RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026745
(234 letters)
>4f3q_A Transcriptional regulatory protein CBU_1566; YEBC family; 2.15A
{Coxiella burnetii}
Length = 247
Score = 160 bits (408), Expect = 3e-49
Identities = 64/213 (30%), Positives = 109/213 (51%), Gaps = 14/213 (6%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRAS-EKGQEAFIEKVYEVYGYGGV 78
+ GG + SN L AV++KA ++PKD + R IKR + + +E YE YG GV
Sbjct: 39 ARLGGEDIDSNPRLRAVVDKAFAANMPKDTITRAIKRGAGSGAGDNLVEVRYEGYGPSGV 98
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 138
+++V+ LTD R+VA VR C G + GSV + F++ ++ ++D++++++I
Sbjct: 99 AVMVDCLTDNKNRTVAEVRHAFSKCDGNLGTEGSVAYLFKQRGLITFP-PNSDEEKIMEI 157
Query: 139 ALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELL 198
AL+ GAEDV N+D V + +++ I ++ A + +L
Sbjct: 158 ALEVGAEDVTT---NDDG--------SIDVTTLPEDFEKIRNAMKAADLNPS-HAEVTVL 205
Query: 199 PITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
T + +D ++ E L L +LDDV VY+
Sbjct: 206 ASTEVGLDKDSAEQMLRLTEMLEDLDDVQNVYS 238
>1kon_A Protein YEBC, YEBC; alpha/beta, two-domains, montreal-kingston
bacterial structural genomics initiative, BSGI,
structural genomics; 2.20A {Escherichia coli} SCOP:
e.39.1.1
Length = 249
Score = 160 bits (408), Expect = 3e-49
Identities = 64/213 (30%), Positives = 97/213 (45%), Gaps = 15/213 (7%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRAS-EKGQEAFIEKVYEVYGYGGV 78
K GG +P +N L A ++KA ++ +D + R I R +YE YG GG
Sbjct: 39 AKLGGGDPDANPRLRAAVDKALSNNMTRDTLNRAIARGVGGDDDANMETIIYEGYGPGGT 98
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 138
+I++E L+D R+VA VR CGG + GSV + F + V I F D+D +++
Sbjct: 99 AIMIECLSDNRNRTVAEVRHAFSKCGGNLGTDGSVAYLFSKKGV--ISFEKGDEDTIMEA 156
Query: 139 ALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELL 198
AL+AGAEDV + V + + + L AG+ + ++
Sbjct: 157 ALEAGAEDV-----------VTYDDGAIDVYTAWEEMGKVRDALEAAGLKAD-SAEVSMI 204
Query: 199 PITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
P T ++D E LI L + DDV VY
Sbjct: 205 PSTKADMDAETAPKLMRLIDMLEDCDDVQEVYH 237
>1lfp_A Hypothetical protein AQ_1575; NEW fold, thermostability, structural
genomics, BSGC structure funded by NIH, protein
structure initiative, PSI; 1.72A {Aquifex aeolicus}
SCOP: e.39.1.1
Length = 249
Score = 157 bits (399), Expect = 7e-48
Identities = 64/214 (29%), Positives = 108/214 (50%), Gaps = 15/214 (7%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRAS-EKGQEAFIEKVYEVYGYGGV 78
+ GGPNP N L +E+AK+ ++P + +ER IK+ + E E F E +YE Y GGV
Sbjct: 36 TRLGGPNPEFNPRLRTAIEQAKKANMPWENIERAIKKGAGELEGEQFEEVIYEGYAPGGV 95
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 138
+++V TD R+ + VR V GG + G V + F R + + + +++LL+
Sbjct: 96 AVMVLATTDNRNRTTSEVRHVFTKHGGNLGASGCVSYLFERKGYIEVPAKEVSEEELLEK 155
Query: 139 ALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELL 198
A++ GAEDV E+ + + + + ++ L + G+P E
Sbjct: 156 AIEVGAEDVQ--------PGEE----VHIIYTVPEELYEVKENLEKLGVPIE-KAQITWK 202
Query: 199 PITTIEVDD-EAMELNKELIAKLLELDDVDAVYT 231
PI+T++++D E + +L+ L ELDDV V
Sbjct: 203 PISTVQINDEETAQKVIKLLNALEELDDVQQVIA 236
>1mw7_A Hypothetical protein HP0162; structural genomics, PSI, protein
structure initiative, northeast structural genomics
consortium, NESG; 2.00A {Helicobacter pylori} SCOP:
e.39.1.1
Length = 240
Score = 156 bits (396), Expect = 1e-47
Identities = 60/218 (27%), Positives = 98/218 (44%), Gaps = 20/218 (9%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVS 79
K GG P +N L + AK ++PKD ++ IKRAS K E YE GV
Sbjct: 34 AKDGGSEPDTNAKLRTAILNAKAQNMPKDNIDAAIKRASSKE-GNLSEITYEGKANFGVL 92
Query: 80 IVVEVLTDKITRSVAAVREVV-KDCGGKMADPGSVMFKFRRARVVNIKFTDADK-----D 133
I++E +TD TR++A ++ K G + GS+ F F R V + + +
