RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3671
(266 letters)
>1tza_A APAG protein, SOR45; structural genomics, PSI, protein structure
initiative, NORT structural genomics consortium, NESG,
unknown function; 2.40A {Shewanella oneidensis} SCOP:
b.1.23.1
Length = 134
Score = 121 bits (304), Expect = 9e-35
Identities = 34/95 (35%), Positives = 47/95 (49%), Gaps = 1/95 (1%)
Query: 172 ETTENVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLET 231
++RV V Y+ + SP Y + Y I + NLGE +L RHW I +G
Sbjct: 3 ALDNSIRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSE 62
Query: 232 VRGRGVVGQEPVLSKSLPAFQYSSHVSLQAPSGHM 266
V+G GVVG+ P + A+QY+S L P G M
Sbjct: 63 VQGAGVVGETPTI-PPNTAYQYTSGTVLDTPFGIM 96
>1xvs_A Protein APAG; MCSG APC26324, midwest center for structural
genomics, structure initiative, PSI, structural
genomics, unknown FUN; 2.01A {Vibrio cholerae} SCOP:
b.1.23.1
Length = 126
Score = 114 bits (287), Expect = 2e-32
Identities = 30/94 (31%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 173 TTENVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETV 232
+ +++ V Y+ + +P + + Y I ++NL TVQL R W I G V
Sbjct: 4 SLPCIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLITDADGKQTVV 63
Query: 233 RGRGVVGQEPVLSKSLPAFQYSSHVSLQAPSGHM 266
G GVVG++P + K+ + YSS +L P G M
Sbjct: 64 EGDGVVGEQPRI-KANDEYTYSSGTALDTPVGVM 96
>2f1e_A Protein APAG; APAG protein, xanthomonas axonopodis PV.citri,
structural genomics, unknown function; NMR {Xanthomonas
axonopodis PV}
Length = 127
Score = 114 bits (286), Expect = 3e-32
Identities = 34/96 (35%), Positives = 51/96 (53%), Gaps = 1/96 (1%)
Query: 171 KETTENVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLE 230
+ V V V P ++ + +P Y + Y IR++N G + +L RHW+I +G E
Sbjct: 3 DDPRYRVEVEVSPRFLAHQSTPDEGRYAFAYSIRIQNAGAVPARLVARHWQITDGNGRTE 62
Query: 231 TVRGRGVVGQEPVLSKSLPAFQYSSHVSLQAPSGHM 266
V G GVVG++P L + AF Y+S V L+ G M
Sbjct: 63 QVDGEGVVGEQPWL-RPGEAFHYTSGVLLETEQGQM 97
>1xq4_A Protein APAG; all beta protein, structural genomics, protein
structure initiative, PSI, northeast structural genomics
consortium, NESG; 2.70A {Bordetella pertussis} SCOP:
b.1.23.1
Length = 139
Score = 114 bits (286), Expect = 4e-32
Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 1/94 (1%)
Query: 173 TTENVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETV 232
++ V+V P Y+ + P+ Y + Y +R+ N G Q+ RHW I ++ V
Sbjct: 9 KPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEV 68
Query: 233 RGRGVVGQEPVLSKSLPAFQYSSHVSLQAPSGHM 266
RG GVVGQ+P+L+ F+Y+S L P G M
Sbjct: 69 RGLGVVGQQPLLAPG-ETFEYTSGCPLPTPIGTM 101
>1vbv_A Hypothetical protein B0966; protein degradation, structural
genomics, unknown function; 2.70A {Escherichia coli}
SCOP: b.34.17.1
Length = 105
Score = 47.2 bits (112), Expect = 2e-07
