RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780952|ref|YP_003065365.1| DNA helicase II [Candidatus
Liberibacter asiaticus str. psy62]
(685 letters)
>gnl|CDD|162191 TIGR01073, pcrA, ATP-dependent DNA helicase PcrA. Designed to
identify pcrA members of the uvrD/rep subfamily.
Length = 726
Score = 537 bits (1385), Expect = e-153
Identities = 246/650 (37%), Positives = 362/650 (55%), Gaps = 32/650 (4%)
Query: 27 LKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQ 86
L LN +Q AV + PLLI+AGAG+GKT VL R+ HLI K + P ILA+TFTN+
Sbjct: 2 LAHLNPEQREAV-KTTEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNK 60
Query: 87 AIQEMKNRLACYLGE--KIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQ 144
A +EMK R+ LG + I TFHS C ILR+ + +G+ +F+I+D + +++K
Sbjct: 61 AAREMKERVEKLLGPVAEDIWISTFHSMCVRILRRDIDRIGINRNFSIIDPTDQLSLMKT 120
Query: 145 LLKDLQIDDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAYLQKT 204
+LKD +D K ++P ++ I +N P+D + + ++ +Y +Y L +
Sbjct: 121 ILKDKNLDPKKFEPRSILGTISNAKNELLPPEDFAKEATNYFEKVVAEVYQEYQKRLLRN 180
Query: 205 KSCDFGGLIIKTIEVLHH-PHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQ 263
+ DF LI+ TI + P VL+ Y K YI VDEYQD N QY L+RLL +
Sbjct: 181 NALDFDDLIMTTINLFQRVPDVLEYYQRKFQYIHVDEYQDTNRAQYTLVRLLASR----- 235
Query: 264 GARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTANKLISH 323
+C VGD +Q IY WRGA +IL+F+KD+ +A I LEQNYRST +IL AN++I H
Sbjct: 236 FRNLCVVGDADQSIYGWRGADIQNILSFEKDYPNATTILLEQNYRSTKNILQAANEVIEH 295
Query: 324 NKQRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIINIQNTG-MSLNNIAILVRT 382
N R K L+T+ K++ + + ++ E + EI + G + AIL RT
Sbjct: 296 NSNRKPKNLWTENS--SGDKITYYEADTERDEAQFVAGEIDKLVKNGERKYGDFAILYRT 353
Query: 383 SWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINCPKR 441
+ Q+R FE+ L+ IP+K++GG FYDR+EI+D LAY R++ D RIIN PKR
Sbjct: 354 NAQSRVFEETLLKANIPYKIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKR 413
Query: 442 GIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSKKMD 501
GIG SL KI +A + +ISL +A ++ + G + +L F I + +
Sbjct: 414 GIGASSLEKIVNYALELNISLFEAIGEIDEIGGLAAKSANALLAFATMIENLRQQQEYLS 473
Query: 502 PAPIANMILEQSGYMAMWKNNKSSEKSQERLDNLRELLSII----EKHE--TLEGFVLQA 555
P + +L++SGY M K + +E++Q RL+NL E LS+ ++ E +L F+
Sbjct: 474 PTELVEEVLDKSGYREMLK-AEKTEEAQSRLENLDEFLSVTKEFEDESEDKSLIDFLTDL 532
Query: 556 PLRENLGSF--IPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSIN-EGNVEGER 612
L +L + + +MTLHAAKGLEF VF+ G E+G+ PH S+ E +E ER
Sbjct: 533 ALVSDLDELEETEEGGAVTLMTLHAAKGLEFPVVFLIGMEEGVFPHSRSLMDEKELEEER 592
Query: 613 RLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQ--VSQFLLELYDP 660
RLAYVGITRA+++ +L TH R + S+FL E+
Sbjct: 593 RLAYVGITRAEEELYL-------THATMRTLFGRIQMNPPSRFLNEIPAE 635
>gnl|CDD|183307 PRK11773, uvrD, DNA-dependent helicase II; Provisional.
Length = 721
Score = 480 bits (1239), Expect = e-136
Identities = 239/654 (36%), Positives = 364/654 (55%), Gaps = 30/654 (4%)
Query: 27 LKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQ 86
L LN +Q AV P +L+LAGAG+GKT VL+ R+ L+ + P I+A+TFTN+
Sbjct: 7 LDSLNDKQREAVAAPLG-NMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNK 65
Query: 87 AIQEMKNRLACYLGEKIPR--IQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQ 144
A EM++R+ LG + TFH +LR H + LP DF ILDS + ++K+
Sbjct: 66 AAAEMRHRIEQLLGTSQGGMWVGTFHGLAHRLLRAHWQDANLPQDFQILDSDDQLRLLKR 125
Query: 145 LLKDLQIDDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAYLQKT 204
L+K L +D+K + P + I+ ++ G P+ I + K IY Y +
Sbjct: 126 LIKALNLDEKQWPPRQAQWYINGQKDEGLRPQHIQSYGDPVEQTWLK-IYQAYQEACDRA 184
Query: 205 KSCDFGGLIIKTIEV-LHHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQ 263
DF L+++ E+ L+ PH+L+ Y E+ +I+VDE+QD N QY +RLL +
Sbjct: 185 GLVDFAELLLRAHELWLNKPHILQHYQERFTHILVDEFQDTNAIQYAWIRLL-----AGD 239
Query: 264 GARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTANKLISH 323
++ VGD++Q IY WRGAQ +I F DF A I+LEQNYRST +IL AN LI++
Sbjct: 240 TGKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTANILKAANALIAN 299
Query: 324 NKQRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIINIQNTGMSLNNIAILVRTS 383
N R K+L+T D D +S++ + ++ E +++ I Q+ G +L++ AIL R++
Sbjct: 300 NNGRLGKELWT--DGGDGEPISLYCAFNELDEARFVVERIKTWQDNGGALSDCAILYRSN 357
Query: 384 WQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINCPKRG 442
Q+R E+A L+ IP+++ GG F++RQEI+DALAY RL+ + D F+R++N P RG
Sbjct: 358 AQSRVLEEALLQAGIPYRIYGGMRFFERQEIKDALAYLRLIANRNDDAAFERVVNTPTRG 417
Query: 443 IGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDP 502
IG +L ++ A ++L QA L+ + +LQ F++ I + M
Sbjct: 418 IGDRTLDVVRQTARDRQLTLWQACRALLQEKVLAGRAASALQRFIELIDALAQETADMPL 477
Query: 503 APIANMILEQSGYMAMWKNNKSSEKSQERLDNLRELLSI---------IEKHETLEGFVL 553
+ +++ SG AM++ K EK Q R++NL EL++ E L+ F+
Sbjct: 478 HEQTDRVIKDSGLRAMYEQEK-GEKGQARIENLEELVTATRQFSYPDEDEDLTPLQAFLS 536
Query: 554 QAPLRENLGSFIPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINE-GNVEGER 612
A L G + +Q+MTLH+AKGLEF VFI G E+GL P Q+S+ E G +E ER
Sbjct: 537 HAALEAGEGQADAHEDAVQLMTLHSAKGLEFPLVFIVGMEEGLFPSQMSLEEGGRLEEER 596
Query: 613 RLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLELYDPSHTQEI 666
RLAYVGITRA +K L Y +RR + E Y + S+F+ E+ +E+
Sbjct: 597 RLAYVGITRAMQKLTLTYAESRRLYG---KEVY--HRPSRFIREI-PEECVEEV 644
>gnl|CDD|130146 TIGR01074, rep, ATP-dependent DNA helicase Rep. Designed to
identify rep members of the uvrD/rep subfamily.
