLSISDGYLIMVDFIRSIF-SDFYQ 137
Query: 166 QTEINTREDIVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYK 225
E E GK+ D+ +GK K
Sbjct: 138 PIEHFEVETSYCPGKF-----------------------------------DLSINGK-K 161
Query: 226 ISGTAAKLGRPSSYHHCTLLVNVNKSRLSQSL 257
+G A + + L V ++ SQ +
Sbjct: 162 FAGLAQRRIKNGIAVSIYLSVCGDQKGRSQMI 193
>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 = 33.3 bits (75), Expect = 0.075
Identities = 45/335 (13%), Positives = 89/335 (26%), Gaps = 113/335 (33%)
Query: 13 PHVTLQLAVPKLLPSSGVA---------------TSRFYSSKPRAP--VH---------- 45
P++ L+ A+ +L P+ V Y + + +
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195
Query: 46 NDETKIQKSVFISQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNP---CVVIGRH-QN 101
++ + + N + + + L ++ P C+++ + QN
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN 255
Query: 102 P--WQETNLG--VLYDEGIEIARRNS------GGGTVYHDSGNLNVTFFTPRERYNRRNN 151
W NL +L + R T H S + + TP E
Sbjct: 256 AKAWNAFNLSCKIL------LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE------V 303
Query: 152 LEIISRTLE-------RE----------------------WN-------------IQTEI 169
++ + L+ RE W+ I++ +
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363
Query: 170 NTREDIVYDGKYK--VIIP--TLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYK 225
N E Y + + P I L W + + + KY
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTI--------LLSLIWFDVIKSDVMVVVNKLHKYS 415
Query: 226 ISGTAAKLGRPSSY--HHCTLLVNVNKSRLSQSLH 258
+ K + S+ L + V K +LH
Sbjct: 416 L---VEKQPKESTISIPSIYLELKV-KLENEYALH 446
Score = 27.1 bits (59), Expect = 7.8
Identities = 18/124 (14%), Positives = 38/124 (30%), Gaps = 21/124 (16%)
Query: 143 RERYNR----RNNLEIISRTLEREWNIQTEINTREDIVYDGKYKVII--PTLISYQTYQE 196
R+ ++R + I + L W + + + KY ++ P +
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS- 430
Query: 197 IISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKLGRPSSYHHCTLLVNVNKSRLSQS 256
I L+ + + ++ IV Y I P ++ L+
Sbjct: 431 -IYLELKVKLENEYALHRS--IV--DHYNI---------PKTFDSDDLIPPYLDQYFYSH 476
Query: 257 LHHH 260
+ HH
Sbjct: 477 IGHH 480
>1nf2_A Phosphatase; structural proteomics, HAD NEW fold, structural
genomics, BSGC structure funded by NIH structure
initiative, PSI; 2.20A {Thermotoga maritima} SCOP:
c.108.1.10
Length = 268
Score = 29.8 bits (68), Expect = 0.77
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 175 IVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVY 220
IVY + VI+ I + ++II + Q I+ D++Y
Sbjct: 69 IVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHWQAYID---DVLY 111
>2b30_A Pvivax hypothetical protein; SGPP, structural genomics, PSI,
protein structure initiative; 2.70A {Plasmodium vivax}
SCOP: c.108.1.10
Length = 301
Score = 29.5 bits (67), Expect = 1.1
Identities = 15/59 (25%), Positives = 23/59 (38%)
Query: 175 IVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKL 233
IVYD ++ I Y E+IS +E+ QT + E K + K+
Sbjct: 101 IVYDQIGYTLLDETIETDVYAELISYLVEKNLVNQTIFHRGESNYVTEDNKYADFLQKM 159
>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 = 28.9 bits (64), Expect = 2.1
Identities = 23/123 (18%), Positives = 41/123 (33%), Gaps = 38/123 (30%)
Query: 35 FYSSKPRAPVHNDETKIQKSVFISQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNPCV 94
Y + A + V+ N A ++ + F+ ++ NNP
Sbjct: 1635 LYKTSKAA----------QDVW---------NRA-DNHFKDTYGFSILDIV---INNPVN 1671
Query: 95 VI-------GR--HQN----PWQETNLGVLYDEGI-EIARRNSGGGTVYHDSGNLNVTFF 140
+ G+ +N ++ G L E I + +S T + G L+ T F
Sbjct: 1672 LTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQF 1731
Query: 141 T-P 142
T P
Sbjct: 1732 TQP 1734
Score = 28.5 bits (63), Expect = 3.1
Identities = 23/138 (16%), Positives = 43/138 (31%), Gaps = 44/138 (31%)
Query: 7 SAVFKFPHVTLQLAVPKL---LPSSGVATSRFYSSKPRAPVHN--DETKIQKSVFISQSS 61
++ F L A + L + V+ F + + PV++ D + ++ S
Sbjct: 424 ASPFHSHL--LVPASDLINKDLVKNNVS---FNAKDIQIPVYDTFDGSDLRVL-----SG 473
Query: 62 NIFTNLALE------DWLYKNFDFTNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLYDE- 114
+I + W F H+ + G P + LGVL
