RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2892
(452 letters)
>gnl|CDD|235907 PRK07004, PRK07004, replicative DNA helicase; Provisional.
Length = 460
Score = 751 bits (1941), Expect = 0.0
Identities = 307/452 (67%), Positives = 389/452 (86%), Gaps = 1/452 (0%)
Query: 1 MLVPFNTENKKFRVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHI 60
M P + + + +VPPHSIE+EQSVLGGLLLDN AWD+IAD L+ FYRYDHR+IF+HI
Sbjct: 1 MNAPADPQLESLKVPPHSIEAEQSVLGGLLLDNAAWDRIADFLSQSDFYRYDHRIIFEHI 60
Query: 61 IKLINSSHPADVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGIL 120
+LI ++ PADVITV+++L+ +G AEE+GGL+YLN+LAQN PSAANIRRYAEIVRDR +L
Sbjct: 61 GRLIAATRPADVITVYEALTTSGKAEEVGGLAYLNALAQNTPSAANIRRYAEIVRDRAVL 120
Query: 121 RKLITVTDEISSQAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKR 180
R+L++V DEIS+ AF +GKEV+Q+LDEAESK+FSIAE+ +GF +I PLL +V++R
Sbjct: 121 RRLVSVADEISADAFNPQGKEVRQLLDEAESKVFSIAEEGARGTQGFLEIGPLLTQVVER 180
Query: 181 INKLHNRGTNDNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAI 240
I+ L++ N +DVTG TGF +LD++TSG+ G+LIIVAGRPSMGKTAFS+NIGE++A+
Sbjct: 181 IDTLYHT-ANPSDVTGTPTGFVDLDRMTSGMHGGELIIVAGRPSMGKTAFSMNIGEYVAV 239
Query: 241 ENKLPVAIFSMEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLY 300
E LPVA+FSMEM G QLAMRMLGSVG+LDQH++RTGRL+ +DWP++ +++K++++QL+
Sbjct: 240 EYGLPVAVFSMEMPGTQLAMRMLGSVGRLDQHRMRTGRLTDEDWPKLTHAVQKMSEAQLF 299
Query: 301 IDETPSLNVIELRANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGL 360
IDET LN +ELR+ +RRL+RQCGK+G+IIIDYLQLMS +S+GENRATEISEISR+LK L
Sbjct: 300 IDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSL 359
Query: 361 AKEINCPILALSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADK 420
AKE++ P++ALSQLNR LEQR NKRP+MSDLRESGAIEQDADVILFIYRDEVYN +S DK
Sbjct: 360 AKELDVPVIALSQLNRGLEQRPNKRPVMSDLRESGAIEQDADVILFIYRDEVYNPDSPDK 419
Query: 421 GIAEIIVSKQRNGPIGNIRLTFSGQYTKFNNF 452
G AEII+ KQRNGPIG +RLTF GQYTKF+NF
Sbjct: 420 GTAEIIIGKQRNGPIGPVRLTFLGQYTKFDNF 451
>gnl|CDD|233080 TIGR00665, DnaB, replicative DNA helicase. This model describes
the helicase DnaB, a homohexameric protein required for
DNA replication. The homohexamer can form a ring around
a single strand of DNA near a replication fork. An
intein of > 400 residues is found at a conserved
location in DnaB of Synechocystis PCC6803, Rhodothermus
marinus (both experimentally confirmed), and
Mycobacterium tuberculosis. The intein removes itself by
a self-splicing reaction. The seed alignment contains
inteins so that the model built from the seed alignment
will model a low cost at common intein insertion sites
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 434
Score = 681 bits (1760), Expect = 0.0
Identities = 241/438 (55%), Positives = 324/438 (73%), Gaps = 7/438 (1%)
Query: 14 VPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADVI 73
VPPH+IE+EQ+VLG +LLDN A D +A+ L + FYR H+LIF+ I+ L P D++
Sbjct: 1 VPPHNIEAEQAVLGAILLDNEAIDDVAEILKPEDFYRPAHQLIFEAILDLYEKGEPIDLV 60
Query: 74 TVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISSQ 133
TV + L G EE+GGL+YL LA N+PSAANI YAEIV+++ ILR+LI EI
Sbjct: 61 TVKEELEKDGQLEEVGGLAYLAELADNVPSAANIEYYAEIVKEKAILRRLIQAGTEIVEL 120
Query: 134 AFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRGTNDND 193
A+ +V+++LDEAE KIF IAE + GF+ I+ +L ++ I +L+
Sbjct: 121 AY-DPEGDVEELLDEAEQKIFEIAESRT--SGGFKSIKEVLKETVEEIEELYE---RKGG 174
Query: 194 VTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEM 253
+TG+ TGF +LDK+TSGLQP DLII+A RPSMGKTAF+LNI E+ AI+ PVA FS+EM
Sbjct: 175 ITGVPTGFTDLDKLTSGLQPSDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLEM 234
Query: 254 SGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELR 313
S QL MRML S ++D KLRTG+LS +DW ++ + K++++ LYID+TP L + ELR
Sbjct: 235 SAEQLVMRMLSSESRVDSQKLRTGKLSDEDWEKLTSAAGKLSEAPLYIDDTPGLTITELR 294
Query: 314 ANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALSQ 373
A +RRL R+ G +G+I+IDYLQLMS + R ENR E+SEISR+LK LAKE+N P++ALSQ
Sbjct: 295 AKARRLKREHG-LGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKELNVPVIALSQ 353
Query: 374 LNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQRNG 433
L+RS+EQR++KRP +SDLRESG+IEQDAD+++F+YRDE YN +S DKGIAEII++KQRNG
Sbjct: 354 LSRSVEQREDKRPQLSDLRESGSIEQDADIVMFLYRDEYYNPDSEDKGIAEIIIAKQRNG 413
Query: 434 PIGNIRLTFSGQYTKFNN 451
P G ++L F G+YT+F N
Sbjct: 414 PTGTVKLAFQGEYTRFEN 431
>gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional.
