RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780277|ref|YP_003064690.1| DNA polymerase I [Candidatus
Liberibacter asiaticus str. psy62]
(976 letters)
>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 1072 bits (2775), Expect = 0.0
Identities = 406/987 (41%), Positives = 581/987 (58%), Gaps = 125/987 (12%)
Query: 4 ENHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAV 63
L L+DGSS ++RAFYA R DGLP A+ GF NML KLL ++E +H AV
Sbjct: 1 MKTLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLL---KEEK-PTHVAV 56
Query: 64 IFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIAT 123
FD TFR+E+YP+YKANRP +PE L Q+PL+R +A GIP +E++G+EADD+I T
Sbjct: 57 AFDAKGKTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGT 116
Query: 124 YTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTV---KEEKIDIEHVIKKWGIPPEKMV 180
AE G+ V I++ DKDL+QLV L DT+ K E++D E V++K+G+ PE+++
Sbjct: 117 LAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEELDPEEVVEKYGVTPEQII 176
Query: 181 CLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETA 240
AL GDS DNIPG+PGIG KTAA LLQEYG+L E + E +
Sbjct: 177 DYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSL----------------EGLYENLDE- 219
Query: 241 RLSRKLVMLRTDVPITIPLEHLILEDCNGPRLISFLKALEFTKLIN--------RVATTY 292
+K + KL R T
Sbjct: 220 -----------------------------------IKGKKKEKLRENKEQAFLSRKLATI 244
Query: 293 DCDAANIEPVVLDINTTENKGIAIETEIDRDTTI---KTSQFSSLSDQTSKINSEQTPQK 349
D P+ +D+ E + DR+ I K +F SL
Sbjct: 245 KTDV----PLEVDLEDLELQ------PPDREKLIALFKELEFKSL--------------- 279
Query: 350 LFLERLQKLSQYPINNDSYTKIVNTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAI 409
L R P++ + Y I++ ++++ W+ KL+ G +F T ++D ++ + +
Sbjct: 280 --LRRAAAAEAAPLDEEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMQAELVGL 337
Query: 410 AISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNI 469
+ + E +I L + L +E+L+ LK E+ K+G N+
Sbjct: 338 SFAVEPG--------EAAYIPL-----------DQLDREVLAALKPLLEDPAIKKVGQNL 378
Query: 470 KYDKLVLHRYGISMRG-FEDIMLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKSRKSSI 528
KYD VL RYGI +RG D ML SY+LD GR H + S+A+++L + + +
Sbjct: 379 KYDLHVLARYGIELRGIAFDTMLASYLLDPGRR-HGLDSLAERYLGHKTISFEEVAGKQL 437
Query: 529 PIDKISDSQVQEHAIENSNVILQLWLLLRPKLIVE-KLLHVYERLDKPMIDVVSQMEITG 587
++ + E+A E+++V L+L +L+PKL+ E LL +YE ++ P++ V+++ME G
Sbjct: 438 TFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYEEIELPLVPVLARMERNG 497
Query: 588 IQIDQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKT 647
I++D++ LK++SAE+++ L LE+ IY+L+GE+FN++SPKQLG+ILF KL P G KTKT
Sbjct: 498 IKVDREYLKELSAELAQRLAELEQEIYELAGEEFNINSPKQLGEILFEKLGLPVGKKTKT 557
Query: 648 GQWKTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLAS 707
G + T A+ LE++ D+PI ILE+RQLSK+KSTY D+LP IN T R+HT ++
Sbjct: 558 G-YSTDAEVLEKLA-DDHPIPDKILEYRQLSKLKSTYTDALPKLINPDTGRIHTSFNQTV 615
Query: 708 TMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPL 767
T TGRL+S +PNLQNIPI+T+ G++IR+AF++P KL+SADYSQIELRILAH++ L
Sbjct: 616 TATGRLSSSDPNLQNIPIRTEEGRRIRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGL 675
Query: 768 YQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSE 827
+ F DIH A+E+FGV +E+V+ + RR AK INF IIYG+S F LA QL I R E
Sbjct: 676 IEAFAEGEDIHTATASEVFGVPLEEVTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKE 735
Query: 828 AADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAA 887
A +YI RYF R+PG+ EY+E+T R+ GYVET+FGRR + +INS + R ERAA
Sbjct: 736 AKEYIDRYFERYPGVKEYMERTVEQAREKGYVETLFGRRRYLPDINSRNGNRRAFAERAA 795
Query: 888 INAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHS 947
INAPIQGSAADI + AMI V K+L++ L ++MLLQ+HDELVFEVPE+E+ +++
Sbjct: 796 INAPIQGSAADIIKLAMIRVDKALKEEGLKSRMLLQVHDELVFEVPEDELEEVKKLVKEV 855
Query: 948 MEKACLPKINLRVPLKVNIKVSNNWQE 974
ME A + L VPL V++ V +NW E
Sbjct: 856 MENA----VELSVPLVVDVGVGDNWDE 878
>gnl|CDD|161944 TIGR00593, pola, DNA polymerase I. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University).