Sbjct: 474 SISERIVDCIIRLPVKWE-TTTQFKATHI---------LDFG----PGGASGLGVLTHRN 519
Query: 115 ----GIEIARRNSGGGTV 128
G+ + GT+
Sbjct: 520 KDGTGVRVIV----AGTL 533
>1nbw_A Glycerol dehydratase reactivase alpha subunit; molecular chaperone,
actin-like ATPase domain, beta/BETA/alpha swiveling
domain, hydrolase; 2.40A {Klebsiella pneumoniae} SCOP:
c.8.6.1 c.55.1.6 c.55.1.6
Length = 607
Score = 28.7 bits (64), Expect = 2.3
Identities = 10/52 (19%), Positives = 21/52 (40%)
Query: 168 EINTREDIVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIV 219
+ T Y + V+I + + ++ L+R N+ I ++D V
Sbjct: 120 RLATLPAAQYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGV 171
>1nrw_A Hypothetical protein, haloacid dehalogenase-like hydrolase;
structural genomics, PSI, protein structure initiative;
1.70A {Bacillus subtilis} SCOP: c.108.1.10
Length = 288
Score = 28.4 bits (64), Expect = 2.3
Identities = 8/51 (15%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 175 IVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYK 225
+++D + ++ I + +I+S N E+ T I +
Sbjct: 71 VIHDPEGRLYHHETIDKKRAYDILS--WLESENYYYEVFTGSAIYTPQNGR 119
>2d0o_A DIOL dehydratase-reactivating factor large subunit; chaperone; HET:
ADP; 2.00A {Klebsiella oxytoca} SCOP: c.8.6.1 c.55.1.6
c.55.1.6 PDB: 2d0p_A
Length = 610
Score = 28.0 bits (62), Expect = 3.4
Identities = 9/47 (19%), Positives = 19/47 (40%)
Query: 173 EDIVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIV 219
D Y +++ + + +I+ +L + I I R+D V
Sbjct: 123 LTRPADAPYILVVSSAFDFADIASVINASLRAGYQITGVILQRDDGV 169
>3mpo_A Predicted hydrolase of the HAD superfamily; SGX, PSI, structural
genomics, protein structure initiative; 2.90A
{Lactobacillus brevis}
Length = 279
Score = 27.9 bits (63), Expect = 3.4
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 175 IVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVY 220
+ KV+ ++Y+ Y ++ + + + Q E D +Y
Sbjct: 75 VAQTISGKVLTNHSLTYEDYIDLEAWARKVRAHFQIETP---DYIY 117
>3gzb_A Putative snoal-like polyketide cyclase; YP_001182657.1, STRU
genomics, joint center for structural genomics, JCSG;
HET: MSE; 1.44A {Shewanella putrefaciens} PDB: 3lza_A*
Length = 154
Score = 26.7 bits (58), Expect = 6.6
Identities = 18/84 (21%), Positives = 29/84 (34%), Gaps = 13/84 (15%)
Query: 160 EREWNIQTEINTREDIVYDGKYKVIIPTLISYQTYQEIISR-------TLEREWNIQTEI 212
E ++ R+ I +D Y + II LE ++NI+
Sbjct: 35 EHDYKTLITFYNRDSIFFDKTANR------KYTGGRFIIDFLERAHQGVLEYDFNIEHMY 88
Query: 213 NTREDIVYDGKYKISGTAAKLGRP 236
N +V G Y G + G+P
Sbjct: 89 NAGSLVVMIGNYHFKGPGEQFGKP 112
>1wyu_B Glycine dehydrogenase subunit 2 (P-protein); alpha(2)beta(2)
tetramer, riken structural genomics/proteomi initiative,
RSGI; HET: PLP; 2.10A {Thermus thermophilus} SCOP:
c.67.1.7 PDB: 1wyt_B* 1wyv_B*
Length = 474
Score = 27.2 bits (61), Expect = 7.1
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 6/36 (16%)
Query: 106 TN---LGVLYDEGI-EIARR-NSGGGTVYHDSGNLN 136
TN LG+ ++ I EI+R G +Y+D NLN
Sbjct: 210 TNPNTLGL-FERRILEISRLCKEAGVQLYYDGANLN 244
>3o6x_A Glutamine synthetase; type III, beta barrel,dodecamer, ligas; HET:
P3S ADP; 3.50A {Bacteroides fragilis}
Length = 729
Score = 26.9 bits (59), Expect = 8.3
Identities = 14/63 (22%), Positives = 20/63 (31%), Gaps = 13/63 (20%)
Query: 136 NVTFFTPRERYNRRNNLEIISRTLEREW-----NIQTEINTREDIVYDGKYKVIIPTLIS 190
+ N E+ R LE E +Q E D+ I+P +S
Sbjct: 570 SRAVL---IGERIFNETELACR-LEVELEKYTMKVQIESRVLGDLAI----NHIVPIAVS 621
Query: 191 YQT 193
YQ
Sbjct: 622 YQN 624
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
0.319 0.134 0.405
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,086,832
Number of extensions: 235703
Number of successful extensions: 422
Number of sequences better than 10.0: 1
Number of HSP's gapped: 411
Number of HSP's successfully gapped: 29
Length of query: 261
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 169
Effective length of database: 4,133,061
Effective search space: 698487309
Effective search space used: 698487309
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 (21.8 bits)
S2: 56 (25.7 bits)