Length = 448
Score = 628 bits (1623), Expect = 0.0
Identities = 225/441 (51%), Positives = 321/441 (72%), Gaps = 9/441 (2%)
Query: 13 RVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADV 72
RVPP SIE+EQ+VLG + LD A +++ L+ D FYR+ HRLIF+ ++KL + P DV
Sbjct: 8 RVPPQSIEAEQAVLGAIFLDPDALITVSEYLSPDDFYRHAHRLIFRAMLKLSDRGEPIDV 67
Query: 73 ITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISS 132
+TV + L + G+ EE+GGLSYL LA ++P+AANI YA+IV ++ +LR+LI EI++
Sbjct: 68 VTVTEILDDQGDLEEVGGLSYLAELANSVPTAANIEYYAKIVAEKAMLRRLIRTATEIAN 127
Query: 133 QAFISRGKEVKQILDEAESKIFSIAEKEICINK-GFQQIQPLLNRVIKRINKLHNRGTND 191
A+ + +ILDEAE KIF ++E+ NK GF+ I+ +L + RI LHN+
Sbjct: 128 DAY-EPEDDADEILDEAEKKIFEVSERR---NKSGFKNIKDVLVKAYDRIEMLHNQ---T 180
Query: 192 NDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSM 251
D+TGI TGF +LDK+TSGLQP DLIIVA RPS+GKTAF+LNI +++A + VAIFS+
Sbjct: 181 GDITGIPTGFTDLDKMTSGLQPNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSL 240
Query: 252 EMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIE 311
EM L MRML + G +D +LRTG+L+ DDWP++ ++ ++ + +YID+TP + V E
Sbjct: 241 EMGAESLVMRMLCAEGNIDAQRLRTGQLTDDDWPKLTIAMGSLSDAPIYIDDTPGIKVTE 300
Query: 312 LRANSRRLSRQCGKIGVIIIDYLQLMSANSR-GENRATEISEISRNLKGLAKEINCPILA 370
+RA RRL+++ G +G+I+IDYLQL+ + R GENR E+SEISR+LK LAKE+ P++A
Sbjct: 301 IRARCRRLAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKELKVPVIA 360
Query: 371 LSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQ 430
LSQL+R +EQRQ+KRP+MSD+RESG+IEQDAD++ F+YRD+ Y++ + +K EII++KQ
Sbjct: 361 LSQLSRGVEQRQDKRPVMSDIRESGSIEQDADIVAFLYRDDYYDEETENKNTIEIIIAKQ 420
Query: 431 RNGPIGNIRLTFSGQYTKFNN 451
RNGP+G + L F +Y KF N
Sbjct: 421 RNGPVGTVELAFQKEYNKFVN 441
>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 545 bits (1407), Expect = 0.0
Identities = 212/439 (48%), Positives = 307/439 (69%), Gaps = 7/439 (1%)
Query: 13 RVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADV 72
R+PP IE+EQ+VLGG+LLD A +++++ L + FYR HRLI++ I+ L P D+
Sbjct: 1 RLPPQDIEAEQAVLGGILLDPDAIERVSERLRPEDFYRPAHRLIYQAILDLYGQGEPIDL 60
Query: 73 ITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISS 132
+TV + LS+ G IGG +YL +L PSAANI YA+IV+++ +LR+LI +EI +
Sbjct: 61 VTVSEELSDRGLLTRIGGANYLATLIDRTPSAANIDYYAKIVKEKALLRELIEAGNEIVN 120
Query: 133 QAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRGTNDN 192
+ S +++LD AE KIF +AE++ ++ F I LL + I G
Sbjct: 121 LGYESEKDLDEEVLDAAEKKIFDVAERKN--SEDFVHIGDLLKETMDEIEARFENG---- 174
Query: 193 DVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSME 252
+ G+ TGF +LD+ITSG +PGDLIIVA RP MGKTA +LNI + A + + PVAIFS+E
Sbjct: 175 GLIGVPTGFTDLDEITSGFRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAIFSLE 234
Query: 253 MSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIEL 312
MS QL MR+L S ++ KLRTGRLS D+W R+ + +++++ ++ID+TP L + E+
Sbjct: 235 MSEEQLVMRLLSSESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFIDDTPGLTITEI 294
Query: 313 RANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALS 372
R+ +RRL + +G+I+IDYLQLM+ + ENR E+SEISR+LKGLAKE+ P++ALS
Sbjct: 295 RSKARRLKLKHN-LGLIVIDYLQLMTGGKKSENRKQEVSEISRSLKGLAKELGVPVIALS 353
Query: 373 QLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQRN 432
QLNRS+EQR +KRP++SDLRESGA+EQDAD+++F++RDE Y +++ D+G AE+IV+K RN
Sbjct: 354 QLNRSVEQRTDKRPMLSDLRESGALEQDADIVIFLHRDEAYLKDTPDRGEAEVIVAKNRN 413
Query: 433 GPIGNIRLTFSGQYTKFNN 451
GP G ++L F Q+TKF N
Sbjct: 414 GPTGTVKLAFDPQFTKFKN 432
>gnl|CDD|181562 PRK08840, PRK08840, replicative DNA helicase; Provisional.
Length = 464
Score = 484 bits (1248), Expect = e-170
Identities = 226/450 (50%), Positives = 323/450 (71%), Gaps = 3/450 (0%)
Query: 4 PFNTENKKFRVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKL 63
+ + +VPPHS+E+EQSV+GGLLLDN WD +A+ + + FY HRLIF+ + +
Sbjct: 9 IPDAQVDAIKVPPHSLEAEQSVIGGLLLDNERWDTVAEKVVASDFYSRPHRLIFEGVKSI 68
Query: 64 INSSHPADVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKL 123
+ + P D+IT+ + L E++GG +YL LA+N PSAANI YA+IV +R ++R L
Sbjct: 69 LEAGKPLDLITLSEHLERREQLEDVGGFAYLADLAKNTPSAANINAYADIVAERALVRNL 128
Query: 124 ITVTDEISSQAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINK 183
I V +EI+ + +G+ + +LD AESK+F+IAE N+G Q + +L + ++RI
Sbjct: 129 IGVANEIADAGYDPQGRTSEDLLDMAESKVFAIAEARTSENEGPQNVDSILEKTLERIEL 188
Query: 184 LHNRGTNDNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENK 243
L+ T + VTG+ TGF +L+K T+GLQ DLIIVA RPSMGKT F++N+ E+ A++
Sbjct: 189 LYK--TPQDGVTGVDTGFTDLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQD 246
Query: 244 LPVAIFSMEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKI-NKSQLYID 302
PV IFS+EM QL MRML S+ ++DQ K+RTG+L +DW RI+ ++ + K +YID
Sbjct: 247 KPVLIFSLEMPAEQLMMRMLASLSRVDQTKIRTGQLDDEDWARISSTMGILMEKKNMYID 306
Query: 303 ETPSLNVIELRANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAK 362
++ L E+R+ +RR++R+ G + +I++DYLQLM + +NR EI+EISR+LK LAK
Sbjct: 307 DSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLKALAK 366
Query: 363 EINCPILALSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGI 422
E+N P++ALSQLNRSLEQR +KRP+ SDLRESG+IEQDAD+I+FIYRDEVYN +S KG
Sbjct: 367 ELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEVYNPDSPLKGT 426
Query: 423 AEIIVSKQRNGPIGNIRLTFSGQYTKFNNF 452
AEII+ KQRNGPIG++RLTF GQY++F+N+
Sbjct: 427 AEIIIGKQRNGPIGSVRLTFQGQYSRFDNY 456
>gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional.