Length = 887
Score = 823 bits (2129), Expect = 0.0
Identities = 382/977 (39%), Positives = 549/977 (56%), Gaps = 101/977 (10%)
Query: 7 LFLVDGSSFIYRAFYA---TPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAV 63
L L+DG S +RA++A PL + K G P NA+ GF ML KLL KE ++ AV
Sbjct: 1 LLLIDGHSLAFRAYFALKNKPLTNSK--GEPTNAVYGFTKMLLKLL----KEEKPTYVAV 54
Query: 64 IFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIAT 123
FD TFR+E Y +YKANR PE L+ Q+PL++ A GIP +E++G+EADD+IAT
Sbjct: 55 AFDSGTPTFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIAT 114
Query: 124 YTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDT---VKEEKIDIEHVIKKWGIPPEKMV 180
AEKEG+ V IIS DKDL+QLVS + +I E+V++K+G+ P+++V
Sbjct: 115 LAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEYVVEKYGVTPDQLV 174
Query: 181 CLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETA 240
L+AL GDS DNIPG+ GIG KTAA LLQE+G+LENI N +IK K RE ++ + E A
Sbjct: 175 DLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDA 234
Query: 241 RLSRKLVMLRTDVPITIPLEHLILEDCNGPRLISFLKALEFTKLINRVATTYDCDAANIE 300
LS++L + TDVP+ + LE L L + + RL + L
Sbjct: 235 FLSKELATIVTDVPLEVDLEDLRLSEPDRERLYALL------------------------ 270
Query: 301 PVVLDINTTENKGIAIETEIDRDTTIKT--SQFSSLSDQTSKINSEQTPQKLFLERLQKL 358
E++ + + + S + D + + +E+T E L
Sbjct: 271 -----------------QELEFKSLLDRLENLESPVIDDHAPVLTEKTSCAKESEEAAPL 313
Query: 359 SQYPINNDSYTKIVNTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKD 418
+ + +G + + + K +A+A +T +Q
Sbjct: 314 A--------------------NPAEKAEVG----GFVLERLLDQLKKALALAFATENQSY 349
Query: 419 DTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHR 478
+ E I L + D ++ NE KIGH+ K+ +L R
Sbjct: 350 VA-YASEADGIPLLTILTDDK-------------FARWLLNEQIKKIGHDAKFLMHLLKR 395
Query: 479 YGISMRG-FEDIMLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKSRKSSIPIDKISDSQ 537
GI + G D ML +Y+LD + S + ++A+++L K +
Sbjct: 396 EGIELGGVIFDTMLAAYLLDPAQVST-LDTLARRYLVEELILDEKIGGKLAKFAFPPLEE 454
Query: 538 VQEHAIENSNVILQLWLLLRPKLIVEKLLHVYERLDKPMIDVVSQMEITGIQIDQDLLKQ 597
E+ + +L L +L KLL +Y ++ P+ V+++ME TGI++D D L++
Sbjct: 455 ATEYLARRAAATKRLAEELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQE 514
Query: 598 VSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKTGQWKTTAQDL 657
+S E + + LEE IY+L+GE+FN++SPKQLG++LF KL P G KTKTG + T A L
Sbjct: 515 LSQEFGEEIADLEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVGKKTKTG-YSTDADVL 573