Length = 664
Score = 447 bits (1152), Expect = e-126
Identities = 233/647 (36%), Positives = 341/647 (52%), Gaps = 32/647 (4%)
Query: 29 GLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAI 88
LN QQ AV P L+LAGAG+GKT V+ ++ +LI + I A+TFTN+A
Sbjct: 1 KLNPQQQEAVEYVTG-PCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAA 59
Query: 89 QEMKNRLACYLGEKIPR---IQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQL 145
+EMK R+A LG+ R I TFH+ I+++ +G ++F++ D + ++K+L
Sbjct: 60 REMKERVAKTLGKGEARGLTISTFHTLGLDIIKREYNALGYKSNFSLFDETDQLALLKEL 119
Query: 146 LKDLQIDDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAYLQKTK 205
+ L DDKD ++I I W+N P+ S+ E + Y Y A+L+
Sbjct: 120 TEGLIKDDKDL-LDKLISTISNWKNDLLTPEQALASARGEREQTFAHCYALYQAHLRAYN 178
Query: 206 SCDFGGLIIKTIEVLH-HPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQG 264
+ DF LI+ +L + V ++ KI Y++VDEYQD NT QY L++LL
Sbjct: 179 ALDFDDLILLPTLLLQQNEEVRNRWQNKIRYLLVDEYQDTNTSQYELVKLLVGDR----- 233
Query: 265 ARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTANKLISHN 324
AR VGD++Q IY WRGA+ +++ ++DF +IKLEQNYRST IL AN LI++N
Sbjct: 234 ARFTVVGDDDQSIYSWRGARPENLVLLKEDFPQLKVIKLEQNYRSTGRILKAANILIANN 293
Query: 325 KQRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIINIQ-NTGMSLNNIAILVRTS 383
F+KKLF++ K+ + ++ E I EII + + AIL R +
Sbjct: 294 PHVFEKKLFSELG--YGEKIKVIECNNEEHEAERIAGEIIAHKLVNKTQYKDYAILYRGN 351
Query: 384 WQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINCPKRG 442
Q+R E A ++ IP+K+ GG SF+ R EI+D L+Y RL+ D F RI+N PKR
Sbjct: 352 HQSRLLEKALMQNRIPYKLSGGTSFFSRPEIKDLLSYLRLLVNPDDDAAFLRIVNTPKRE 411
Query: 443 IGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDP 502
IG +L K+ A + + SL AS + + +SLQ F + +++ +P
Sbjct: 412 IGPATLEKLGELAMERNKSLFTASFDMGLLQTLSGRGYESLQRFTDWLVEIRRLAERSEP 471
Query: 503 APIANMILEQSGYMAMWKNNKSSEKSQE-RLDNLRELLSII---------EKHETLEGFV 552
++E Y S K+ E R+ N+ L S ++ TL V
Sbjct: 472 IEAVRSLIEDIDYENWLYETSPSPKAAEMRMKNVNTLFSWFKEMLEGDEEDEPMTLTQVV 531
Query: 553 LQAPLRENLGSFIPD--SNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEG 610
+ LR+ L + + +Q+MTLHA+KGLEF VFI G E+G+LPHQ SI E NVE
Sbjct: 532 TRLTLRDMLERGEDEEELDQVQLMTLHASKGLEFPYVFIVGMEEGILPHQSSIEEDNVEE 591
Query: 611 ERRLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLEL 657
ERRLAYVGITRA+K+ RR + E +P S+FL EL
Sbjct: 592 ERRLAYVGITRAQKELTFTLCKERRQYG----ELVRPEP-SRFLDEL 633
>gnl|CDD|130147 TIGR01075, uvrD, DNA helicase II. Designed to identify uvrD
members of the uvrD/rep subfamily.
Length = 715
Score = 445 bits (1145), Expect = e-125
Identities = 238/649 (36%), Positives = 353/649 (54%), Gaps = 37/649 (5%)
Query: 27 LKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQ 86
L GLN +Q AV P LL+LAGAG+GKT VL R+ L+ + P I+A+TFTN+
Sbjct: 2 LDGLNDKQREAVAAPPGN-LLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNK 60
Query: 87 AIQEMKNRLACYLGEKIPR------IQTFHSFCASILRKHGEVVGLPTDFAILDSAESRT 140
A EM++R+ G + I TFH +LR H GLP DF ILDS +
Sbjct: 61 AAAEMRHRI----GALLGTSARGMWIGTFHGLAHRLLRAHHLDAGLPQDFQILDSDDQLR 116
Query: 141 IIKQLLKDLQIDDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAY 200
++K+L+K L +D+K + P + + I+ ++ G P I + K IY Y
Sbjct: 117 LLKRLIKALNLDEKQWPPRQAMWYINNQKDEGLRPSHIQAFDNPVERTWIK-IYQAYQEA 175
Query: 201 LQKTKSCDFGGLIIKTIEVL-HHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKE 259
+ DF L+++ E+L + PH+L+ Y E+ +I+VDE+QD N QY +RLL
Sbjct: 176 CDRAGLVDFAELLLRAHELLRNKPHILQHYQERFTHILVDEFQDTNKIQYAWIRLLAGNT 235
Query: 260 DSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTANK 319
+ VGD++Q IY WRGAQ +I F KDF A I+LEQNYRST +IL AN
Sbjct: 236 -----GNVMIVGDDDQSIYGWRGAQVENIQKFLKDFPGAETIRLEQNYRSTANILAAANA 290
Query: 320 LISHNKQRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIINIQNTGMSLNNIAIL 379
LI++N +R K L+T D +S++ + ++ E ++ I Q G +L+ A+L
Sbjct: 291 LIANNDERLGKNLWT--DGEVGEPISLYSAFNELDEARFVVSRIKTWQRNGGALDECAVL 348
Query: 380 VRTSWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINC 438
R++ Q+R E+A L+ IP+++ GG F++RQEI+DALAY RL+ + D F+R+IN
Sbjct: 349 YRSNAQSRVLEEALLQASIPYRIYGGMRFFERQEIKDALAYLRLIANRNDDAAFERVINT 408
Query: 439 PKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSK 498
P RGIG +L ++ A ++L QA+ +L + +LQ FV+ I N +
Sbjct: 409 PTRGIGDRTLDVVRQAARDRGLTLWQAARELTQEKVLAGRAASALQRFVELIEALANETA 468
Query: 499 KMDPAPIANMILEQSGYMAMWKNNKSSEKSQERLDNLRELLSI---------IEKHETLE 549
M + +++ SG M++ K EK Q R++NL EL++ E L
Sbjct: 469 DMPLHVQTDHVIKDSGLREMYQQEK-GEKGQARIENLEELVTATRQFSLPENDEDMTPLT 527
Query: 550 GFVLQAPLRENLGSFIPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINE-GNV 608
F+ A L G + +Q+MTLH+AKGLEF VF+ G E+G+ P Q+S++E G +
Sbjct: 528 AFLSHAALEAGEGQADAGQDAVQLMTLHSAKGLEFPLVFLVGMEEGMFPSQMSLDEGGRL 587
Query: 609 EGERRLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLEL 657
E ERRLAYVGITRA +K + Y RR + S+F+ EL
Sbjct: 588 EEERRLAYVGITRAMQKLTITYAETRRLYGKEVYHI-----PSRFIREL 631
>gnl|CDD|182838 PRK10919, PRK10919, ATP-dependent DNA helicase Rep; Provisional.