Length = 476
Score = 483 bits (1245), Expect = e-169
Identities = 226/443 (51%), Positives = 310/443 (69%), Gaps = 5/443 (1%)
Query: 11 KFRVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPA 70
+ RVPPHS+E+EQ+VLGGL+L A D++ D L + FYR DHRLI++ I +L P
Sbjct: 29 QLRVPPHSVEAEQAVLGGLMLAPDALDRVNDQLTENDFYRRDHRLIYRAIRELSEKDRPF 88
Query: 71 DVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEI 130
D +T+ + + G E++G +YL LA PSAANI YAEIVRD+ +LR+LI V I
Sbjct: 89 DAVTLGEWFESQGKLEQVGDGAYLIELASTTPSAANIAAYAEIVRDKAVLRQLIEVGTTI 148
Query: 131 SSQAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRGTN 190
+ F G+E ++L AE +F IAE F + L + +L NR N
Sbjct: 149 VNDGFQPEGRESIELLASAEKAVFKIAEAGARGRTDFVAMPGALKDAFE---ELRNRFEN 205
Query: 191 DNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFS 250
++TG+ TG+ + D +T+GLQP DLII+A RP+MGKT F+LNI E+ AI++K VA+FS
Sbjct: 206 GGNITGLPTGYNDFDAMTAGLQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFS 265
Query: 251 MEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVI 310
MEMS QLAMR++ S G+++ +LRTG L +DW R+ +IK + +++++ID+TP ++
Sbjct: 266 MEMSASQLAMRLISSNGRINAQRLRTGALEDEDWARVTGAIKMLKETKIFIDDTPGVSPE 325
Query: 311 ELRANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILA 370
LR+ RRL R+ +G+I+IDYLQLMS ENRATEISEISR+LKGLAKE+N P++A
Sbjct: 326 VLRSKCRRLKRE-HDLGLIVIDYLQLMSVPGNSENRATEISEISRSLKGLAKELNVPVIA 384
Query: 371 LSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQ-NSADKGIAEIIVSK 429
LSQLNRSLE R +KRP+M+DLRESGAIEQDAD+I+FIYRD+ YN+ NS DKG+AEII+ K
Sbjct: 385 LSQLNRSLETRTDKRPVMADLRESGAIEQDADMIVFIYRDDYYNKENSPDKGLAEIIIGK 444
Query: 430 QRNGPIGNIRLTFSGQYTKFNNF 452
R GP G+ +L F G+YT+F+N
Sbjct: 445 HRGGPTGSCKLKFFGEYTRFDNL 467
>gnl|CDD|136106 PRK06904, PRK06904, replicative DNA helicase; Validated.
Length = 472
Score = 477 bits (1229), Expect = e-167
Identities = 230/442 (52%), Positives = 323/442 (73%), Gaps = 4/442 (0%)
Query: 14 VPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADVI 73
+PPHSIE+EQ+VLGG++LDN WD +A+ + +D FY ++HR+IF+ + L + P D++
Sbjct: 22 IPPHSIEAEQAVLGGIMLDNRHWDSVAERVIADDFYTFEHRIIFQEMELLFRQNTPIDLL 81
Query: 74 TVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISSQ 133
T+ +L G ++E+GG +YL L+ N PSAANI YA+IVR++ ILR+LI+V + I+
Sbjct: 82 TLDQALKTKGKSDEVGGFAYLAELSNNTPSAANILAYADIVREKAILRELISVGNNIAKN 141
Query: 134 AFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRGTNDND 193
A+ +G+++K ILDEAE +FSIAEK N+G Q + LL I +I L TN N
Sbjct: 142 AYSPKGQDIKDILDEAERDVFSIAEKRTTANEGPQNVINLLENTIDKIENLAATPTN-NG 200
Query: 194 VTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEM 253
VTG++TGF +LDK T+GLQP DLIIVA RPSMGKT F++N+ E+ A+ ++ PV +FS+EM
Sbjct: 201 VTGVTTGFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLEM 260
Query: 254 SGIQLAMRMLGSVGKLDQHKLRTGR-LSSDDWPRINDSIKKIN-KSQLYIDETPSLNVIE 311
Q+ MRML S+ ++DQ K+RTG+ L DW +I+ ++ K LYID++ L E
Sbjct: 261 PAEQIMMRMLASLSRVDQTKIRTGQNLDQQDWAKISSTVGMFKQKPNLYIDDSSGLTPTE 320
Query: 312 LRANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILAL 371
LR+ +RR+ R+ G + +I++DYLQLM A +NR EI+EISR+LK LAKE+ P++AL
Sbjct: 321 LRSRARRVYRENGGLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKELKVPVVAL 380
Query: 372 SQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSAD-KGIAEIIVSKQ 430
SQLNR+LE R +KRP+ SDLRESG+IEQDAD+I+FIYRDEVYN+ + D KG+AEII+ KQ
Sbjct: 381 SQLNRTLENRGDKRPVNSDLRESGSIEQDADLIMFIYRDEVYNETTEDNKGVAEIIIGKQ 440
Query: 431 RNGPIGNIRLTFSGQYTKFNNF 452
RNGPIG +RL F GQY++F+N
Sbjct: 441 RNGPIGRVRLAFQGQYSRFDNL 462
>gnl|CDD|181193 PRK08006, PRK08006, replicative DNA helicase; Provisional.
Length = 471
Score = 476 bits (1225), Expect = e-166
Identities = 226/450 (50%), Positives = 326/450 (72%), Gaps = 3/450 (0%)
Query: 4 PFNTENKKFRVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKL 63
+ + +VPPHSIE+EQSVLGGL+LDN WD +A+ + +D FY HR IF + +L
Sbjct: 16 ERDPQVAGLKVPPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARL 75
Query: 64 INSSHPADVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKL 123
S P D+IT+ +SL G + +GG +YL L++N PSAANI YA+IVR+R ++R++
Sbjct: 76 QESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRERAVVREM 135
Query: 124 ITVTDEISSQAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINK 183
I+V +EI+ + +G+ + +LD AES++F IAE ++G + I +L+ + RI +
Sbjct: 136 ISVANEIADAGYDPQGRTSEDLLDLAESRVFQIAESRANKDEGPKNIADILDATVARIEQ 195
Query: 184 LHNRGTNDNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENK 243
L + + VTG++TG+ +L+K T+GLQP DLIIVA RPSMGKT F++N+ E+ A+
Sbjct: 196 LFQQ--PHDGVTGVNTGYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMLQD 253
Query: 244 LPVAIFSMEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIK-KINKSQLYID 302
PV IFS+EM G Q+ MRML S+ ++DQ ++RTG+L +DW RI+ ++ + K +YID
Sbjct: 254 KPVLIFSLEMPGEQIMMRMLASLSRVDQTRIRTGQLDDEDWARISGTMGILLEKRNMYID 313
Query: 303 ETPSLNVIELRANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAK 362
++ L E+R+ +RR+ R+ G + +I+IDYLQLM S +NR EI+EISR+LK LAK
Sbjct: 314 DSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALAK 373
Query: 363 EINCPILALSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGI 422
E+ P++ALSQLNRSLEQR +KRP+ SDLRESG+IEQDAD+I+FIYRDEVY++NS KGI
Sbjct: 374 ELQVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEVYHENSDLKGI 433
Query: 423 AEIIVSKQRNGPIGNIRLTFSGQYTKFNNF 452
AEII+ KQRNGPIG +RLTF+GQ+++F+N+
Sbjct: 434 AEIIIGKQRNGPIGTVRLTFNGQWSRFDNY 463
>gnl|CDD|235525 PRK05595, PRK05595, replicative DNA helicase; Provisional.