Query: 658 EQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLE 717
E++ +PII ILE+RQL+K+KSTY D LP +N T R+HT ++ T TGRL+S
Sbjct: 574 EKLRE-KHPIIALILEYRQLTKLKSTYVDGLPELVNPDTGRIHTTFNQTGTATGRLSSSN 632
Query: 718 PNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDI 777
PNLQNIPI+++ G+KIR+AF++ LISADYSQIELR+LAH+++ L + F+N DI
Sbjct: 633 PNLQNIPIRSEEGRKIRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGEDI 692
Query: 778 HRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFH 837
H A+ +FGV IE V+P MRR AKTINF ++YG+S F LA +L I R EA ++I+RYF
Sbjct: 693 HTETASRLFGVEIEDVTPNMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFIERYFA 752
Query: 838 RFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAA 897
R+PG+ +YIE T R+ GYVET+FGRR + +INS ++R ER AINAPIQGSAA
Sbjct: 753 RYPGVKDYIENTVEEARKKGYVETLFGRRRYIPDINSRNRNVREAAERMAINAPIQGSAA 812
Query: 898 DITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSMEKACLPKIN 957
DI + AMI + K L++ KL ++LLQ+HDEL+FE PEEE + ++ ME A
Sbjct: 813 DIMKIAMIKLDKRLKERKLKARLLLQVHDELIFEAPEEEAEEVAALVKEVMEHA----YP 868
Query: 958 LRVPLKVNIKVSNNWQE 974
L VPL+V + NW E
Sbjct: 869 LAVPLEVEVGTGKNWGE 885
>gnl|CDD|128751 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 315 bits (809), Expect = 4e-86
Identities = 133/262 (50%), Positives = 178/262 (67%), Gaps = 10/262 (3%)
Query: 5 NHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVI 64
L LVDGSS +RA++A P L + G P NA+ GF ML KL+ KE ++ AV+
Sbjct: 1 KKLLLVDGSSLAFRAYFALPPL-KNSKGEPTNAVYGFLRMLLKLI----KEEKPTYVAVV 55
Query: 65 FDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATY 124
FD TFR+E+YP+YKANRPK P+ LL Q+PL++ A GIP +E++G+EADD+IAT
Sbjct: 56 FDAKGKTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATL 115
Query: 125 TYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEK----IDIEHVIKKWGIPPEKMV 180
AE EG+ V I+S DKDL+QLVS + D K K E+VI+K+G+ PE+++
Sbjct: 116 AKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQII 175
Query: 181 CLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETA 240
+AL GDS DNIPG+PGIG KTAA LL+E+G+LENIL N ++K KK RE +L + E A
Sbjct: 176 DYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLK-KKLREKLLAHKEDA 234
Query: 241 RLSRKLVMLRTDVPITIPLEHL 262
+LSRKL + TDVP+ + LE L
Sbjct: 235 KLSRKLATIETDVPLEVDLEDL 256
>gnl|CDD|128758 smart00482, POLAc, DNA polymerase A domain.
