RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780882|ref|YP_003065295.1| site-specific tyrosine
recombinase XerC [Candidatus Liberibacter asiaticus str. psy62]
(328 letters)
>1a0p_A Site-specific recombinase XERD; DNA binding, DNA recombination;
2.50A {Escherichia coli} SCOP: a.60.9.1 d.163.1.1
Length = 290
Score = 123 bits (307), Expect = 8e-29
Identities = 85/302 (28%), Positives = 147/302 (48%), Gaps = 17/302 (5%)
Query: 15 LKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAF 74
L + +L L +E+ L++ TL +Y D + +L +T+ T +++A
Sbjct: 3 LARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLH---HRGLTLATA---QSDDLQAL 56
Query: 75 ISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQA 134
+++R S R LS ++ +YL + K + ++ + K LP+ L+E Q
Sbjct: 57 LAERLEGGYKATSSARLLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQ- 115
Query: 135 LTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKG 194
LL + ++ R+ A+L +LY GLR+SE + LT +I Q +R+ GKG
Sbjct: 116 ----VERLLQAPLIDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKG 171
Query: 195 DKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI-RGKPLNPGVFQRYIRQLRRY 253
+K R+VPL + Y + L + + + R + + F I+
Sbjct: 172 NKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVL 231
Query: 254 LGLPLST-TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMME 312
G+ + H LRH+FATHLL++G DLR +Q +LGH LSTTQIYT+V ++ + +
Sbjct: 232 AGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATER----LRQ 287
Query: 313 IY 314
++
Sbjct: 288 LH 289
>1xo0_A Recombinase CRE; CRE recombinase, holliday junction,
recombination,complex (recombinase/DNA), hydrolase,
ligase/DNA complex; 2.00A {Enterobacteria phage P1}
SCOP: a.60.9.1 d.163.1.1 PDB: 3crx_A* 1kbu_A 1ma7_A
1q3u_A* 1q3v_A* 2crx_A* 1ouq_A* 1nzb_A* 1xns_A 5crx_A*
1f44_A* 2hof_A 2hoi_A 4crx_A* 1drg_A 3c29_A* 3c28_A
1crx_A* 1pvr_A 1pvq_A ...
Length = 324
Score = 106 bits (264), Expect = 7e-24
Identities = 38/310 (12%), Positives = 91/310 (29%), Gaps = 32/310 (10%)
Query: 18 RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISK 77
R+N + + S+ T + R + + ++R ++
Sbjct: 5 RKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCK---LNNRKW---FPAEPEDVRDYLLY 58
Query: 78 RRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTL 137
+ + + +++++ L + + + + + + + + ++ KQAL
Sbjct: 59 LQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAF 118
Query: 138 ----VDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-- 191
D V + + D RN A L + Y L+I+E + ++I +
Sbjct: 119 ERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLKIAEIARIRVKDISRTDGGRMLIHI 178
Query: 192 -----GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLP-------LFRGIRGKPLN 239
L V K + + + + N L + L+
Sbjct: 179 GRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLS 238
Query: 240 PGVFQRYIRQLRRYLG--------LPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFR 291
+ R + L+ + H+ R A + G + I G
Sbjct: 239 TRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTN 298
Query: 292 LSTTQIYTNV 301
++ Y
Sbjct: 299 VNIVMNYIRN 308
>2a3v_A Site-specific recombinase INTI4; protein-DNA complex,
recombination; HET: DNA; 2.80A {Vibrio cholerae o1
biovar eltor str}
Length = 320
Score = 105 bits (261), Expect = 2e-23
Identities = 62/320 (19%), Positives = 115/320 (35%), Gaps = 43/320 (13%)
Query: 13 ELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIR 72
+ L + ++Q R +K T+++Y +++ F + + E+
Sbjct: 4 QFLLSVREFMQ----TRYYAKKTIEAYLHWITRYIHFHN--------KKHPSLMGDKEVE 51
Query: 73 AFISKRRTQ-KIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMR-------------- 117
F++ Q K+ ++ +L+ + K + K ++ E +