Length = 672
Score = 370 bits (951), Expect = e-103
Identities = 234/653 (35%), Positives = 349/653 (53%), Gaps = 47/653 (7%)
Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89
LN Q AV P L+LAGAG+GKT V+ ++ HLI I A+TFTN+A +
Sbjct: 3 LNPGQQQAVEFVTG-PCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAR 61
Query: 90 EMKNRLACYLGEKIPR---IQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQLL 146
EMK R+A LG K R I TFH+ I+++ +G+ ++F++ D + ++K+L
Sbjct: 62 EMKERVAQTLGRKEARGLMISTFHTLGLDIIKREYAALGMKSNFSLFDDTDQLALLKELT 121
Query: 147 KDLQIDDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAYLQKTKS 206
+ L DDK ++I I W+N P + E I Y Y A+L+
Sbjct: 122 EGLIEDDKVL-LQQLISTISNWKNDLKTPAQAAAGAKGERDRIFAHCYGLYDAHLKACNV 180
Query: 207 CDFGGLIIK-TIEVLHHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQGA 265
DF LI+ T+ + + V +++ KI Y++VDEYQD NT QY L++LL A
Sbjct: 181 LDFDDLILLPTLLLQRNEEVRERWQNKIRYLLVDEYQDTNTSQYELVKLLV-----GSRA 235
Query: 266 RICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTANKLISHNK 325
R VGD++Q IY WRGA+ +++ +DF +IKLEQNYRS+ IL AN LI++N
Sbjct: 236 RFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALQVIKLEQNYRSSGRILKAANILIANNP 295
Query: 326 QRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIIN---IQNTGMSLNNIAILVRT 382
F+K+LF++ D+ KV + ++ E + E+I + T + AIL R
Sbjct: 296 HVFEKRLFSELGYGDELKVL--SANNEEHEAERVTGELIAHHFVNKTQYK--DYAILYRG 351
Query: 383 SWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINCPKR 441
+ Q+R FE ++ IP+K+ GG SF+ R EI+D LAY R++ D F RI+N PKR
Sbjct: 352 NHQSRVFEKFLMQNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVNTPKR 411
Query: 442 GIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRW-NNCSKKM 500
IG +L K+ A + SL AS + S + +SL F W +
Sbjct: 412 EIGPATLQKLGEWAMTRNKSLFTASFDMGLSQTLSGRGYESLTRFT----HWLAEIQRLA 467
Query: 501 DPAPIANM--ILEQSGYMAMWKNNKSSEKSQE-RLDNLRELLSIIEKHETLEGFVLQAP- 556
+ P+A + ++ Y + S K+ E R+ N+ +L S + E LEG L P
Sbjct: 468 EREPVAAVRDLIHGIDYESWLYETSPSPKAAEMRMKNVNQLFSWMT--EMLEGSELDEPM 525
Query: 557 ----------LRENL--GSFIPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSIN 604
LR+ + G + + +Q+MTLHA+KGLEF V++ G E+GLLPHQ SI+
Sbjct: 526 TLTQVVTRFTLRDMMERGESEEELDQVQLMTLHASKGLEFPYVYLVGMEEGLLPHQSSID 585
Query: 605 EGNVEGERRLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLEL 657
E N++ ERRLAYVGITRA+K+ L +T+ + + + R +P S+FLLEL
Sbjct: 586 EDNIDEERRLAYVGITRAQKE--LTFTLCKERRQYGELVRPEP---SRFLLEL 633
>gnl|CDD|161956 TIGR00609, recB, exodeoxyribonuclease V, beta subunit. All
proteins in this family for which functions are known
are DNA-DNA helicases that are used as part of an
exonuclease-helicase complex (made up of RecBCD
homologs) that function to generate substrates for the
initiation of recombination and recombinational repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University).