Length = 206
Score = 294 bits (755), Expect = 8e-80
Identities = 111/206 (53%), Positives = 147/206 (71%)
Query: 730 GQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVN 789
G++IRRAF++PP L+SADYSQIELRILAH++ L + F N DIH AA++FGV
Sbjct: 1 GREIRRAFVAPPGYVLVSADYSQIELRILAHLSGDENLLEAFNNGGDIHSKTAAQVFGVP 60
Query: 790 IEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPGIHEYIEKT 849
E+V+ ++RR AK INF IIYG+ LA QL I +EA + IK YF RFPG+ YI++T
Sbjct: 61 EEEVTKELRRAAKAINFGIIYGMGAKGLAEQLGISEAEAKELIKAYFARFPGVKRYIKRT 120
Query: 850 KNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAADITRRAMISVHK 909
R+ GYV T+FGRR + +I+S +R ERAA+NAPIQGSAADI + AMI + +
Sbjct: 121 LEEARRKGYVTTLFGRRRYIPDIDSRNPVLRAAAERAAVNAPIQGSAADILKLAMIKMDE 180
Query: 910 SLEDHKLATKMLLQIHDELVFEVPEE 935
+L++ L ++LLQ+HDELVFEVPEE
Sbjct: 181 ALKEKGLRARLLLQVHDELVFEVPEE 206
>gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase;
Provisional.
Length = 553
Score = 273 bits (699), Expect = 2e-73
Identities = 140/510 (27%), Positives = 233/510 (45%), Gaps = 53/510 (10%)
Query: 488 DIMLMSYVL--DSGRSSHDIASIAQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIEN 545
D+ML S +L GR+ +++ A + L K ++S D + Q+ +A +
Sbjct: 74 DLMLASQLLLGSEGRAGSSLSAAAARALGEGLD---KPPQTSALSDPPDEEQL-LYAAAD 129
Query: 546 SNVILQLWLLLRPKLIVEKLLHVYERLDKPMID-------VVSQMEITGIQIDQDLLKQV 598
++V+L+L+ +L +L RL + + ++ME+ G+ D D+ + +
Sbjct: 130 ADVLLELYAVLADQLNRIAAAAHPGRL-RLLAAAESAGALAAAEMELAGLPWDTDVHEAL 188
Query: 599 SAEIS----------KNLLSLEENIYDLSGE-KFNLSSPKQLGDIL-FTKLKFPSGAKTK 646
AE+ L L I + G + N SP+Q+ L ++ PS
Sbjct: 189 LAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRRAGIELPS----- 243
Query: 647 TGQWKTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLA 706
T +W +L +I D+P ++ +LE+R+LSK+ S + ++ R R H Y
Sbjct: 244 TRKW-----ELREI---DHPAVEPLLEYRKLSKLLSANGWAWLDYWV-RDGRFHPEYVPG 294
Query: 707 STMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITP 766
+TGR AS PN Q IP + IR AF++ P KL+ AD SQIELR+LA +
Sbjct: 295 GVVTGRWASRGPNAQQIP------RDIRSAFVADPGWKLVVADASQIELRVLAAYSGDER 348
Query: 767 LYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRS 826
+ + F D+HR+ A+ FG E+ + R AK NF IYG + L +
Sbjct: 349 MIEAFRTGGDLHRLTASVGFGKPEEEK--EERALAKAANFGAIYGATSKGLQEYAK-NYG 405
Query: 827 EAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERA 886
EAA ++R +P ++E+ + G V T+ GR R
Sbjct: 406 EAARLLERLRRAYPRAVGWVERAAREGERGGVVRTLLGRTSPPPGFAWRARRRARSRGRF 465
Query: 887 AINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVH 946
N P+QG+AAD + A+ + + L + L +++ +HDE+V E PEEE + I
Sbjct: 466 TRNFPVQGTAADWAKLALALLRRRLAEG-LDAELVFFVHDEVVVECPEEEAEEVAAAIEE 524
Query: 947 SMEKACLPKINL-RVPLKVNIKVSNNWQEE 975
+ME+A ++ VP V + V ++ E
Sbjct: 525 AMEEA--GRLLFGPVPFPVEVAVVESYAEA 552
>gnl|CDD|184939 PRK14976, PRK14976, 5'-3' exonuclease; Provisional.