Identities = 20/127 (15%), Positives = 36/127 (28%), Gaps = 36/127 (28%)
Query: 12 VQGKYSTGQLFLHRVFGYRGIVLFPWLARVYDRDIPNKRDKPSDVNGSVGKEVKSKTHTF 71
+ K+ GQ H + GY G+V+ DI + + + +
Sbjct: 2 IASKFGIGQQVRHSLLGYLGVVV----------DIDPVYSLSEPSPDELAVNDELRAAPW 51
Query: 72 YQVLIDSRDCPYIRAQTEAVTFLGNQNSNKSLYAIPGLDYVAHEDILP-YSCSH-EQPLH 129
Y V+++ + + Y+A + H EQP
Sbjct: 52 YHVVMEDDNGLPVHT------------------------YLAEAQLSSELQDEHPEQPSM 87
Query: 130 HELFDKF 136
EL
Sbjct: 88 DELAQTI 94
>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 = 37.9 bits (87), Expect = 0.003
Identities = 31/186 (16%), Positives = 62/186 (33%), Gaps = 39/186 (20%)
Query: 69 HTFYQVLIDSRDCPYIRAQTEAVTFLGNQNSNKSLYAIPGLDYVAHEDILPYSCSHEQPL 128
F +D+ DC ++ +++ S + + + I+ + L
Sbjct: 23 SVFEDAFVDNFDCKDVQDMPKSIL------SKEEI-----------DHIIMSKDAVSGTL 65
Query: 129 HHELFDKFLVHMPDKDPPFVAQQTLRTWQRKNHPWLELSDVHKETTENVRVTVIPFYMGC 188
LF L K + Q+ + R N+ +L +S + E + +T + Y+
Sbjct: 66 R--LFWTLL----SK-QEEMVQKFVEEVLRINYKFL-MSPIKTEQRQPSMMTRM--YIEQ 115
Query: 189 RDSP--TSSVYWWRYCIRLENLGELTVQLRE-RHWRIFSLSG---------TLETVRGRG 236
RD + V+ RL+ +L L E R + + G L+
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 237 VVGQEP 242
V +
Sbjct: 176 VQCKMD 181
Score = 29.4 bits (65), Expect = 1.6
Identities = 24/160 (15%), Positives = 44/160 (27%), Gaps = 54/160 (33%)
Query: 73 QVLIDSRDCPYIRAQTEAVTFLGNQNSNKSLYAIPGLDYVAHEDILPYSCSHEQPLHHEL 132
++L+ +R K + H + +S + L
Sbjct: 267 KILLTTRF--------------------KQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306
Query: 133 FDKFLVHMPDKDPPFVAQQTLRTWQRKNHPWLELSDVHKETTENVRVTVIPFYMGCRDSP 192
K+L +D P T +P LS +I + RD
Sbjct: 307 LLKYL-DCRPQDLPREVLTT--------NP-RRLS-------------IIAESI--RDGL 341
Query: 193 TSSVYWWRY-CIRLENLGELTVQ------LRERHWR--IF 223
+ W C +L + E ++ R+ R +F
Sbjct: 342 ATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF 381
>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 = 33.5 bits (76), Expect = 0.081
Identities = 45/279 (16%), Positives = 79/279 (28%), Gaps = 96/279 (34%)
Query: 17 STGQLFLHRVFGYRGIVLFPW--LARVYDRDIPNKRDKPSDVNGSVGKEVKSKTHTFYQV 74
G L +FG +G + L +Y D +K T ++
Sbjct: 150 GEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDL-----------IKFSAETLSEL 198
Query: 75 LIDSRDCPYIRAQT-EAVTFLGNQNSNKSLYAIPGLDYVAHEDILPYSCSHEQPL----- 128
+ + D + Q + +L N ++ P DY+ +P SC PL
Sbjct: 199 IRTTLDAEKVFTQGLNILEWLENPSN------TPDKDYLLS---IPISC----PLIGVIQ 245
Query: 129 --------------HHELFDKF---LVHMPDKD---PPFVAQQTLRTWQRKNHPWLELSD 168
EL H + +A+ +W+ +
Sbjct: 246 LAHYVVTAKLLGFTPGELRSYLKGATGHS--QGLVTAVAIAETD--SWES----FFVSV- 296
Query: 169 VHKETTENVRVTVIPFYMGCR-------DSPTSSVYWWRYCIRLENLGELTVQLRERHWR 221
+ + F++G R S S+ + N G + L
Sbjct: 297 --------RKAITVLFFIGVRCYEAYPNTSLPPSIL--EDSLE-NNEGVPSPML------ 339
Query: 222 IFSLSG-TLETVRGRGVVGQEPVLSKSLPAFQYSSHVSL 259