Length = 1087
Score = 96.0 bits (239), Expect = 3e-20
Identities = 152/822 (18%), Positives = 261/822 (31%), Gaps = 226/822 (27%)
Query: 38 VTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPP---SKILAMTFTNQAIQEMKNR 94
+TIP + LI A AGTGKT + L L+ E P +IL +TFTN A +E+K R
Sbjct: 4 LTIPLNGTFLIEASAGTGKTFTIAQLYLRLL--LEGGPLTVEEILVVTFTNAATEELKTR 61
Query: 95 L---------AC----------------YLGEKIPR----------------IQTFHSFC 113
+ A EK+ + I T H FC
Sbjct: 62 IRGRIHQALRALKAALTSQELPEPLKEAIQDEKVKQAITRLRNALATMDEAAIYTIHGFC 121
Query: 114 ASILRKHGEVVGLP-TDFAILDSAESRTII------------------------------ 142
+L +H I D + I
Sbjct: 122 QRMLEQHAFESDEIFDVELIEDESLLLAEITKDFWRRNFYNLPFDIAQIVLKTKKSPQAV 181
Query: 143 -KQLLKDLQIDDKDYDPHEVI--EKIDYWQNRGWNPKDIPQSSLTEDAE----------- 188
Q+L DL + P + E++ W + + D ++ E+ +
Sbjct: 182 LTQILADLLLQSYLAFPSPPLDLEQLIKWHEQIYKDLDKLDHAVFEEIDKLNAERNNLFC 241
Query: 189 IPKAIYIQYVAYLQKT--------KSCDFGGLII---KTIEVLHHPHVLKKYHEKIPYIM 237
+ +++ + +Q+ + F L+ ++ + + E+ P +
Sbjct: 242 LKDRVFLTLLKEVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIAL 301
Query: 238 VDEYQDINTPQYLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKD 297
+DE+QD + QY + L + + + +GD Q IY +RGA L + D
Sbjct: 302 IDEFQDTDPQQYRIFSKLFIAQKT--TSLFL-IGDPKQAIYSFRGADIFTYLQAKSKA-D 357
Query: 298 ANIIKLEQNYRSTTHILNTANKLISHNKQRFDKKLFTQRDCHDDAKVSIHVSQSDNSEL- 356
A L N+RST ++ + NKL S F L V H S S +
Sbjct: 358 ARYT-LGTNWRSTPALVGSLNKLFSLISNPF---LEK----PIFIPVLAHQKNSKGSFVI 409
Query: 357 STIIQEIINIQNTGMSLNNIAILVRTSWQT----------------RKFEDAFLEQEIPH 400
+ Q I+ T + + +T Q F F + +
Sbjct: 410 NGQEQPPIHFFTTEVESEGVDDYRQTIAQKCAREIALWLASAALGLANFIATFGGRPLRA 469
Query: 401 KVIGGSFYDRQE---IRDALAYFRLV---CQE----HRDEDFKRIINCPKRGIGKESLHK 450
I R+E IR AL ++ + E+ + ++ + + E+
Sbjct: 470 GDIAVLVRGRKEANQIRKALKKAQIPSVYLSDKSSVFATEEAQELLALLEALLEPENEGT 529
Query: 451 IQYHASQH--HISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDPAPIANM 508
++ + +S L+ D + + V+ R +++
Sbjct: 530 LRAALASSIFGLSALELETLNQDE--------ITWERVVEKFREYHD------------- 568
Query: 509 ILEQSGYMAM------WKNNK----SSEKSQERLDNLRELLSIIEKHETLEGFVLQAPLR 558
I + G +AM K S + L NL L ++ E + L
Sbjct: 569 IWRKIGVLAMFQRLMLEKGIGERLLSQPGGERILTNLLHLAELL--QEAAHQERNKLSLL 626
Query: 559 ENLGSFI--------------PDSNCIQIMTLHAAKGLEFDTVFI--------------- 589
L I D+ ++I+T+H +KGLE+ VF+
Sbjct: 627 RWLEDQISNEEEEEEEIIRLESDAELVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLH 686
Query: 590 ---SGWEQGLLPHQLSINEGNVEGER-----RLAYVGITRAKKKCHLF--YTINRRTHDF 639
S Q +Q N+ ER RL YV +TRAKK+ + I + +
Sbjct: 687 DQHSHEYQLYDFNQSEENQKLARVERLAEDLRLLYVALTRAKKQLFIGIAPLITSKLSNL 746
Query: 640 TRVERYQPSQVSQFLLELYDPSHTQEIIYDDIYGTFSEHWNQ 681
+ + Q E D+I G +
Sbjct: 747 AYSALHNSALGYQ--------KQDGET--DNITG-LKQCLAA 777
>gnl|CDD|163019 TIGR02785, addA_Gpos, recombination helicase AddA, Firmicutes type.
AddAB, also called RexAB, substitutes for RecBCD in
several bacterial lineages. These DNA recombination
proteins act before synapse and are particularly
important for DNA repair of double-stranded breaks by
homologous recombination. The term AddAB is used
broadly, with AddA homologous between the Firmicutes (as
modeled here) and the alphaproteobacteria, while the
partner AddB proteins show no strong homology across the
two groups of species.
Length = 1232
Score = 86.7 bits (215), Expect = 2e-17
Identities = 108/548 (19%), Positives = 199/548 (36%), Gaps = 137/548 (25%)
Query: 225 VLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQ 284
+ Y EK ++VDEYQD N Q +L+LL K + + VGD Q IY +R A
Sbjct: 381 AAEFYREKFKEVLVDEYQDTNLLQESILQLL--KRGEEDEGNLFMVGDVKQSIYRFRQAD 438
Query: 285 FSHILNFQKDFKDAN-----IIKLEQNYRSTTHILNTANKLISH---------------- 323
S L F I L +N+RS +L+T N L
Sbjct: 439 PSLFLEKYHRFAQEGNEHGKRIDLAENFRSRKEVLDTTNYLFKQLMDEEVGEIDYDEEAQ 498
Query: 324 ----NKQ----RFDKKLFTQRDCHDDAKVSIHVSQSDNSELST--------------IIQ 361
N + +K + + + L +I+
Sbjct: 499 LKFGNAKYPENPDNKTELLLYEKLAIEEEEEEEIDEEEEILDKAQQEATMVAERIKALIK 558
Query: 362 EIINI------QNTGMSLNNIAILVRTSWQTRKFEDAFLEQEIPHKVIGGSFY-DRQEIR 414
E + + ++ +I IL R+ + + F + IP V Y E+R
Sbjct: 559 EGFKVYDKKTGEYRPVTYRDIVILTRSRGWNLQIMEEFKKYGIPVFVNDAENYFQTTEVR 618
Query: 415 DALAYFRLVCQEHRDEDFKRIINCPKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQ 474
L+ R++ ++D ++ P G +E L I+ S +A + + + +
Sbjct: 619 VMLSLLRVIDNPYQDIPLVAVLRSPIVGFDEEELALIRLQ--NKDSSFYEAVKSYVKAQK 676
Query: 475 FR-PQIRQSLQNFVKDIRRWNNCSKKMDPAPIANMI---LEQSGYM-------------- 516
++ + L+NF+ +++W ++ I+ +I +GY
Sbjct: 677 LIEDELYEKLKNFLDSLQKWREFARTH---SISELIWKIYNDTGYYDYVGGLPNGKQRQA 733
Query: 517 ---AMWKNNKSSEKSQERLDNLRELLSIIEKHETLEGFVLQAPLRE---NLGSFI---PD 567
A+++ + EK+ + L + + IE+ ++E +L S +
Sbjct: 734 NLYALYERARQYEKTSFK--GLFQFIRFIER------------MQERQKDLASAVAVGEA 779
Query: 568 SNCIQIMTLHAAKGLEFDTVFISGWEQG----------LLPHQLSINEGNVEGERRLA-- 615
N +++MT+H +KGLEF VF+ G + LL QL + ++ + RL+
Sbjct: 780 ENAVRLMTIHKSKGLEFPVVFVLGMGKQFNKQDLNSSYLLNRQLGLGITYIDPQERLSYP 839
Query: 616 -----------------------YVGITRAKKKCHLFYTINRRTHDFTRVERYQPS-QVS 651
YV +TRAK+K L ++ +++ + VS
Sbjct: 840 SLPKVAIKQKMKRELLSEEMRVLYVALTRAKEKLILVGSVKDEK---KESKKWLAALAVS 896
Query: 652 QFLLELYD 659
++L D
Sbjct: 897 GWVLPAND 904
Score = 74.4 bits (183), Expect = 1e-13
Identities = 39/122 (31%), Positives = 64/122 (52%), Gaps = 19/122 (15%)
Query: 46 LLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQEMKNRLACYLGEKIPR 105
+L+ A AG+GKT VL+ R++ I + + ++L +TFTN A +EMK R+ L + + +
Sbjct: 17 ILVSASAGSGKTAVLVERIIKKIL-RGVDIDRLLVVTFTNAAAREMKERIEEALQKALQQ 75
Query: 106 ------------------IQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQLLK 147
I T HSFC ++RKH ++ L F IL E +IK+++
Sbjct: 76 EPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQLLLIKEVVD 135
Query: 148 DL 149
D+
Sbjct: 136 DV 137
>gnl|CDD|182930 PRK11054, helD, DNA helicase IV; Provisional.