Sbjct: 52 EFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEI 111
Query: 118 -------------NLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLY 164
+K L E L + D + + + + L
Sbjct: 112 RRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAK 171
Query: 165 GCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLN 224
+ E ++L + D G + P+ +Y F
Sbjct: 172 ELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYL---FPSFQL 228
Query: 225 IQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQ 284
P +R +N V Q+ +R+ + G+ + T HTLRHSFATHLL G D+R++Q
Sbjct: 229 SLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQ 288
Query: 285 SILGHFRLSTTQIYTNVNSK 304
LGH + TTQIYT+V +
Sbjct: 289 EQLGHTDVKTTQIYTHVLDR 308
>3nkh_A Integrase; alpha-fold, MRSA protein, structural genomics, PSI-2,
protei structure initiative; 2.50A {Staphylococcus
aureus subsp}
Length = 244
Score = 95.3 bits (236), Expect = 2e-20
Identities = 39/204 (19%), Positives = 75/204 (36%), Gaps = 28/204 (13%)
Query: 129 LNEKQALTLVDNVLLHTSHETKWIDARN----SAILYLLYGCGLRISEALSLTPQNIMDD 184
L + +++ ++ I R + + G+RI E L++ ++I D
Sbjct: 26 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDFD 85
Query: 185 QSTLRIQG-------------------KGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNI 225
+L I G R + L + + + D N
Sbjct: 86 NKSLNINGTIHWFHDESGGFGVKDTTKTESSYRTIGLSSRSCEILKKAILENKKDSKWND 145
Query: 226 QLP----LFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLR 281
+F +G P+ F + +R+ + +G+ ++H LRHS + L G L+
Sbjct: 146 GYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDKEVSSHILRHSHISLLSQQGVSLK 205
Query: 282 SIQSILGHFRLSTT-QIYTNVNSK 304
+I +GH TT IY++V +
Sbjct: 206 AIMDRVGHSDHRTTLSIYSHVTEQ 229
>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA complex;
HET: PTR; 3.80A {Enterobacteria phage lambda} SCOP:
d.10.1.4 d.163.1.1 PDB: 1z1g_A 1kjk_A 2wcc_3*
Length = 356
Score = 82.6 bits (202), Expect = 1e-16
Identities = 46/289 (15%), Positives = 85/289 (29%), Gaps = 24/289 (8%)
Query: 19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKR 78
+ + L RG+ + TL +Y + L E IT + I +
Sbjct: 81 DRYEKILA-SRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAA---------MLNG 130
Query: 79 RTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLV 138
+ S K S + + T +++ R K R
Sbjct: 131 YIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRL---------T 181
Query: 139 DNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIR 198
+ L + + L G R+ + + +I+D + G K
Sbjct: 182 ADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVK-I 240
Query: 199 IVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPL 258
+P + + + + + R +PL+ G RY + R+ GL
Sbjct: 241 AIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSF 300
Query: 259 ST---TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSK 304
T H LR + L + Q +LGH + Y + +
Sbjct: 301 EGDPPTFHELRS-LSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGR 348
>1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA complex;
HET: PTR; 2.80A {Enterobacteria phage lambda} PDB:
1p7d_A*
Length = 283
Score = 79.6 bits (194), Expect = 9e-16
Identities = 50/287 (17%), Positives = 88/287 (30%), Gaps = 24/287 (8%)
Query: 21 WLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRT 80
+ + L RG+ + TL +Y + L + ++ EI A ++
Sbjct: 10 YEKILA-SRGIKQKTLINYMSKIKAIRRGLP--------DAPLEDITTKEIAAMLNGYI- 59
Query: 81 QKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDN 140
+ S K S + + T +++ R K R +
Sbjct: 60 DEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRL---------TAD 110
Query: 141 VLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIV 200
L + + L G R+ + + +I+D + G KI I