Sbjct: 93 IIMECMTDNPTRTIANLKSYFNKTQGASIVPNGSLEFMFNRKSVFECLKNEVENLKLSLE 152
Query: 134 QLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDN 193
L +D G E++ E ED + +++ + +P
Sbjct: 153 DLEFALIDYGLEELEE--------VED----KIIIRGDYNSFKLLNEGFESLKLPIL-KA 199
Query: 194 GSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
+ + T IE++DE MEL ++L+ ++ + DDV A+YT
Sbjct: 200 SLQRIATTPIELNDEQMELTEKLLDRIEDDDDVVALYT 237
>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 = 36.0 bits (82), Expect = 0.009
Identities = 33/240 (13%), Positives = 67/240 (27%), Gaps = 80/240 (33%)
Query: 45 VPKDIVER-----NIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREV 99
K V R +++A + + A + V + G G K + A+ +V
Sbjct: 126 FAKYNVSRLQPYLKLRQALLELRPA--KNVL-IDGVLGSG--------K---TWVAL-DV 170
Query: 100 VKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQL---------LDIALDAGAEDVIEP 150
+ + + +N+K ++ + L +D + ++
Sbjct: 171 CLSYKVQCKMDFKIFW-------LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223
Query: 151 PVNEDDT-DEDR---AERYYK------------------------VVSTSD-NYTDI--- 178
+ E R + Y+ +++T TD
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA 283
Query: 179 -TTK---LREAGIPFETDNGSELLP-ITTIEVDD---EAMELNK---ELIAKLLELDDVD 227
TT L + D LL D E + N +IA+ + D +
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR-DGLA 342
Score = 35.6 bits (81), Expect = 0.012
Identities = 35/241 (14%), Positives = 79/241 (32%), Gaps = 76/241 (31%)
Query: 33 LAAVLEKAKELD---VPKDIVERN------IKRASEKGQEAFIEKVYEV-YGYGGVSIVV 82
++L K +E+D + KD V + E+ + F+E+V + Y +
Sbjct: 42 PKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF------- 93
Query: 83 EVLTDKI---TRSVAAVREVVKDCGGKMADPGSVMFKF---RRARVVNIK-----FTDAD 131
L I R + + + + ++ + V K+ R + ++ A
Sbjct: 94 --LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAK 151
Query: 132 -----------KDQL-LDIALDAGAEDVIEPPV-----NEDDTDEDRAER----YYKVVS 170
K + LD+ L + ++ + ++ E E Y++
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211
Query: 171 TSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAK-----LLELDD 225
+ +D ++ ++ + + EL + L +K LL L +
Sbjct: 212 NWTSRSDHSSNIK-------------------LRIHSIQAELRRLLKSKPYENCLLVLLN 252
Query: 226 V 226
V
Sbjct: 253 V 253
Score = 34.1 bits (77), Expect = 0.042
Identities = 23/138 (16%), Positives = 40/138 (28%), Gaps = 26/138 (18%)
Query: 113 VMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTD------EDRAER-Y 165
++ F A V N D D I + +I T + E
Sbjct: 21 ILSVFEDAFVDNFDCKDVQ-DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMV 79
Query: 166 YKVVSTS--DNYTDITTKLR-EAGIP------FETD-----NGSELLPITTIEVDDEAME 211
K V NY + + ++ E P + N +++ + ++
Sbjct: 80 QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK 139
Query: 212 LNKELIAKLLELDDVDAV 229
L + LLEL V
Sbjct: 140 LRQ----ALLELRPAKNV 153
>1w25_A Stalked-cell differentiation controlling protein; two-component
system, ggdef domain, cyclic dinucleotide, cyclic-digmp;
HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1
c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*
Length = 459
Score = 31.3 bits (71), Expect = 0.23
Identities = 18/109 (16%), Positives = 35/109 (32%), Gaps = 3/109 (2%)
Query: 125 IKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLRE 184
+ T D L++GA D + P+++ R + D R
Sbjct: 79 VLITALDGRGDRIQGLESGASDFLTKPIDDVMLFA-RVRSLTRFKLVIDELRQREASGRR 137
Query: 185 AGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYTDQ 233
G+ + L + VDD + +A L ++ + +D
Sbjct: 138 MGVIAGAAARLDGLGGRVLIVDDNER--QAQRVAAELGVEHRPVIESDP 184
>1zsy_A Mitochondrial 2-enoyl thioester reductase; medium-chain
dehydrogenase/reductase, oxidoreductase, 2-ENOY