Length = 281
Score = 222 bits (568), Expect = 4e-58
Identities = 107/285 (37%), Positives = 159/285 (55%), Gaps = 11/285 (3%)
Query: 3 KENHLFLVDGSSFIYRAFYAT--PLLSRK-HDGLPVNAIAGFCNMLWKLLQNSRKESIAS 59
L+DG+S I+R++YAT K + GLP NAI F M++K+L+ S
Sbjct: 1 MMKKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNP----S 56
Query: 60 HFAVIFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADD 119
+ + FD TFR+++Y +YK R K PE L+ Q+PL++ + GI E G+EADD
Sbjct: 57 YILIAFDAGRKTFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADD 116
Query: 120 IIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEH---VIKKWGIPP 176
+I + K+ V I S+DKDL+QLV+ T + K I + + +GI P
Sbjct: 117 LIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILNTNNFFELYGIEP 176
Query: 177 EKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEY 236
++++ + L GDS DNI G+ GIG KTA LL +YGN+ENI N +IK KK + + E
Sbjct: 177 KQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIK-KKIKNKLSEA 235
Query: 237 AETARLSRKLVMLRTDVPITIPLEHLILEDCNGPRLISFLKALEF 281
E A LS+KL ++TDVP+ +E + L+ + P L + LE
Sbjct: 236 KEKALLSKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIFEELEL 280
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 190 bits (484), Expect = 2e-48
Identities = 90/264 (34%), Positives = 140/264 (53%), Gaps = 12/264 (4%)
Query: 5 NHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVI 64
NHL ++D + I R P S V + KL+++S+ +H +
Sbjct: 3 NHLLIIDALNLIRRIHAVQP--SPNDINACVETCQHALD---KLIRHSQ----PTHAVAV 53
Query: 65 FDY--PAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIA 122
FD + +R+++ PDYKA R +PE L LP +R A + GI + G EADD+IA
Sbjct: 54 FDGDARSSGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIA 113
Query: 123 TYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCL 182
T + G TI+STDK QL+SPT + D ++ +D + +++G+ P+++
Sbjct: 114 TLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYFQKRWLDAPFIEQEFGVEPQQLPDY 173
Query: 183 QALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARL 242
L G S IPG+ GIG K+AA LL ++ +LENI + + +K R+ + E+ E ARL
Sbjct: 174 WGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALP-EKWRKKLEEHKEMARL 232
Query: 243 SRKLVMLRTDVPITIPLEHLILED 266
RKL L+TD+P+ L+ L L
Sbjct: 233 CRKLAQLQTDLPLGGNLQQLRLNR 256
>gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease
proofreading domain present in DNA polymerase I, Werner
syndrome helicase, RNase D and other enzymes.
Length = 172
Score = 80.9 bits (200), Expect = 2e-15
Identities = 46/192 (23%), Positives = 87/192 (45%), Gaps = 24/192 (12%)
Query: 371 IVNTKDIQQWVQKLET-IGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFI 429
+ +++ +++ ++KL G + T ++++ K + I IS E FI
Sbjct: 4 VTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTG---------EGAFI 54
Query: 430 DLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGFEDI 489
+ + L LK E+E K+GHN K+D VL R+GI + D
Sbjct: 55 IDPLAL-----------GDDLEILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDT 103
Query: 490 MLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVI 549
ML +Y+L G S H +A++ + Y E+ K + S + + ++A E+++ +
Sbjct: 104 MLAAYLLLGGPSKHGLATLLK---EYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADAL 160
Query: 550 LQLWLLLRPKLI 561
L+L+ L +L
Sbjct: 161 LRLYEKLEKELE 172
>gnl|CDD|177280 PHA00439, PHA00439, exonuclease.