Sbjct: 111 EYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIP 170
Query: 201 PLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLST 260
L I L L + + R +PL+ G RY + R+ GL
Sbjct: 171 TALHIDALGISMKETLDKCKEILGGE-TIIASTRREPLSSGTVSRYFMRARKASGLSFEG 229
Query: 261 ---TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSK 304
T H LR + L + Q +LGH + Y + +
Sbjct: 230 DPPTFHELRS-LSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGR 275
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 63.0 bits (153), Expect = 8e-11
Identities = 74/452 (16%), Positives = 131/452 (28%), Gaps = 181/452 (40%)
Query: 1 MEGNN-------LPEIVSFELLKERQNWLQN---------LEIERGLSKLTLQSYECDTR 44
+EGN+ L + L+K + ++N ++ + ++
Sbjct: 96 LEGNDIHALAAKLLQENDTTLVK-TKELIKNYITARIMAKRPFDKKSNSALFRAVG--EG 152
Query: 45 QFLIFLAF--------YTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDR--SLKRSLSG 94
+ F Y EE +R L Y + + + L R+
Sbjct: 153 NAQLVAIFGGQGNTDDYFEE------LRDL-YQTYHVLV-GDLIKFSAETLSELIRTTLD 204
Query: 95 IKSF-------LKYLKKRKITTESN-------------ILNM-------RNLKKSNSLPR 127
+ L++L+ T + + ++ + + L + P
Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFT---PG 261
Query: 128 ALNEK-QALT-----LVDNVLLHTSHETKW---IDARNSAILYLLYGCGLRISEA---LS 175
L + T LV V + + W + AI L + G+R EA S
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAET--DSWESFFVSVRKAITVLFF-IGVRCYEAYPNTS 318
Query: 176 LTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVR----KAILEYYDLCPFDLNLNIQLP--- 228
L P + D +G P+L S+ + + +Y + N LP
Sbjct: 319 LPPSILEDSLE----NNEG---VPSPML-SISNLTQEQVQDYVNKT------NSHLPAGK 364
Query: 229 -----LFRGIR-----GKP-----LN---------PGVFQRYI----RQLR---RYLGLP 257
L G + G P LN G+ Q I R+L+ R+L P
Sbjct: 365 QVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL--P 422
Query: 258 LSTTAHT-------------LRHS-------------FATHLLSNGGDLRSIQ-SILGH- 289
+++ H+ L + + T +G DLR + SI
Sbjct: 423 VASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTF---DGSDLRVLSGSISERI 479
Query: 290 FRLSTTQIYTNVNSKNGGDWMMEI---YDQTH 318
V W E + TH
Sbjct: 480 VDCIIRL---PVK------W--ETTTQFKATH 500
Score = 43.0 bits (101), Expect = 1e-04
Identities = 36/224 (16%), Positives = 60/224 (26%), Gaps = 82/224 (36%)
Query: 25 LEIERGLSKLTLQSYECDTRQFLIFLAFYTEEK-ITIQTI---RQLSYT----EIRAFIS 76
L I L++ +Q Y T L K + I + + L + +
Sbjct: 339 LSI-SNLTQEQVQDYVNKTNSHL------PAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 77 KRRTQKIG---DRSL----KRSLSGIKSFL--------KYLKK-------------RKIT 108
R K D+S +R L FL L
Sbjct: 392 TLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFN 451
Query: 109 TESNIL-----------NMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNS 157
+ + ++R L + R +VD + KW
Sbjct: 452 AKD--IQIPVYDTFDGSDLRVL-SGSISER---------IVDCI---IRLPVKWETTTQF 496
Query: 158 AILYLL-YGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIV 200
++L +G G S LT +N G G +R++
Sbjct: 497 KATHILDFGPG-GASGLGVLTHRN---------KDGTG--VRVI 528
Score = 34.9 bits (80), Expect = 0.025
Identities = 46/259 (17%), Positives = 80/259 (30%), Gaps = 88/259 (33%)
Query: 45 QFLIFLAFYTEEKITIQTIRQLSYTEI---------RAFISKRRTQKIGDRSLKRSLSGI 95
+FL +++ E + + ++ ++ I +L L
Sbjct: 63 KFLGYVSSLVEPS------KVGQFDQVLNLCLTEFENCYL---EGNDI--HALAAKLLQE 111
Query: 96 KSFLKYLKKRKITT--ESNILNMRNL-KKSNS-LPRALNEKQA-LTLV----DNVLLHTS 146
K I + I+ R KKSNS L RA+ E A L + N
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNT----- 166
Query: 147 HETKWIDARNSAILYLLYGCGLR-----ISEAL-SLTPQNIMDDQSTLRIQGKG-DKIRI 199
+ + + R+ LY Y + +E L L ++ +G +
Sbjct: 167 -DDYFEELRD---LYQTYHVLVGDLIKFSAETLSELIR----TTLDAEKVFTQGLN---- 214
Query: 200 VPLLPSVRKAILEYYDLCP---FDLNLNIQLPLFRGI----------R--GKPLNPGVFQ 244