Length = 444
Score = 437 bits (1126), Expect = e-151
Identities = 202/439 (46%), Positives = 299/439 (68%), Gaps = 7/439 (1%)
Query: 13 RVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADV 72
R P SIE+EQSVLG +++D T+ + A+ L S+ FYR H++IF II+L D+
Sbjct: 6 RSLPQSIEAEQSVLGAMIIDKTSIAEAAEVLKSEDFYRDSHKVIFSAIIELYQKDIAVDM 65
Query: 73 ITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISS 132
+T+ ++L +T E GG++Y+ L+ +I S ANI+ Y +IV+D+ LR+LI + EI
Sbjct: 66 LTLTENLKSTDKLEAAGGVTYITELSNSIVSTANIQSYIKIVKDKSTLRRLIKSSTEIIE 125
Query: 133 QAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRGTNDN 192
++ + +V++++D AE KIF I+EK F+ + +L R ++I L N N
Sbjct: 126 NSY-NNQDDVEKVIDSAEKKIFDISEKRT--TSDFEPLSNVLERGFEQIENLFN---NKG 179
Query: 193 DVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSME 252
+ TG+++GF ELD TSG Q GD+I++A RPSMGKT F+LNI E+ A+ VAIFS+E
Sbjct: 180 ETTGVASGFRELDAKTSGFQKGDMILIAARPSMGKTTFALNIAEYAALREGKSVAIFSLE 239
Query: 253 MSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIEL 312
MS QLA ++L S +D +LRTG L DW I + + ++++ID+T ++V+E+
Sbjct: 240 MSKEQLAYKLLCSEANVDMLRLRTGNLEDKDWENIARASGPLAAAKIFIDDTAGVSVMEM 299
Query: 313 RANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALS 372
R+ RRL + G I +I+IDYLQLMS E+R E+SEISR++K LAKE+ CP++ALS
Sbjct: 300 RSKCRRLKIEHG-IDMILIDYLQLMSGGKGSESRQQEVSEISRSIKALAKEMECPVIALS 358
Query: 373 QLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQRN 432
QL+R+ EQR + RP++SDLRESG+IEQDADV++F+YRDE YN+ + DK +AE I++KQRN
Sbjct: 359 QLSRAPEQRADHRPMLSDLRESGSIEQDADVVMFLYRDEYYNKETEDKNVAECIIAKQRN 418
Query: 433 GPIGNIRLTFSGQYTKFNN 451
GP G ++L + GQY+KF N
Sbjct: 419 GPTGTVKLAWLGQYSKFGN 437
>gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional.
Length = 497
Score = 428 bits (1104), Expect = e-147
Identities = 179/478 (37%), Positives = 284/478 (59%), Gaps = 39/478 (8%)
Query: 8 ENKKFRVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSS 67
+ R PH+IE+EQ++LG +L++N A D+++D L ++F+ H+ I++ I K+I
Sbjct: 14 AEPEIRELPHNIEAEQALLGAILINNRALDRVSDFLKPEHFFEPLHQRIYEAIAKIIRKG 73
Query: 68 HPADVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVT 127
A +T+ L N E+GG+ YL LA + N R Y I+ D + R+LI +
Sbjct: 74 KLATPVTLKTFLENDEALGELGGVQYLAKLATEAVTIINARDYGRIIYDLALRRELINIG 133
Query: 128 DEISSQAFISR-GKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHN 186
+++ + A+ + ++ +++AE K++ +AE GFQ + + N
Sbjct: 134 EDVVNNAYDAPVDVAPQEQIEDAEQKLYELAETGR-YEGGFQSFGTAITEAVDMANAAFK 192
Query: 187 RGTNDNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIA------- 239
R D ++GISTG +LD GL P DLII+AGRPSMGKTA + NI + A
Sbjct: 193 R---DGHLSGISTGLRDLDSKLGGLHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREA 249
Query: 240 -------IENKLPVAIFSMEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIK 292
N V FS+EMS QLA R+L ++ K+R G++S +D+ ++ D+ +
Sbjct: 250 QPDGSKKAVNGGVVGFFSLEMSAEQLATRILSEQSEISSSKIRRGKISEEDFEKLVDASQ 309
Query: 293 KINKSQLYIDETPSLNVIELRANSRRLSRQCGKIGVIIIDYLQLMSANSR--GENRATEI 350
++ K LYID+TP+L++ +LRA +RRL RQ G + ++++DYLQL+ +S+ +NR EI
Sbjct: 310 ELQKLPLYIDDTPALSISQLRARARRLKRQHG-LDLLVVDYLQLIRGSSKRSSDNRVQEI 368
Query: 351 SEISRNLKGLAKEINCPILALSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRD 410
SEI++ LK LAKE+N P++ALSQL+R +EQR +KRP +SDLRESG+IEQDADV++F+YR+
Sbjct: 369 SEITQGLKALAKELNIPVIALSQLSRQVEQRDDKRPQLSDLRESGSIEQDADVVMFVYRE 428
Query: 411 EVYNQNSADK-----------------GIAEIIVSKQRNGPIGNIRLTFSGQYTKFNN 451
E Y + + AE+I++KQR+GP G ++L F ++T+F +
Sbjct: 429 EYYLKRKEPREGTPKHEEWQEKMEKVHNKAEVIIAKQRHGPTGTVKLAFESEFTRFGD 486
>gnl|CDD|213836 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
HK022 subfamily. Members of this family are phage (or
prophage-region) homologs of the bacterial homohexameric
replicative helicase DnaB. Some phage may rely on host
DnaB, while others encode their own verions. This model
describes the largest phage-specific clade among the
close homologs of DnaB, but there are, or course, other