Length = 684
Score = 76.9 bits (190), Expect = 2e-14
Identities = 37/93 (39%), Positives = 54/93 (58%), Gaps = 2/93 (2%)
Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89
LN Q AV +D+ LL+LAGAG+GKT+VL+AR L+ + P +IL + F QA +
Sbjct: 197 LNPSQARAVVNGEDS-LLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAE 255
Query: 90 EMKNRLACYLGEKIPRIQTFHSFCASILRKHGE 122
EM R+ LG + +TFH+ I++ G
Sbjct: 256 EMDERIRERLGTEDITARTFHALALHIIQ-QGS 287
Score = 64.2 bits (157), Expect = 1e-10
Identities = 42/140 (30%), Positives = 65/140 (46%), Gaps = 11/140 (7%)
Query: 201 LQKTKSCDFGGLIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDINTPQYL-LLRLLCQKE 259
L+ + DF GLI + + L ++ +I+VDE+QDI +PQ LL L ++
Sbjct: 403 LKAENAVDFSGLIHQAVNYLEK----GRFISPWKHILVDEFQDI-SPQRAALLAALRKQ- 456
Query: 260 DSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTANK 319
+ VGD+ Q IY + GA S F + F + + L+ YR + I AN+
Sbjct: 457 --NSQTTLFAVGDDWQAIYRFSGADLSLTTAFHERFGEGDRCHLDTTYRFNSRIGEVANR 514
Query: 320 LISHNKQRFDKKL--FTQRD 337
I N + K L T+ D
Sbjct: 515 FIQQNPHQLKKPLNSLTKGD 534
Score = 51.1 bits (123), Expect = 9e-07
Identities = 27/82 (32%), Positives = 34/82 (41%), Gaps = 29/82 (35%)
Query: 571 IQIMTLHAAKGLEFDTVFI----------------SGWEQGLLPHQLSINEGNVEG---- 610
I MT+HA+KG + D V I S E+ LLP E
Sbjct: 589 IDFMTIHASKGQQADYVIILGLQEGQDGFPAPARESIMEEALLPP--------PEDFPDA 640
Query: 611 -ERRLAYVGITRAKKKCHLFYT 631
ERRL YV +TRAK + L +
Sbjct: 641 EERRLLYVALTRAKHRVWLLFN 662
>gnl|CDD|163018 TIGR02784, addA_alphas, double-strand break repair helicase AddA,
alphaproteobacterial type. AddAB, also called RexAB,
substitutes for RecBCD in several bacterial lineages.
These DNA recombination proteins act before synapse and
are particularly important for DNA repair of
double-stranded breaks by homologous recombination. The
term AddAB is used broadly, with AddA homologous between
the alphaproteobacteria (as modeled here) and the
Firmicutes, while the partner AddB proteins show no
strong homology across the two groups of species.
Length = 1141
Score = 64.3 bits (157), Expect = 9e-11
Identities = 40/140 (28%), Positives = 63/140 (45%), Gaps = 41/140 (29%)
Query: 50 AGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQEMKNRLACYLGE-------- 101
A AG+GKT VL R++ L+ + +PPSKIL +T+T A EM+NR+ LGE
Sbjct: 17 ANAGSGKTHVLTQRVIRLLLNG-VPPSKILCLTYTKAAAAEMQNRVFDRLGEWAVLDDAE 75
Query: 102 ----------KIP----------------------RIQTFHSFCASILRKHGEVVGLPTD 129
K P +IQT H+FC S+L + +
Sbjct: 76 LRARLEALEGKRPDAAKLAEARRLFARALETPGGLKIQTIHAFCESLLHQFPLEANVAGH 135
Query: 130 FAILDSAESRTIIKQLLKDL 149
F+++D + T++ + + L
Sbjct: 136 FSVMDDRAAATLLAEARRAL 155
Score = 58.9 bits (143), Expect = 4e-09
Identities = 39/125 (31%), Positives = 61/125 (48%), Gaps = 18/125 (14%)
Query: 208 DFGGLIIKTIEVLHHPH----VLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQ 263
DF LI +T+ +L P V K I +I+VDE QD + Q+ +++ L ++ S +
Sbjct: 363 DFNDLIERTVALLARPGAGAWVHYKLDRGIDHILVDEAQDTSPEQWDIIQALAEEFFSGE 422
Query: 264 GAR------ICCVGDENQCIYEWRGAQ---FSHI-LNFQKDFKDANI----IKLEQNYRS 309
GAR I VGDE Q IY ++GA F+ F + + + L ++RS
Sbjct: 423 GARSGVERTIFAVGDEKQSIYSFQGADPDRFAEERREFNRKVRAVGAKFEDLSLNYSFRS 482
Query: 310 TTHIL 314
T +L
Sbjct: 483 TPDVL 487
Score = 35.4 bits (82), Expect = 0.043
Identities = 22/92 (23%), Positives = 32/92 (34%), Gaps = 39/92 (42%)
Query: 571 IQIMTLHAAKGLEFDTVFI-----SGWEQGLLPHQLSINEGNVEGE-------------- 611
+++MT+H AKGLE VF+ + + P L G+ E
Sbjct: 776 VRVMTVHGAKGLEAPVVFLVDTGSAPFASQHAPK-LLFTGGSGEASDGKAPLWRPPSAFD 834
Query: 612 -------------------RRLAYVGITRAKK 624
RRL YV +TRA+
Sbjct: 835 PALSAAARERLKERAEDEYRRLLYVAMTRAED 866
>gnl|CDD|184388 PRK13909, PRK13909, putative recombination protein RecB;
Provisional.