Length = 286
Score = 50.9 bits (122), Expect = 1e-06
Identities = 37/144 (25%), Positives = 52/144 (36%), Gaps = 15/144 (10%)
Query: 70 VTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATYTYIAE 129
V +R E+ P YKANR K + + +I G E DD++
Sbjct: 75 VNWRKEVVPTYKANR-KAKRKPVGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPS 133
Query: 130 KEGFA-VTIISTDKDLMQLVSPTTCLYD--TVKEEKIDIEHVIKKWGIPPEKMVCLQALT 186
GF ++S DKD + C + T +W + Q +
Sbjct: 134 LFGFKKAVLVSCDKDFKTI---PNCDFLWCTTGNILTQTPETADRWHL-------FQTIK 183
Query: 187 GDSIDNIPGIPGIGYKTAALLLQE 210
GDS D GIPG G TA L+
Sbjct: 184 GDSTDGYSGIPGWG-DTAEAFLEN 206
>gnl|CDD|128575 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
Length = 36
Score = 50.9 bits (123), Expect = 1e-06
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 176 PEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEY 211
PE+++ L GD DNIPG+ GIG KTA LL+E+
Sbjct: 1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36
>gnl|CDD|163388 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 49.2 bits (118), Expect = 5e-06
Identities = 33/89 (37%), Positives = 49/89 (55%), Gaps = 10/89 (11%)
Query: 150 PTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQ 209
P +Y VK E I++E V+ + GI E+++ + L G D G+ GIG KTA L++
Sbjct: 197 PGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVG--TDYNEGVKGIGPKTALKLIK 254
Query: 210 EYGNLENILINASRIKQKKRRENILEYAE 238
E+G+LE +L K R E+I Y E
Sbjct: 255 EHGDLEKVL--------KARGEDIENYDE 275
>gnl|CDD|179693 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 48.3 bits (116), Expect = 1e-05
Identities = 33/89 (37%), Positives = 50/89 (56%), Gaps = 10/89 (11%)
Query: 150 PTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQ 209
P +Y VK E I++E V+K+ GI E+++ + L G D PGI GIG KTA L++
Sbjct: 150 PGKNVYVEVKPELIELEEVLKELGITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIK 207
Query: 210 EYGNLENILINASRIKQKKRRENILEYAE 238
++G+LE +L ++R I Y E
Sbjct: 208 KHGDLEKVL--------EERGFEIENYDE 228
>gnl|CDD|177397 PHA02567, rnh, RnaseH; Provisional.
Length = 304
Score = 44.7 bits (106), Expect = 1e-04
Identities = 32/91 (35%), Positives = 42/91 (46%), Gaps = 13/91 (14%)
Query: 110 IEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEHVI 169
++I EADDIIA T EG V I+S+D D QL Y VK+ +
Sbjct: 124 MKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHK-----YPGVKQ----WSPMQ 174
Query: 170 KKWGIP----PEKMVCLQALTGDSIDNIPGI 196
KKW P PEK + + + GD D + I
Sbjct: 175 KKWVKPKYGSPEKDLMTKIIKGDKKDGVASI 205
>gnl|CDD|185517 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 38.8 bits (91), Expect = 0.007
Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 17/121 (14%)
Query: 106 GIPAIEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCL------YDTVK 159
GIP IE EA+ A + K+G + + D D L T L + K
Sbjct: 151 GIPVIEAPC-EAE---AQCAELV-KKGKVYAVATEDMD--ALTFGTPVLLRNLNFSEAKK 203
Query: 160 EE--KIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENI 217
+I++ V+++ G+ ++ + L L G D I GIG KTA L+++Y ++E I
Sbjct: 204 RPIQEINLSTVLEELGLSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKLIKKYKSIEEI 261
Query: 218 L 218
L
Sbjct: 262 L 262
>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 32.8 bits (76), Expect = 0.50
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 195 GIPGIGYKTAALLLQEYGNLENILINAS 222
GI +G K A L + +G+LE + AS
Sbjct: 515 GIRHVGEKAAKALARHFGSLEAL-RAAS 541
>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 32.1 bits (74), Expect = 0.63
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 195 GIPGIGYKTAALLLQEYGNLENILINAS 222
+P +G A LL+ +G++E + + AS
Sbjct: 719 SLPDVGPVLARNLLEHFGSVEAV-MTAS 745
>gnl|CDD|182284 PRK10173, PRK10173, glucose-1-phosphatase/inositol phosphatase;
Provisional.