thioester reductase; 1.75A {Homo sapiens} PDB: 2vcy_A
Length = 357
Score = 31.1 bits (71), Expect = 0.28
Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 6/49 (12%)
Query: 116 KFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAER 164
R +N+ D +L D GAE VI + + R E
Sbjct: 189 AALGLRTINVVRDRPDIQKLSDRLKSLGAEHVI------TEEELRRPEM 231
>1gu7_A Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific]
1,mitochondrial; oxidoreductase, thioester reduction,
fatty acids; 1.70A {Candida tropicalis} SCOP: b.35.1.2
c.2.1.1 PDB: 1guf_A* 1n9g_B* 1n9g_A* 1gyr_A 1h0k_A
Length = 364
Score = 30.4 bits (69), Expect = 0.52
Identities = 7/53 (13%), Positives = 18/53 (33%), Gaps = 6/53 (11%)
Query: 116 KFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKV 168
K +++ + D+++ + GA VI + + E +
Sbjct: 189 KLLNFNSISVIRDRPNLDEVVASLKELGATQVI------TEDQNNSREFGPTI 235
>3fiw_A Putative TETR-family transcriptional regulator; TETR-family
transcriptional regulator streptomyces, structur
genomics, PSI-2; 2.20A {Streptomyces coelicolor}
Length = 211
Score = 28.9 bits (65), Expect = 1.1
Identities = 7/44 (15%), Positives = 10/44 (22%), Gaps = 5/44 (11%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTD-----EDRAERYYKV 168
K LL A P+ E D + +
Sbjct: 67 RTKRDLLTAMAQAAMAPHAAEPLPEPGEDWHGWFLRNTRSFRRT 110
>2xpw_A Tetracycline repressor protein class D; transcription,
transcription regulator, helix-turn-helix, ME
coordination; HET: OTC MES; 1.44A {Escherichia coli}
PDB: 1bjy_A* 1bj0_A 1du7_A* 1ork_A* 2fj1_A* 1bjz_A*
2o7o_A* 2x6o_A* 2x9d_A* 2xps_A* 2xpt_A* 2vke_A* 2xpu_A*
2xpv_A* 2tct_A* 2xb5_A* 2trt_A* 2xrl_A* 1qpi_A* 1a6i_A
...
Length = 207
Score = 28.2 bits (63), Expect = 2.1
Identities = 5/44 (11%), Positives = 11/44 (25%), Gaps = 5/44 (11%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTD-----EDRAERYYKV 168
+K LLD + + + A + +
Sbjct: 45 KNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRA 88
>3bqy_A Putative TETR family transcriptional regulator; structural
genomics, strept coelicolor, PSI-2, protein structure
initiative; 1.95A {Streptomyces coelicolor A3}
Length = 209
Score = 27.8 bits (62), Expect = 2.3
Identities = 8/45 (17%), Positives = 12/45 (26%), Gaps = 5/45 (11%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTD-----EDRAERYYKVV 169
A K LL + + V + D D A +
Sbjct: 44 AAKQDLLTAMAEHMVDGVADAAGATGDGDWSERTARLARALRAAL 88
>2hxi_A Putative transcriptional regulator; structural genomics, APC6293,
TET streptomyces coelicolor A3(2), PSI-2; 1.70A
{Streptomyces coelicolor}
Length = 241
Score = 27.9 bits (62), Expect = 2.4
Identities = 6/27 (22%), Positives = 10/27 (37%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDD 156
+K +LL D ++ E D
Sbjct: 71 RNKTELLRAVADRILLSAMDGYRPEGD 97
>2g7g_A RHA04620, putative transcriptional regulator; helix-turn-helix,
structural genomics, PSI, protein structur initiative;
2.01A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1
Length = 213
Score = 27.8 bits (62), Expect = 2.8
Identities = 4/43 (9%), Positives = 11/43 (25%), Gaps = 3/43 (6%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTDED---RAERYYKVV 169
+ ++++ ++ DE A Y
Sbjct: 51 KGRAAVVELVRHRVVREIDGSAFERLPWDEAFSEWARSYRAAF 93
>2opt_A Actii protein; helical protein, TETR family, APO-protein,
transcriptional R transcription; 2.05A {Streptomyces
coelicolor} PDB: 3b6a_A* 3b6c_A*
Length = 234
Score = 27.1 bits (60), Expect = 4.7
Identities = 8/43 (18%), Positives = 15/43 (34%), Gaps = 3/43 (6%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTDED---RAERYYKVV 169
++D+LLD+ D +V P E ++
Sbjct: 48 GNRDELLDLVFDIVLTEVEVPEPEPGRWAEQVKEMCRSLRRMF 90
>2g7l_A TETR-family transcriptional regulator; APC6062, protein structure