Length = 910
Score = 57.7 bits (140), Expect = 9e-09
Identities = 40/141 (28%), Positives = 59/141 (41%), Gaps = 39/141 (27%)
Query: 50 AGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQEMKNRLACYL---------- 99
A AG+GKT L R L L+ K PS+ILA+TFT +A EMK R+ L
Sbjct: 5 ASAGSGKTFALSVRFLALL-FKGANPSEILALTFTKKAANEMKERIIDTLLNLEKEKEES 63
Query: 100 -------------------GEKI--------PRIQTFHSFCASILRKHGEVVGLPTDFAI 132
+K+ +I T +F ILRK +GL DF+I
Sbjct: 64 ELNELEEKLGLSKEELLNKRDKVYQEFLNSELKISTIDAFFQKILRKFCLNLGLSPDFSI 123
Query: 133 LDSAESRTIIKQLLKDLQIDD 153
+ + + ++ L L ++
Sbjct: 124 KEDTKEE-LNEKFLSALSKEE 143
Score = 55.4 bits (134), Expect = 4e-08
Identities = 45/159 (28%), Positives = 74/159 (46%), Gaps = 12/159 (7%)
Query: 231 EKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQGAR----ICCVGDENQCIYEWRGAQFS 286
KI +I++DE+QD + QY +L L + S +G + VGD Q IY +RG +
Sbjct: 327 SKISHILIDEFQDTSVLQYKILLPLIDEIKSGEGQKKFRSFFYVGDVKQSIYRFRGGKKE 386
Query: 287 HILNFQKDFKDANIIKLEQNYRSTTHILNTANKLISHNKQRFDKKLFTQRDCHDDAKVSI 346
KDFK + L+ NYRS I++ N++ + + TQ + +
Sbjct: 387 LFDKVSKDFKQK-VDNLDTNYRSAPLIVDFVNEVFKKKYKNY----KTQYAEQHKSGGYV 441
Query: 347 HVSQSDNSE---LSTIIQEIINIQNTGMSLNNIAILVRT 382
V + + L ++QEI + G+ ++IAIL T
Sbjct: 442 EVVEVADESEELLEQLLQEIQFLLEKGIDPDDIAILCWT 480
Score = 37.3 bits (87), Expect = 0.014
Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 533 DNLRELLSIIEKHETLEGFVLQ-APLRENLGSFIPDSNCIQIMTLHAAKGLEFDTV 587
+NL + L + +E +E F+ + P + + S +S +QIMT+H +KGLEF+ V
Sbjct: 571 ENLLKFLELASGYEDIEEFLFKLEPCDKEIASE--ESKGVQIMTVHKSKGLEFEHV 624
>gnl|CDD|182801 PRK10876, recB, exonuclease V subunit beta; Provisional.
Length = 1181
Score = 41.5 bits (98), Expect = 7e-04
Identities = 33/108 (30%), Positives = 52/108 (48%), Gaps = 14/108 (12%)
Query: 231 EKIPYIMVDEYQDINTPQYLLLRLL--CQKEDSKQGARICCVGDENQCIYEWRGAQFSHI 288
+ P M+DE+QD + QY + R + Q E + + +GD Q IY +RGA I
Sbjct: 376 TRYPVAMIDEFQDTDPQQYRIFRRIYRHQPETA-----LLLIGDPKQAIYAFRGAD---I 427
Query: 289 LNFQKDFKDANI-IKLEQNYRSTTHILNTANKLISHNKQRFDKKLFTQ 335
+ K + + L+ N+RS ++N+ NKL S F LF +
Sbjct: 428 FTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQTDDPF---LFRE 472
Score = 36.5 bits (85), Expect = 0.023
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 24/85 (28%)
Query: 567 DSNCIQIMTLHAAKGLEFDTV---FISGW---EQGLLPHQ---------LSINEGNV--- 608
D + +QI+T+H +KGLE+ V FI+ + +Q H L+ E +V
Sbjct: 732 DKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFY-HDRHSFEAVLDLNAAEESVALA 790
Query: 609 EGER-----RLAYVGITRAKKKCHL 628
E ER RL YV +TR+ C L
Sbjct: 791 EEERLAEDLRLLYVALTRSVWHCSL 815
Score = 33.0 bits (76), Expect = 0.28
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 17/72 (23%)
Query: 47 LILAGAGTGKTTVLIARMLHLIC--------HKEIPPSKILAMTFTNQAIQEMKNR---- 94
LI A AGTGKT + A L L+ + + +IL +TFT A +E++ R
Sbjct: 21 LIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSN 80
Query: 95 -----LACYLGE 101
+AC E
Sbjct: 81 IHELRIACLREE 92
>gnl|CDD|163003 TIGR02760, TraI_TIGR, conjugative transfer relaxase protein TraI.
This protein is a component of the relaxosome complex. In
the process of conjugative plasmid transfer the
realaxosome binds to the plasmid at the oriT (origin of
transfer) site. The relaxase protein TraI mediates the
single-strand nicking and ATP-dependent unwinding
(relaxation, helicase activity) of the plasmid molecule.
These two activities reside in separate domains of the
protein.
Length = 1960
Score = 37.6 bits (87), Expect = 0.010
Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 12/99 (12%)
Query: 6 QKSHFSHILKGD--FVPSCVPNY----------LKGLNAQQTHAVTIPDDTPLLILAGAG 53
+ S HIL G P L Q H + D + + AG
Sbjct: 987 ETSILLHILPGKETVTPLATRAQVFLNLELLERLTHGQKQAIHLIISTKDRFVAVQGLAG 1046
Query: 54 TGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQEMK 92
GKTT+L +R ++ E +++ + T++A+ E+K
Sbjct: 1047 VGKTTMLESRYKPVLQAFESEQLQVIGLAPTHEAVGELK 1085
>gnl|CDD|162365 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model.