+L LE P + L++ I PL G+ + G PG +
Sbjct: 215 --IL-----EWLENPSNTPDKDYLLSIPISCPLI-GVIQLAHYVVTAKLLG--FTPGELR 264
Query: 245 RYIRQLRRYLGLPLSTTAH 263
Y++ G T H
Sbjct: 265 SYLK------G----ATGH 273
Score = 28.0 bits (62), Expect = 3.2
Identities = 7/34 (20%), Positives = 11/34 (32%), Gaps = 7/34 (20%)
Query: 250 LRRYLGLPLSTTAHTLRHSF--ATHLLSNGGDLR 281
R PL+ + +L H T L+
Sbjct: 6 TR-----PLTLSHGSLEHVLLVPTASFFIASQLQ 34
>1ae9_A Lambda integrase; DNA recombination, site-specific recombination;
1.90A {Bacteriophage lambda} SCOP: d.163.1.1
Length = 179
Score = 61.0 bits (146), Expect = 3e-10
Identities = 26/177 (14%), Positives = 53/177 (29%), Gaps = 9/177 (5%)
Query: 132 KQALTL--VDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLR 189
+ LT + W+ + L G R+ + + +I+D +
Sbjct: 1 RSRLTADEYLKIYQAAESSPCWL----RLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVE 56
Query: 190 IQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQ 249
G K +P + + + + + R +PL+ G RY +
Sbjct: 57 QSKTGVK-IAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMR 115
Query: 250 LRRYLGL--PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSK 304
R+ GL S + L + Q +LGH + + + +
Sbjct: 116 ARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQFRDDRGR 172
>3nrw_A Phage integrase/site-specific recombinase; alpha-helical domain,
structural genomics, PSI-2, protein ST initiative; 1.70A
{Haloarcula marismortui}
Length = 117
Score = 48.1 bits (114), Expect = 3e-06
Identities = 15/93 (16%), Positives = 43/93 (46%), Gaps = 7/93 (7%)
Query: 19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKR 78
+L + + + +++S+ + F+ + E+ I +R+L+ ++ + + R
Sbjct: 14 DRYLAHRQ--TDAADASIKSFRYRLKHFVEWA-----EERDITAMRELTGWKLDEYETFR 66
Query: 79 RTQKIGDRSLKRSLSGIKSFLKYLKKRKITTES 111
R + +L + +K++L+YL + + E
Sbjct: 67 RGSDVSPATLNGEMQTLKNWLEYLARIDVVDED 99
>1aih_A HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage
HP1} SCOP: d.163.1.1
Length = 170
Score = 45.5 bits (106), Expect = 2e-05
Identities = 36/163 (22%), Positives = 57/163 (34%), Gaps = 23/163 (14%)
Query: 142 LLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVP 201
LL ++ D I+ + G R SEA + Q+ + K K R VP
Sbjct: 15 LLAECDNSRNPDLG--LIVRICLATGARWSEAET-LTQSQVMPYKITFTNTKSKKNRTVP 71
Query: 202 LLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTT 261
+ + + + D LR + LP
Sbjct: 72 ISDELFDMLPKKRGRLFNDAY--------------------ESFENAVLRAEIELPKGQL 111
Query: 262 AHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSK 304
H LRH+FA+H + NGG++ ++ ILGH + T Y +
Sbjct: 112 THVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPS 154
>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 = 31.5 bits (70), Expect = 0.24
Identities = 18/82 (21%), Positives = 23/82 (28%), Gaps = 52/82 (63%)
Query: 131 EKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI 190
EKQAL K + A S LY A DD +
Sbjct: 18 EKQAL--------------KKLQA--SLKLY-----------A---------DDSA---- 37
Query: 191 QGKGDKIRIVPLLPSVRKAILE 212
P L ++ KA +E
Sbjct: 38 ----------PAL-AI-KATME 47
>3hoa_A Thermostable carboxypeptidase 1; proline-rich loop, hydrolase;
2.10A {Thermus thermophilus HB27} PDB: 1wgz_A
Length = 509
Score = 28.1 bits (62), Expect = 3.3
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 229 LFRGIRGKPLNPGVFQRYIRQLRRYLGL 256
L + G+ + F Y+ + +Y L
Sbjct: 483 LVERVTGEAPSARPFLAYLEK--KYAAL 508
>2xdt_A Endoplasmic reticulum aminopeptidase 1; glycoprotein,
metal-binding, metalloprotease, protease, hydrolase,
adaptive immunity; HET: NAG; 2.70A {Homo sapiens}
Length = 897
Score = 27.4 bits (60), Expect = 4.7
Identities = 8/55 (14%), Positives = 21/55 (38%), Gaps = 10/55 (18%)