initiativ midwest center for structural genomics, MCSG;
2.10A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1
Length = 243
Score = 27.1 bits (60), Expect = 5.1
Identities = 6/36 (16%), Positives = 13/36 (36%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERY 165
A+ +L LDA +V ++ ++
Sbjct: 61 ANTAELHAAVLDALLGEVDLTGAGAEEDWREQLRAV 96
>1z0x_A Transcriptional regulator, TETR family; structural genomics, PSI, P
structure initiative; 2.40A {Enterococcus faecalis}
SCOP: a.4.1.9 a.121.1.1
Length = 220
Score = 26.7 bits (59), Expect = 5.9
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNED 155
+K LL +A E EP + +
Sbjct: 48 KNKQALLQSMAEAIEEHFQEPALCGE 73
>2hxo_A Putative TETR-family transcriptional regulator; TETR
transcriptional regulator, structural genomics, PSI-2,
structure initiative; 2.40A {Streptomyces coelicolor}
Length = 237
Score = 26.4 bits (58), Expect = 7.3
Identities = 7/45 (15%), Positives = 10/45 (22%), Gaps = 5/45 (11%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTD-----EDRAERYYKVV 169
K +LL A DA + A +
Sbjct: 58 TGKAELLGAATDAVVTAAVTAGPTGAADSPQDAVRAVALGLWDAT 102
>3q8g_A CRAL-TRIO domain-containing protein YKL091C; string motif,
signaling protein, directed evoluti SEC14, phospholipid
transporter, lipid; HET: PEE; 1.80A {Saccharomyces
cerevisiae} PDB: 3b7n_A* 3b74_A* 3b7q_A* 3b7z_A*
Length = 320
Score = 26.7 bits (59), Expect = 7.5
Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 11/92 (11%)
Query: 85 LTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIAL---- 140
LT + ++ R ++ + K S + +F RAR +I + + ++
Sbjct: 35 LTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDIN--AS-VEMFVE-TERWRE 90
Query: 141 DAGAEDVIE---PPVNEDDTDEDRAERYYKVV 169
+ GA +IE +D + + + Y
Sbjct: 91 EYGANTIIEDYENNKEAEDKERIKLAKMYPQY 122
>1s9r_A Arginine deiminase; hydrolase, 5-fold pseudo-symmetric domain, 5-
helix bundle domain, raction intermediate; HET: ARG;
1.60A {Mycoplasma arginini} SCOP: d.126.1.4 PDB: 1lxy_A*
Length = 410
Score = 26.7 bits (58), Expect = 7.8
Identities = 17/163 (10%), Positives = 39/163 (23%), Gaps = 26/163 (15%)
Query: 58 SEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVM--- 114
SE+ + + + ++ + + + D M D +
Sbjct: 230 SERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMH---LDTWLTMLDKDKFLYSP 286
Query: 115 --------FKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYY 166
+ + + L + + + P+ + + ER
Sbjct: 287 IANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERET 346
Query: 167 ------------KVVSTSDNYTDITTKLREAGIPFETDNGSEL 197
VV L AGI +G++L
Sbjct: 347 HFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQL 389
>2y2z_A SIM16, SIMR, putative repressor simreg2; transcription,
simocyclinone regulator, TETR-family; 1.95A
{Streptomyces antibioticus} PDB: 2y30_A* 2y31_A* 3zql_A
Length = 267
Score = 26.4 bits (58), Expect = 7.9
Identities = 6/43 (13%), Positives = 13/43 (30%), Gaps = 3/43 (6%)
Query: 130 ADKDQLLDIALDAGAEDVIEPPVNEDDTDED---RAERYYKVV 169
K+ L+++ +D + P D A +
Sbjct: 69 PTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALW 111
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 0.368
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,742,614
Number of extensions: 244513
Number of successful extensions: 872
Number of sequences better than 10.0: 1
Number of HSP's gapped: 858
Number of HSP's successfully gapped: 58
Length of query: 234
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 143
Effective length of database: 4,160,982
Effective search space: 595020426
Effective search space used: 595020426
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: 56 (25.2 bits)