S+S T E V+ V + + LPA V +
Sbjct: 340 --SISNLTQEQVQDY--VNK---TNSHLPA---GKQVEI 368
Score = 32.3 bits (73), Expect = 0.20
Identities = 30/149 (20%), Positives = 49/149 (32%), Gaps = 55/149 (36%)
Query: 57 NGSVGKE----VKSKTHTFYQVLIDSRDCPYIRAQTEAVTFLGNQNSNKSLYAIPGLDYV 112
+GS+ E V + + L ++ F K L P +
Sbjct: 13 HGSL--EHVLLVPTASFFIASQL---QE-----------QFN------KILPE-PTEGFA 49
Query: 113 AHEDILPYSCSHEQPLHHELFDKFLVHM-----PDKDPPF--VAQQTLRTWQRKNHPWLE 165
A ++ P + P EL KFL ++ P K F V L ++ +LE
Sbjct: 50 ADDE--PTT-----PA--ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENC---YLE 97
Query: 166 LSDVH---------KETTENVRVTVIPFY 185
+D+H +TT +I Y
Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNY 126
Score = 28.9 bits (64), Expect = 2.0
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 208 LGELT--VQLRERHWRIFSLSGTLETVRGRGVVGQEPV 243
LGE L + + S+ +E V RG+ Q V
Sbjct: 1764 LGEYAALASLAD----VMSIESLVEVVFYRGMTMQVAV 1797
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 30.0 bits (67), Expect = 0.60
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 24/66 (36%)
Query: 172 ETTENVRVTVI-PFYMGCRDSPTSSVYWWRYCIRLENLGEL------TVQLRERH----- 219
N+ + + P C+ P V R+ + G++ V L ++
Sbjct: 13 RRGPNLNIVLTCP---ECKVYPPKIVE--RF-----SEGDVVCALCGLV-LSDKLVDTRS 61
Query: 220 -WRIFS 224
WR FS
Sbjct: 62 EWRTFS 67
>3to3_A Petrobactin biosynthesis protein ASBB; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG,
alpha-beta structure; HET: MSE ATP; 2.38A {Bacillus
anthracis}
Length = 619
Score = 29.2 bits (65), Expect = 1.7
Identities = 8/39 (20%), Positives = 20/39 (51%)
Query: 125 EQPLHHELFDKFLVHMPDKDPPFVAQQTLRTWQRKNHPW 163
++ DK ++++ + + AQQ++RT + +P
Sbjct: 256 ISNYAEDIQDKGIIYLGESADDYCAQQSMRTLRNVTNPK 294
>3ttc_A HYPF, transcriptional regulatory protein; Zn finger, nucleotide
binding, hydrogenase maturation factor transferase; HET:
ADP; 1.86A {Escherichia coli} PDB: 3tsp_A* 3tsu_A*
3ttf_A* 3ttd_A 3tsq_A
Length = 657
Score = 27.0 bits (60), Expect = 7.1
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 14/43 (32%)
Query: 107 PGLDYVAHEDILPYSCSHEQPLHHELFDKFLVHMPDKDPPFVA 149
PGL+ V +LP + PL H L + P V
Sbjct: 203 PGLNEVGV--MLPAN-----PLQHLLLQEL-------QCPLVM 231
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
0.321 0.137 0.432
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,090,321
Number of extensions: 231698
Number of successful extensions: 337
Number of sequences better than 10.0: 1
Number of HSP's gapped: 331
Number of HSP's successfully gapped: 17
Length of query: 266
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 174
Effective length of database: 4,133,061
Effective search space: 719152614
Effective search space used: 719152614
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 (25.5 bits)