Length = 413
Score = 30.5 bits (69), Expect = 2.5
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 668 IKNILEWRQLSKIKSTYADSL 688
IK +W+ LSK+K+ Y DSL
Sbjct: 253 IKTDQQWKVLSKLKNGYQDSL 273
>gnl|CDD|184786 PRK14671, uvrC, excinuclease ABC subunit C; Provisional.
Length = 621
Score = 30.1 bits (68), Expect = 2.6
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 195 GIPGIGYKTAALLLQEYGNLENI 217
I GIG KTA LL+ +G++E +
Sbjct: 573 DIAGIGEKTAEKLLEHFGSVEKV 595
>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 689
Score = 29.7 bits (67), Expect = 4.1
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 195 GIPGIGYKTAALLLQEYGNLENILI 219
GIP +G TA L +E+G E I+
Sbjct: 532 GIPEVGPTTARNLAREFGTFEAIMD 556
>gnl|CDD|179065 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 29.3 bits (67), Expect = 4.7
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 195 GIPGIGYKTAALLLQEYGNLENILINAS 222
IPGIG K LL+ +G+L+ I AS
Sbjct: 547 DIPGIGPKRRKALLKHFGSLKAIK-EAS 573
>gnl|CDD|183710 PRK12737, gatY, tagatose-bisphosphate aldolase; Reviewed.
Length = 284
Score = 29.3 bits (66), Expect = 5.4
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 793 VSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPG 841
V + + A I GI +AT+L+I S+A +K+YF+ P
Sbjct: 213 VPDEDVKKA------ISLGICKVNVATELKIAFSDA---VKKYFYENPK 252
>gnl|CDD|150116 pfam09340, NuA4, Histone acetyltransferase subunit NuA4. The NuA4
histone acetyltransferase (HAT) multisubunit complex is
responsible for acetylation of histone H4 and H2A
N-terminal tails in yeast. NuA4 complexes are highly
conserved in eukaryotes and play primary roles in
transcription, cellular response to DNA damage, and cell
cycle control.
Length = 80
Score = 28.7 bits (65), Expect = 6.6
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 12/73 (16%)
Query: 593 DLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDIL-----FTKLKFPSGAKTKT 647
+LL++ ++ K L +LE IYD E SS G+I+ + K S
Sbjct: 6 ELLQK-KKKLEKELAALERQIYDKETEYLEDSSS--GGNIIKGFDGYLK----SSKNGSA 58
Query: 648 GQWKTTAQDLEQI 660
+ K D ++I
Sbjct: 59 QRRKRKFTDDDRI 71
>gnl|CDD|129319 TIGR00215, lpxB, lipid-A-disaccharide synthase. Lipid-A precursor
biosynthesis producing lipid A disaccharide in a
condensation reaction. transcribed as part of an operon
including lpxA.
Length = 385
Score = 28.7 bits (64), Expect = 7.1
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 1/85 (1%)
Query: 154 LYDTVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGN 213
L D + K D + +K GI L L G + + + K A LL Q+ +
Sbjct: 167 LLDAIPLYKPDRKSAREKLGIDHNGE-TLALLPGSRGSEVEKLFPLFLKAAQLLEQQEPD 225
Query: 214 LENILINASRIKQKKRRENILEYAE 238
L +L + ++ + + EY
Sbjct: 226 LRRVLPVVNFKRRLQFEQIKAEYGP 250
>gnl|CDD|173132 PRK14669, uvrC, excinuclease ABC subunit C; Provisional.
Length = 624
Score = 28.3 bits (63), Expect = 9.4
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 196 IPGIGYKTAALLLQEYGNLENI 217
IPG+G KT LL+ +G+LE +
Sbjct: 557 IPGVGAKTVQRLLKHFGSLERV 578
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.135 0.381
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 15,716,906
Number of extensions: 1040271
Number of successful extensions: 2085
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2050
Number of HSP's successfully gapped: 45
Length of query: 976
Length of database: 5,994,473
Length adjustment: 103
Effective length of query: 873
Effective length of database: 3,768,849
Effective search space: 3290205177
Effective search space used: 3290205177
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 (21.7 bits)
S2: 62 (27.6 bits)