DnaB homologs from phage that fall outside the scope of
this model [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 420
Score = 419 bits (1079), Expect = e-144
Identities = 181/426 (42%), Positives = 282/426 (66%), Gaps = 7/426 (1%)
Query: 18 SIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADVITVFD 77
SIE+EQ+VLGGLLLDN +++ L ++FY DHR+IF+ ++ + ++ P D +T+ D
Sbjct: 1 SIEAEQAVLGGLLLDNDFIERVMAILKPEHFYSQDHRIIFEAMLDMFAANRPVDPLTLAD 60
Query: 78 SLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISSQAFIS 137
L G AE++GGL+YL ++ N PSAANI YA IVR++ RKLI I A
Sbjct: 61 KLEAEGEAEKVGGLAYLAEISNNTPSAANISSYARIVREKAKERKLIAACQRIIDLACSD 120
Query: 138 RGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINK-LHNRGTNDNDVTG 196
G+ +Q ++EA++ + ++ + +GF +L VI+ ++K + +G ++TG
Sbjct: 121 GGQTAEQKVEEAQAALLALTMSD-GQERGFVTFGEVLEDVIRDLDKRFNPKG----ELTG 175
Query: 197 ISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGI 256
+STG +LD++T+GL GDLI++ RPSMGKT +LNI E++A+ PV FS+EMS
Sbjct: 176 LSTGLPKLDRLTNGLVKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEMSAE 235
Query: 257 QLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELRANS 316
QL R+L S ++ +RTGR + ++ R+ +++ ++++ LYID+T L V ++R+ +
Sbjct: 236 QLGERLLASKSGINTGNIRTGRFNDSEFNRLLNAVDRLSEKDLYIDDTGGLTVAQIRSIA 295
Query: 317 RRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALSQLNR 376
RR+ R+ G + +I++DY+QLM A +RG +R E+ ISR LK LAKE++ P++ L+QLNR
Sbjct: 296 RRIKRKKGGLDLIVVDYIQLM-APARGRDRNEELGGISRGLKALAKELDVPVVLLAQLNR 354
Query: 377 SLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQRNGPIG 436
E+R +KRPIMSDLR+SGAIEQDADVI I+R+ Y+ G+AE+I++K R+GP G
Sbjct: 355 GSEKRTDKRPIMSDLRDSGAIEQDADVIGLIHREGYYDAREPPAGVAELILAKNRHGPTG 414
Query: 437 NIRLTF 442
+ L F
Sbjct: 415 TVELLF 420
>gnl|CDD|236093 PRK07773, PRK07773, replicative DNA helicase; Validated.
Length = 886
Score = 427 bits (1100), Expect = e-142
Identities = 168/393 (42%), Positives = 256/393 (65%), Gaps = 7/393 (1%)
Query: 13 RVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADV 72
R PP + +EQSVLGG+LL A ++ + L FYR H+ I+ I+ L PAD+
Sbjct: 22 RQPPQDLAAEQSVLGGMLLSKEAIARVLERLRPGAFYRPAHQNIYDAILDLYGRGEPADL 81
Query: 73 ITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISS 132
+TV L G E IGG YL++L +P+AAN YA IV ++ +LR+LI I
Sbjct: 82 VTVAAELDRRGLLERIGGAPYLHTLISTVPTAANADYYARIVAEKALLRRLIEAGTRIVQ 141
Query: 133 QAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRGTNDN 192
+ + G +V +++D A+++I+ + ++ + ++ F ++ LL I+ + + G
Sbjct: 142 YGY-AEGADVAEVVDRAQAEIYDVTDRRL--SEDFVALEDLLQPTFDEIDAIASSGGL-- 196
Query: 193 DVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSME 252
G+ TGF ELD +T+GL PG LIIVA RPSMGKT F L+ + AI ++L VAIFS+E
Sbjct: 197 -ARGVPTGFTELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSLE 255
Query: 253 MSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIEL 312
MS QL MR+L + K+ +R+GR+S DDW R+ ++ +I+++ ++ID+TP+L V+E+
Sbjct: 256 MSKEQLVMRLLSAEAKIKLSDMRSGRMSDDDWTRLARAMGEISEAPIFIDDTPNLTVMEI 315
Query: 313 RANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALS 372
RA +RRL RQ +G+I++DYLQLM++ + ENR E+SEISR+LK LAKE+ P++ALS
Sbjct: 316 RAKARRL-RQEANLGLIVVDYLQLMTSGKKYENRQQEVSEISRHLKLLAKELEVPVVALS 374
Query: 373 QLNRSLEQRQNKRPIMSDLRESGAIEQDADVIL 405
QL+R +EQR +KRP++SDLRESG + D ++
Sbjct: 375 QLSRGVEQRTDKRPMLSDLRESGCLTGDTLILR 407
Score = 89.0 bits (221), Expect = 8e-19
Identities = 25/56 (44%), Positives = 37/56 (66%)
Query: 396 AIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQRNGPIGNIRLTFSGQYTKFNN 451
+IEQDADV++ +YR + Y+++ G AE IV+K RNGP G + L F ++F N
Sbjct: 827 SIEQDADVVILLYRPDYYDRDDPRGGEAEFIVAKHRNGPTGTVTLAFQLHLSRFAN 882
>gnl|CDD|217733 pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerisation of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This C-terminal domain contains an ATP-binding
site and is therefore probably the site of ATP
hydrolysis.