Query: 52 FYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRK 106
F T + E++ F S + R +++++ I+ + ++ K
Sbjct: 837 FSTRTR----------LEEVKGFFSSLKENGSQLRCVQQTIETIEENIGWMDKNF 881
>2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA binding
protein; 2.00A {Unidentified phage}
Length = 103
Score = 27.1 bits (59), Expect = 5.0
Identities = 15/100 (15%), Positives = 33/100 (33%), Gaps = 10/100 (10%)
Query: 21 WLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRT 80
+ + L RG+ + TL +Y + + + ++ EI A ++
Sbjct: 10 YEKILA-SRGIKQKTLINYMSKIKAIR--------RGLPDAPLEDITTKEIAAMLNGYI- 59
Query: 81 QKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLK 120
+ S K S + + T +++ R K
Sbjct: 60 DEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAK 99
>3i1m_O 30S ribosomal protein S15; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 2qan_O* 2qb9_O* 2qbb_O* 2qbd_O 2qbf_O
2qbh_O* 2qbj_O* 2qou_O* 2qow_O* 2qoy_O* 2qp0_O* 2vaz_F
2z4k_O* 2z4m_O* 2qal_O 3i1o_O 3i1q_O 3i1s_O 3i1z_O
3i21_O ...
Length = 89
Score = 27.0 bits (60), Expect = 6.1
Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 54 TEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNI 113
TE ++ + T + ++ + R L R +S + L YLK++ + + +
Sbjct: 25 TEVQVALLTAQINHLQG---HFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQL 81
Query: 114 LNMRNLKK 121
+ L++
Sbjct: 82 IERLGLRR 89
>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding
motif, ATP- binding, nucleotide-binding, transferase;
HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB:
3a4l_A* 3a4n_A
Length = 260
Score = 27.0 bits (59), Expect = 6.2
Identities = 9/38 (23%), Positives = 18/38 (47%)
Query: 79 RTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNM 116
+++K+ +K + K FLK +KK + +L
Sbjct: 207 KSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRVLKE 244
>3l1n_A MP1P, cell WALL antigen; helix-turn-helix, protein-ligand complex;
HET: PLM; 1.30A {Penicillium marneffei}
Length = 194
Score = 26.8 bits (59), Expect = 6.3
Identities = 5/30 (16%), Positives = 15/30 (50%)
Query: 279 DLRSIQSILGHFRLSTTQIYTNVNSKNGGD 308
D+ + + ++ + L+ + ++ GGD
Sbjct: 47 DISAFKKVMQNISLAVNKFNVDIERYVGGD 76
>2h1q_A Hypothetical protein; ZP_00559375.1, structural genomics, PSI-2,
protein structure initiative; 2.01A {Desulfitobacterium
hafniense dcb-2} SCOP: c.67.3.1
Length = 270
Score = 26.4 bits (58), Expect = 9.1
Identities = 9/71 (12%), Positives = 24/71 (33%), Gaps = 3/71 (4%)
Query: 156 NSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYD 215
N+ + +G ++ + + + + KG K+ +V P + + D
Sbjct: 106 NNPQVAREHGVIFSDAKRVEDRMNDPFIM---SQNEVKGKKVGVVGHFPHLESLLEPICD 162
Query: 216 LCPFDLNLNIQ 226
L + +
Sbjct: 163 LSILEWSPEEG 173
>3dwc_A TCMCP-1, metallocarboxypeptidase; cowrin family of
metallocarboxypeptidases, hydrolase; 2.10A {Trypanosoma
cruzi}
Length = 505
Score = 26.2 bits (57), Expect = 9.4
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 229 LFRGIRGKPLNPGVFQRYIRQLRRYL 254
L R G+ LNP ++R++ + RY
Sbjct: 478 LLRQATGETLNPEHYRRHLER--RYR 501
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.320 0.136 0.391
Gapped
Lambda K H
0.267 0.0553 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,697,722
Number of extensions: 120851
Number of successful extensions: 419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 406
Number of HSP's successfully gapped: 32
Length of query: 328
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 235
Effective length of database: 3,438,538
Effective search space: 808056430
Effective search space used: 808056430
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: 57 (26.1 bits)