Length = 586
Score = 37.1 bits (86), Expect = 0.015
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 11/56 (19%)
Query: 574 MTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLF 629
MT+H ++G EFD V + +LP N + R L Y GITRAK + ++
Sbjct: 524 MTVHKSQGSEFDHVIL------ILP-----NGNSPVLTRELLYTGITRAKDQLSVW 568
Score = 29.4 bits (66), Expect = 3.7
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 46 LLILAGAGTGKTTVLIARMLHLI 68
LI G GTGKTT +AR+L +
Sbjct: 163 SLITGGPGTGKTT-TVARLLLAL 184
>gnl|CDD|179308 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 34.0 bits (79), Expect = 0.12
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 113 CASILRKHGEVVGLPTDFAILDSAESRTIIKQLLK 147
SILRK E G+ A+L E + +IK+L +
Sbjct: 400 ICSILRKAAE-AGIDLLLALLTEEEEKELIKKLAE 433
>gnl|CDD|182800 PRK10875, recD, exonuclease V subunit alpha; Provisional.
Length = 615
Score = 32.2 bits (74), Expect = 0.44
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 17/59 (28%)
Query: 574 MTLHAAKGLEFD-TVFISGWEQGLLPHQLS--INEGNVEGERRLAYVGITRAKKKCHLF 629
MT+H ++G EFD T + LP+Q + + R L Y ITRA+++ L+
Sbjct: 542 MTVHKSQGSEFDHTALV-------LPNQFTPVVT-------RELVYTAITRARRRLSLY 586
>gnl|CDD|148043 pfam06201, PITH, C-terminal proteasome-interacting domain of
thioredoxin-like. This family was formerly known as
DUF1000. The full-length, Txnl1, protein which is a
probable component of the 26S proteasome, uses its
C-terminal, PITH, domain to associate specifically with
the 26S proteasome. PITH derives from
proteasome-interacting thioredoxin domain.
Length = 114
Score = 32.1 bits (74), Expect = 0.46
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 624 KKCHLFYTINRRTHDFTRVERYQPSQVSQFLLELYDPSHTQEIIYD 669
K LF INR DF E +P+Q LEL + I Y
Sbjct: 38 KTIKLF--INRPNLDFDDAESLEPTQT----LELSEDDEEGVIEYP 77
>gnl|CDD|184265 PRK13709, PRK13709, conjugal transfer nickase/helicase TraI;
Provisional.
Length = 1747
Score = 30.9 bits (70), Expect = 1.0
Identities = 25/100 (25%), Positives = 45/100 (45%), Gaps = 12/100 (12%)
Query: 4 DDQKSHFSHILKG--------DFVPSCVPNYLKGLNAQQTHAVTIPDDTPLLILAGAGTG 55
+ +KS HIL+G + VP + L T + D ++ AG G
Sbjct: 937 EAEKSILRHILEGKEAVTPLMERVPGELMEGLTSGQRAATRMILESTDRFTVVQGYAGVG 996
Query: 56 KTTVLIARM--LHLICHKEIPPSKILAMTFTNQAIQEMKN 93
KTT A M ++ + E P +++ + T++A+ EM++
Sbjct: 997 KTTQFRAVMSAVNTLPESERP--RVVGLGPTHRAVGEMRS 1034
>gnl|CDD|129743 TIGR00658, orni_carb_tr, ornithine carbamoyltransferase. Most
OTCases are homotrimers, but the homotrimers are
organized into dodecamers built from four trimers in at
least two species; the catabolic OTCase of Pseudomonas
aeruginosa is allosterically regulated, while OTCase of
the extreme thermophile Pyrococcus furiosus shows both
allostery and thermophily.
Length = 304
Score = 30.8 bits (70), Expect = 1.2
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 10/51 (19%)
Query: 641 RVERYQPSQVSQFLLELYDPS----------HTQEIIYDDIYGTFSEHWNQ 681
R++ ++P QV++ L+EL P +E+ + I G S ++Q
Sbjct: 237 RLKLFRPYQVNEELMELAKPEVIFMHCLPAHRGEEVTDEVIEGPHSIVFDQ 287
>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 30.8 bits (69), Expect = 1.2
Identities = 16/95 (16%), Positives = 29/95 (30%), Gaps = 10/95 (10%)
Query: 45 PLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAM-TFTNQAIQEMKNRLACYLGEKI 103
+LI+ G+GKTT +AR L + + + ++ +
Sbjct: 4 VILIVGPPGSGKTT--LARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 104 PRIQTFHSFCASILRKHGEVVGLPTDFAILDSAES 138
A + +V+ ILD S
Sbjct: 62 SGELRLRLALALARKLKPDVL-------ILDEITS 89
>gnl|CDD|180110 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 30.5 bits (70), Expect = 1.7
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 25/62 (40%)
Query: 34 QTHAVTIPDDTPLLILA-------GAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQ 86
Q T+PD +++LA GA TG H PS+++ M+F NQ
Sbjct: 323 QVDEYTLPDGKRIILLAEGRLVNLGAATG--------------H----PSEVMDMSFANQ 364
Query: 87 AI 88
A+
Sbjct: 365 AL 366
>gnl|CDD|163531 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.
Members of this protein family comprise a distinct
clade of putative ATPase associated with an integral
membrane complex likely to act in pilus formation,
secretion, or conjugal transfer. The association of most
members with a nearby gene for a DEAH-box helicase
suggests a role in conjugal transfer.
Length = 340
Score = 30.4 bits (69), Expect = 1.8
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 44 TPLLILAGAGTGKTTVLIARMLHLICHKE 72
LI G G+GKTT+L A +L L+ E
Sbjct: 179 LAFLISGGTGSGKTTLLSA-LLALVAPDE 206
>gnl|CDD|161840 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006).
Length = 405
Score = 29.8 bits (68), Expect = 2.5
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 11/56 (19%)
Query: 45 PLLILAGAGTGKTTVLIARMLHLICH---KEIPPSKILAMT---FTNQAIQEMKNR 94
PL I G G GKT +LH I + + P +K++ ++ FTN + ++N
Sbjct: 138 PLFIYGGVGLGKT-----HLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNN 188
>gnl|CDD|162119 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704).
Length = 406
Score = 28.9 bits (65), Expect = 4.4
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 27 LKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIA--RMLHLICHKEIPPSKILAMTFT 84
+K L + IL G+ L+A R+++L E PS+++ M+F
Sbjct: 290 VKALEELAVEKRNVRPQVDEYIL---KDGRRIYLLAEGRLVNLAA-AEGHPSEVMDMSFA 345
Query: 85 NQAI 88
NQA+
Sbjct: 346 NQAL 349
>gnl|CDD|129857 TIGR00775, NhaD, Na+/H+ antiporter, NhaD family. These proteins
are members of the NhaD Na+:H+ Antiporter (NhaD) Family
(TC 2.A.62). A single member of the NhaD family has been
characterized. This protein is the NhaD protein of
Vibrio parahaemolyticus which has 12 GES predicted
transmembrane regions. It has been shown to catalyze
Na+/H+ antiport, but Li+ can also be a substrate.