Length = 260
Score = 389 bits (1003), Expect = e-135
Identities = 142/258 (55%), Positives = 198/258 (76%), Gaps = 3/258 (1%)
Query: 196 GISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSG 255
G+ TGF +LD++T GLQ GDLII+A RPSMGKTAF+LNI +IA+ PV FS+EMS
Sbjct: 1 GLPTGFTDLDQLTGGLQKGDLIIIAARPSMGKTAFALNIARNIALRQGKPVLFFSLEMSA 60
Query: 256 IQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELRAN 315
QLA R+L + + KLR+G LS +DW R+ ++ ++++ LYID+TP L++ E+RA
Sbjct: 61 EQLAERLLSAESGISSTKLRSGNLSDEDWERLAEAAGELSELPLYIDDTPGLSLSEIRAK 120
Query: 316 SRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALSQLN 375
+RRL R+ +G+I+IDYLQLM + + ENR EISEISR+LK LAKE+N P++ALSQL+
Sbjct: 121 ARRLKRE-HNLGLIVIDYLQLMQGSKKSENRQQEISEISRSLKALAKELNIPVIALSQLS 179
Query: 376 RSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYN--QNSADKGIAEIIVSKQRNG 433
R++EQR +KRP++SDLRESG+IEQDAD+++F+YRDE Y+ +++ G AEII++K RNG
Sbjct: 180 RAVEQRPDKRPMLSDLRESGSIEQDADIVMFLYRDEYYDKEEDNKPYGEAEIIIAKNRNG 239
Query: 434 PIGNIRLTFSGQYTKFNN 451
P G + LTF+G YT+F N
Sbjct: 240 PTGTVTLTFNGWYTRFVN 257
>gnl|CDD|236278 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 370 bits (953), Expect = e-125
Identities = 174/456 (38%), Positives = 266/456 (58%), Gaps = 35/456 (7%)
Query: 17 HSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADVITVF 76
+ ++ E++VL +L +++IA L FY H+ IF+ ++KL N P D +
Sbjct: 5 YDLDIERAVLSSILFSPDKFEEIASVLEPKDFYLPAHQDIFEAMLKLHNEDEPIDEEFIR 64
Query: 77 DSLSNTGN-AEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISSQAF 135
L EEI L LA N NI Y E ++++ I R+L+++ + I QA
Sbjct: 65 KKLPKDKKIDEEI----LLEILATN--PIDNIEAYVEEIKEKSIKRELLSLANTIPEQA- 117
Query: 136 ISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRGTNDNDVT 195
+ ++ ILDE E +++SI ++ F+ + ++ ++ I K G + D+
Sbjct: 118 VEEDQKSSDILDEVERELYSITNGSN--SEDFKDSKEVIESTMEHIKKQKRLG--NKDII 173
Query: 196 GISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSG 255
G+ TGF EL+K+T G GDLII+A RPSMGKT LN+ + VA FS+EM
Sbjct: 174 GLDTGFVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMALKA-LNQDKGVAFFSLEMPA 232
Query: 256 IQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELRAN 315
QL +RML + + LRTG L D+W R++D+ +++K +L++ ++ +N+ ++RA
Sbjct: 233 EQLMLRMLSAKTSIPLQNLRTGDLDDDEWERLSDACDELSKKKLFVYDSGYVNIHQVRAQ 292
Query: 316 SRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALSQLN 375
R+L Q +IG+ +IDYLQLMS + ++R +ISEISR LK LA+E++ PI+ALSQLN
Sbjct: 293 LRKLKSQHPEIGLAVIDYLQLMSGSGNFKDRHLQISEISRGLKLLARELDIPIIALSQLN 352
Query: 376 RSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYN--------QNSADKGI----- 422
RSLE R +KRP++SDLRESGAIEQDAD+ILF+YRD+VY + + +G
Sbjct: 353 RSLESRADKRPMLSDLRESGAIEQDADIILFVYRDDVYKEREEKEKEKKAKKEGKEERRI 412
Query: 423 ---------AEIIVSKQRNGPIGNIRLTFSGQYTKF 449
AEII+ K RNGP G ++L F ++T+F
Sbjct: 413 HFQNKSIEEAEIIIGKNRNGPTGTVKLRFQKEFTRF 448
>gnl|CDD|238484 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric
helicase DnaB unwinds the DNA duplex at the chromosome
replication fork. Although the mechanism by which DnaB
both couples ATP hydrolysis to translocation along DNA
and denatures the duplex is unknown, a change in the
quaternary structure of the protein involving
dimerization of the N-terminal domain has been observed
and may occur during the enzymatic cycle. This
C-terminal domain contains an ATP-binding site and is
therefore probably the site of ATP hydrolysis.
Length = 242
Score = 361 bits (930), Expect = e-124
Identities = 136/242 (56%), Positives = 184/242 (76%), Gaps = 1/242 (0%)
Query: 203 ELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGIQLAMRM 262
+LD +T GLQPGDLII+A RPSMGKTAF+LNI E+IA + PV FS+EMS QL R+
Sbjct: 2 DLDNLTGGLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQRL 61
Query: 263 LGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELRANSRRLSRQ 322
L S + KLRTG LS +DW R+ ++I ++ + +YID++ SL V ++R+ +RRL ++
Sbjct: 62 LASESGISLSKLRTGSLSDEDWERLAEAIGELKELPIYIDDSSSLTVSDIRSRARRLKKE 121
Query: 323 CGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALSQLNRSLEQRQ 382
+G+I+IDYLQLMS + + NR E++EISR+LK LAKE+N P++ALSQL+R +E R
Sbjct: 122 -HGLGLIVIDYLQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQLSRGVESRA 180
Query: 383 NKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQRNGPIGNIRLTF 442
+KRP++SDLRESG+IEQDADV++F+YRDE YN+ S KGIAEIIV+K RNGP G + L F
Sbjct: 181 DKRPMLSDLRESGSIEQDADVVMFLYRDEYYNKESESKGIAEIIVAKNRNGPTGTVELRF 240
Query: 443 SG 444
G
Sbjct: 241 DG 242
>gnl|CDD|180528 PRK06321, PRK06321, replicative DNA helicase; Provisional.
Length = 472
Score = 356 bits (915), Expect = e-119
Identities = 183/462 (39%), Positives = 275/462 (59%), Gaps = 20/462 (4%)
Query: 7 TENKKFRVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINS 66
+ + PP+S ESE VLG +L + A+ L D FY +H++IF+ + S
Sbjct: 8 PQPTQLLSPPNSKESEMIVLGCMLTSVNYLNLAANQLQEDDFYFLEHKIIFRVLQDAFKS 67
Query: 67 SHPADVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITV 126
P DV + L IGG SYL +LA+ ++A I YAEI+R + ILRK+I
Sbjct: 68 DKPIDVHLAGEELKRRNQLNVIGGPSYLITLAEFAGTSAYIEEYAEIIRSKSILRKMIQT 127
Query: 127 TDEISSQAFISRGKEVKQILDEAESKIFSIAE----------KEICINKGFQQIQPLLNR 176
EI +A + K+V LDEA++ +F I++ + + +P L +
Sbjct: 128 AKEIEKKA-LEEPKDVATALDEAQNLLFKISQTTNLAQYVLVADKLKGLTSSKDKPFLLQ 186
Query: 177 VIKRINKL--HNRGTNDNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNI 234
+ +R +G + ++GI T F +LDK+ +G P +L+I+A RP+MGKTA +LNI
Sbjct: 187 LQERQEAFQQSAQGDSSPMISGIPTHFIDLDKMINGFSPSNLMILAARPAMGKTALALNI 246
Query: 235 GEHIAIENKLPVAIFSMEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKI 294
E+ +N+LPV IFS+EM+ QL R++ S +++ K+ G LS D+ RI + ++
Sbjct: 247 AENFCFQNRLPVGIFSLEMTVDQLIHRIICSRSEVESKKISVGDLSGRDFQRIVSVVNEM 306
Query: 295 NKSQLYIDETPSLNVIELRANSRRLSRQCGKIGVIIIDYLQLMSA---NSRGENRATEIS 351
+ L ID+ P L + +LRA +RR+ ++ I +IIDYLQL+S E+R TEIS
Sbjct: 307 QEHTLLIDDQPGLKITDLRARARRM-KESYDIQFLIIDYLQLLSGSGNLRNSESRQTEIS 365
Query: 352 EISRNLKGLAKEINCPILALSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDE 411
EISR LK LA+E+N PIL LSQL+R +E R N RP+MSDLRESG+IEQD+D+++F+ R E
Sbjct: 366 EISRMLKNLARELNIPILCLSQLSRKVEDRANHRPMMSDLRESGSIEQDSDLVMFLLRRE 425
Query: 412 VYNQNSADK-GIAEIIVSKQRNGPIGNIRLTFSGQYTKFNNF 452
Y+ N DK G AE+IV+K R+G IG++ L F ++ +F N+
Sbjct: 426 YYDPN--DKPGTAELIVAKNRHGSIGSVPLVFEKEFARFRNY 465
>gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional.