Length = 420
Score = 28.7 bits (64), Expect = 4.6
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 211 GLIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLC 256
GL+ + +H PH K+ H ++P+I+ DI++ + + LL
Sbjct: 254 GLVWLFSDWIHSPHGEKRLHLRVPHILTR--IDISSLTFFIGILLA 297
>gnl|CDD|151205 pfam10712, NAD-GH, NAD-specific glutamate dehydrogenase. The
members of this are annotated as being NAD-specific
glutamate dehydrogenase encoded in antisense gene pair
with DnaK-J. However, this could not be confirmed.
Length = 576
Score = 28.4 bits (64), Expect = 5.8
Identities = 7/38 (18%), Positives = 13/38 (34%), Gaps = 5/38 (13%)
Query: 631 TINRRT--HDFTRVE---RYQPSQVSQFLLELYDPSHT 663
++ F RV+ R ++ LL+L
Sbjct: 201 GLDGGAEGDHFVRVDALVRLLAEELLHLLLDLRHAGLA 238
>gnl|CDD|181748 PRK09275, PRK09275, aspartate aminotransferase; Provisional.
Length = 527
Score = 28.3 bits (64), Expect = 6.1
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 666 IIYDDIYGTFSEHWNQI 682
II DD+YGTF + + +
Sbjct: 279 IITDDVYGTFVDDFRSL 295
>gnl|CDD|163513 TIGR03801, asp_4_decarbox, aspartate 4-decarboxylase. This enzyme,
aspartate 4-decarboxylase (EC 4.1.1.12), removes the
side-chain carboxylate from L-aspartate, converting it
to L-alanine plus carbon dioxide. It is a PLP-dependent
enzyme, homologous to aspartate aminotransferase (EC
2.6.1.1).
Length = 521
Score = 28.4 bits (64), Expect = 6.9
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 666 IIYDDIYGTFSEH 678
I+ DD+YGTF +
Sbjct: 278 ILTDDVYGTFVDD 290
>gnl|CDD|182699 PRK10751, PRK10751, molybdopterin-guanine dinucleotide
biosynthesis protein B; Provisional.
Length = 173
Score = 28.1 bits (63), Expect = 7.7
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 45 PLL-ILAGAGTGKTTVLIARMLHLICHKEIPPSKI 78
PLL I A +GTGKTT L+ +++ +C + I P I
Sbjct: 7 PLLAIAAWSGTGKTT-LLKKLIPALCARGIRPGLI 40
>gnl|CDD|184033 PRK13404, PRK13404, dihydropyrimidinase; Provisional.
Length = 477
Score = 28.1 bits (63), Expect = 7.8
Identities = 14/43 (32%), Positives = 16/43 (37%), Gaps = 4/43 (9%)
Query: 118 RKHGEVVGLPTDFAILDSAESRTIIKQLLKDLQIDDKDYDPHE 160
RK +G D AI D TI L DY P+E
Sbjct: 387 RKGAIAIGADADIAIWDPDREVTITNADLHHAA----DYTPYE 425
>gnl|CDD|130585 TIGR01522, ATPase-IIA2_Ca, golgi membrane calcium-translocating
P-type ATPase. The calcium P-type ATPases have been
characterized as Type IIA based on a phylogenetic
analysis which distinguishes this group from the Type
IIB PMCA calcium pump modelled by TIGR01517. A separate
analysis divides Type IIA into sub-types, SERCA and PMR1
the former of which is modelled by TIGR01116.
Length = 884
Score = 27.9 bits (62), Expect = 9.0
Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 85 NQAIQEMKNRLACYLGEKIPRIQTFHSFC--ASILRKHGEVVGLPTDFAILDSAE 137
+ + L + + RI + C A + ++G PTD A+++
Sbjct: 363 FGEVIVDGDVLHGFYTVAVSRILEAGNLCNNAKFRNEADTLLGNPTDVALIELLM 417
>gnl|CDD|129069 smart00836, DALR_1, DALR anticodon binding domain. This all alpha
helical domain is the anticodon binding domain of
Arginyl tRNA synthetase. This domain is known as the
DALR domain after characteristic conserved amino acids
PUBMED:10447505.
Length = 122
Score = 27.9 bits (63), Expect = 9.1
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 110 HSFCASILRKHGE-VVGLP----TDFAILDSAESRTIIKQLLK---DLQIDDKDYDPH 159
H+ SILRK GE + LP D ++L E +++ L + L+ + +PH
Sbjct: 5 HARICSILRKAGEAGLTLPDIADADLSLLTEPEELALLRLLARFPEVLEAAAETLEPH 62
>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR;
Provisional.
Length = 441
Score = 27.7 bits (61), Expect = 9.2
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 37 AVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQE 90
A+ P + +LI +GTGK L+AR +H + P L N+++ E
Sbjct: 156 ALVAPSEATVLIHGDSGTGKE--LVARAIHASSARSEKPLVTLNCAALNESLLE 207
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.8 bits (62), Expect = 9.7
Identities = 28/137 (20%), Positives = 48/137 (35%), Gaps = 32/137 (23%)
Query: 47 LILAGA-GTGKTTVLIARML-HLICHKEIP-----PSKILAMTFTNQAIQEMKN---RLA 96
+ILA G+GKT + L L K P++ LA + + + + ++
Sbjct: 27 VILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPSLGLKVV 86
Query: 97 CYLG--EKIPRIQTFHSFCASI-------LRKHGEVVGLPT---DFAILD---------- 134
G K +++ S I L E L D ILD
Sbjct: 87 GLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGF 146
Query: 135 SAESRTIIKQLLKDLQI 151
+ ++K L K++Q+
Sbjct: 147 GDQLEKLLKLLPKNVQL 163
>gnl|CDD|183227 PRK11608, pspF, phage shock protein operon transcriptional
activator; Provisional.
Length = 326
Score = 27.7 bits (62), Expect = 10.0
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 41 PDDTPLLILAGAGTGKTTVLIARMLH 66
P D P+LI+ GTGK LIA LH
Sbjct: 27 PLDKPVLIIGERGTGKE--LIASRLH 50
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
0.321 0.136 0.409
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 11,207,175
Number of extensions: 731299
Number of successful extensions: 1659
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1594
Number of HSP's successfully gapped: 62
Length of query: 685
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 585
Effective length of database: 3,833,673
Effective search space: 2242698705
Effective search space used: 2242698705
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: 61 (27.3 bits)