Length = 505
Score = 356 bits (914), Expect = e-118
Identities = 160/446 (35%), Positives = 277/446 (62%), Gaps = 7/446 (1%)
Query: 8 ENKKFRVPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSS 67
E + FR PP+ E+EQ VLG +LL I + L + FYR H+LIF+ II L + +
Sbjct: 63 EYRDFRQPPYDNEAEQGVLGAMLLSPDTVIDIVEVLTPEDFYRPAHQLIFQAIIDLFSDN 122
Query: 68 HPADVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVT 127
D + V L T + E +GG YL++L Q++P+AAN R YAEIV ++ +LR+L+
Sbjct: 123 KEIDPVIVAGRLDRTNDLERVGGAPYLHTLIQSVPTAANARYYAEIVSEKAVLRRLVDAG 182
Query: 128 DEISSQAFI-SRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHN 186
+ + G E+ ++D A+ ++F++++K ++ + + +L+ + + L
Sbjct: 183 TRVVQLGYEGDEGAEIDSVIDRAQQEVFAVSQKNQ--SEDYAVLADILDPTMDELEMLS- 239
Query: 187 RGTNDNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPV 246
+ TGI TGF +LD +T+GL+ G +IIVA RP +GK+ +L+ +I++
Sbjct: 240 --SQGGIATGIPTGFKDLDDLTNGLRGGQMIIVAARPGVGKSTLALDFMRSASIKHNKAS 297
Query: 247 AIFSMEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPS 306
IFS+EMS ++ MR+L + ++ +R G++ D W ++ + KI ++ ++ID++ +
Sbjct: 298 VIFSLEMSKSEIVMRLLSAEAEVRLSDMRGGKMDEDAWEKLVQRLGKIAQAPIFIDDSAN 357
Query: 307 LNVIELRANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINC 366
L ++E+R+ +RRL ++ + +I++DYLQLMS+ R E+R E+SE SR LK LAKE++
Sbjct: 358 LTMMEIRSKARRLKQKHD-LKLIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDV 416
Query: 367 PILALSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEII 426
P++A+SQLNR E R +KRP ++DLRESG++EQDAD+++ +YR + +++ G A+II
Sbjct: 417 PLIAISQLNRGPESRTDKRPQLADLRESGSLEQDADMVMLLYRPDSQDKDDERAGEADII 476
Query: 427 VSKQRNGPIGNIRLTFSGQYTKFNNF 452
++K R GPI +++ Y++F +
Sbjct: 477 LAKHRGGPIDTVQVAHQLHYSRFVDM 502
>gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional.
Length = 428
Score = 294 bits (753), Expect = 1e-95
Identities = 161/441 (36%), Positives = 259/441 (58%), Gaps = 26/441 (5%)
Query: 18 SIESEQSVLGGLLLDNTAWDKIADC-LNSDYFYRYDHRLIFKHIIKLINSSHPADVITVF 76
++E+E++VLG LLLD + I +C L YF H+ IF+ + K+ + P D++T F
Sbjct: 5 NVEAEKTVLGSLLLDG---ELIKECRLTEQYFSMPVHKSIFQLMRKMEDEGQPIDLVT-F 60
Query: 77 DSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEISSQAFI 136
S + + IGG+ Y L +P+ +N Y +VR + QA +
Sbjct: 61 TSRVDPNFLKGIGGMEYFIGLMDGVPTTSNFSYYEGLVRGAWKMY-----------QAGV 109
Query: 137 SRGKEVKQILDEAESKIFSIAEKEICI--NKGFQQIQPLLNRVIKRINKLHNRGTNDNDV 194
K ++++ E KI +C K L + ++ +LH + ++
Sbjct: 110 LGHKMGERLIAEKSEKIIGETITALCELEEKDCVCEFDLKDALVDLYEELH---QDAKEI 166
Query: 195 TGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMS 254
TGI TG+ L+K+T GLQ GD +++ RPSMGKTAF+LN+G H A ++ V +FS+EMS
Sbjct: 167 TGIETGYTSLNKMTCGLQEGDFVVLGARPSMGKTAFALNVGLHAA-KSGAAVGLFSLEMS 225
Query: 255 GIQLAMRMLGSVGKLDQHKLRT--GRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIEL 312
QL RM VG++ +L+ R + +DW +++ + +I + L I + + V ++
Sbjct: 226 SKQLLKRMASCVGEVSGGRLKNPKHRFAMEDWEKVSKAFAEIGELPLEIYDNAGVTVQDI 285
Query: 313 RANSRRLSRQCG-KIGVIIIDYLQLMSANSRGE-NRATEISEISRNLKGLAKEINCPILA 370
+R+L R+ G K +II+DYLQL++ + + + NR EISEISR LK LA+E+N ++A
Sbjct: 286 WMQTRKLKRKHGDKKILIIVDYLQLITGDPKHKGNRFQEISEISRKLKLLARELNVCVVA 345
Query: 371 LSQLNRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDEVYNQNSADKGIAEIIVSKQ 430
LSQL+RS+E RQ+KRP++SDLRE+G IEQDADVI+ +YR++ Y++ + K + EI V+K
Sbjct: 346 LSQLSRSVESRQDKRPLLSDLRETGQIEQDADVIMLMYREDYYDKETMQKEMTEIHVAKH 405
Query: 431 RNGPIGNIRLTFSGQYTKFNN 451
RNGP+G+ +L F ++ +F
Sbjct: 406 RNGPVGSFKLRFLKEFGRFVE 426
>gnl|CDD|216111 pfam00772, DnaB, DnaB-like helicase N terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerisation of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This N-terminal domain is required both for
interaction with other proteins in the primosome and for
DnaB helicase activity.
Length = 103
Score = 134 bits (340), Expect = 2e-38
Identities = 55/103 (53%), Positives = 71/103 (68%)
Query: 14 VPPHSIESEQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLINSSHPADVI 73
VPPHSIE+EQ+VLG LLLD A D++AD L + FY HRLIF+ I++L P D +
Sbjct: 1 VPPHSIEAEQAVLGALLLDPEAIDEVADILKPEDFYDPAHRLIFEAILELYEKGKPIDPV 60
Query: 74 TVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRD 116
TV + L G EE+GG++YL LA N+PSAANI YA IV++
Sbjct: 61 TVAEELERKGKLEEVGGIAYLAELAANVPSAANIEYYARIVKE 103
>gnl|CDD|238542 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands.
Length = 271
Score = 75.5 bits (186), Expect = 3e-15
Identities = 53/217 (24%), Positives = 91/217 (41%), Gaps = 9/217 (4%)
Query: 200 GFFELDKITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGIQLA 259
F L+K+T GL+ G+LII+ +GKT F + ++ + V S+E ++ A
Sbjct: 16 PFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVRTA 75
Query: 260 MRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYI--DETPSLNVIELRANSR 317
R+LG H T + + + + + + + D ++ + R
Sbjct: 76 RRLLGQYAGKRLHLPDTVFIYTLE--EFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVR 133
Query: 318 RLSRQCGKIGVIIIDYLQ-LMSANSRGENRATEISEISRNLKGLAKEINCPILALSQLNR 376
++ G I IIID L ++S + + EI L+G A E I +S L R
Sbjct: 134 YMAVSHG-IQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHITLVSHLRR 192
Query: 377 S---LEQRQNKRPIMSDLRESGAIEQDADVILFIYRD 410
+ +SD R S AI Q AD ++ + R+
Sbjct: 193 PDGDKTHEEGGEVSLSDFRGSAAIGQLADNVIALERN 229
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 59.3 bits (144), Expect = 6e-10
Identities = 45/187 (24%), Positives = 83/187 (44%), Gaps = 32/187 (17%)
Query: 206 KITSGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGIQLAMRMLGS 265
++ S L+PGDL+++ RP GKT L + A+++ F++E + + R+
Sbjct: 56 ELFSQLKPGDLVLLGARPGHGKTLLGLELAVE-AMKSGRTGVFFTLEYTEQDVRDRL--- 111
Query: 266 VGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELRANSRRLSRQCGK 325
L + + L D +D+I YI I A++ R +
Sbjct: 112 -RALGADRAQFADLFEFD---TSDAI-----CADYI--------IARLASAPRGT----- 149
Query: 326 IGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEINCPILALSQLNRSLEQRQNKR 385
+++IDYLQL+ + + ++ R LK A+E I+ +SQ++RS +
Sbjct: 150 --LVVIDYLQLLDQRREKPDLSVQV----RALKSFARERGLIIVFISQIDRSFDPSAKPL 203
Query: 386 PIMSDLR 392
P + D+R
Sbjct: 204 PDIRDVR 210
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 54.8 bits (132), Expect = 5e-09
Identities = 37/196 (18%), Positives = 68/196 (34%), Gaps = 33/196 (16%)
Query: 216 LIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGIQLAMRMLGSVGKLDQHKLR 275
LI+V G GKT +L + +IA + V +E +L R++G
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATK-GGKVVYVDIEEEIEELTERLIG----------- 48
Query: 276 TGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELRANSRRLSRQCGKIGVIIIDYLQ 335
+S+K + + + T + R+ G +II+D L
Sbjct: 49 -------------ESLKGALDNLIIVFATADDPAAARLLSKAERLRERGGDDLIILDELT 95
Query: 336 LMSANSR--GENRATEISEISRNLKGLAKEINCPILALSQLNRSLEQRQNKRPIMSDLRE 393
+ R E E+ E R L A++ ++ Q+ + R
Sbjct: 96 RLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKGDPR------LTRG 149
Query: 394 SGAIEQDADVILFIYR 409
+ +E AD ++ + R
Sbjct: 150 AQNLEDIADTVIVLSR 165
>gnl|CDD|222864 PHA02542, 41, 41 helicase; Provisional.
Length = 473
Score = 57.0 bits (138), Expect = 9e-09
Identities = 55/217 (25%), Positives = 97/217 (44%), Gaps = 16/217 (7%)
Query: 204 LDKITSG-LQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGIQLAMRM 262
L+KIT G + L ++ ++GK+ ++ ++ V SMEM+ +A R+
Sbjct: 179 LNKITKGGAERKTLNVLLAGVNVGKSLGLCSLAAD-YLQQGYNVLYISMEMAEEVIAKRI 237
Query: 263 LGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETP--SLNVIELRA--NSRR 318
++ + + LS ++ + ++ + +L I + P + RA N +
Sbjct: 238 DANLLDVSLDDIDD--LSKAEYKAKMEKLRSKTQGKLIIKQYPTGGAHAGHFRALLNELK 295
Query: 319 LSRQCGKIGVIIIDYLQLMSANSR----GENRATEISEISRNLKGLAKEINCPILALSQL 374
L + K VII+DYL + A+SR EN T + I+ L+GLA E + + +Q
Sbjct: 296 LKKNF-KPDVIIVDYLGIC-ASSRLRVSSENSYTYVKAIAEELRGLAVEHDVVVWTAAQT 353
Query: 375 NRSLEQRQNKRPIMSDLRESGAIEQDADVILFIYRDE 411
RS + MSD ES + AD +L + E
Sbjct: 354 TRS--GWDSSDVDMSDTAESAGLPATADFMLAVIETE 388
Score = 33.5 bits (77), Expect = 0.20
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 22 EQSVLGGLLLDNTAWDKIADCLNSDYFYRYDHRLIFKHIIKLIN 65
E+++L L+ + + K+ L ++YF ++IFK I K +N
Sbjct: 2 EETILSNLIFNEDYFRKVWPYLKAEYFESGPEKVIFKLIKKHVN 45
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 48.8 bits (117), Expect = 5e-07
Identities = 31/192 (16%), Positives = 51/192 (26%), Gaps = 63/192 (32%)
Query: 196 GISTGFFELDKITSG-LQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKL---------P 245
+ L + G L G L ++AG P GK+ +L++ +A
Sbjct: 14 DLDAPPPPLRWLVKGLLPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGR 73
Query: 246 VAIFSMEMSGIQLAMRMLGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYIDETP 305
V E S L R
Sbjct: 74 VLYLDGEDSEAGLRRR-------------------------------------------- 89
Query: 306 SLNVIELRANSRRLSRQCGKIGVIIIDYLQLMSANSRGENRATEISEISRNLKGLAKEIN 365
LRA L + +++ID L S EN + + L LA+
Sbjct: 90 ------LRALGEAL-EEIEGPDLVVIDPLA--SLLGGDENDNAAVGALLAALDRLARRTG 140
Query: 366 CPILALSQLNRS 377
+L + ++
Sbjct: 141 AAVLLVHHTGKA 152
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 43.2 bits (102), Expect = 2e-04
Identities = 35/108 (32%), Positives = 55/108 (50%), Gaps = 10/108 (9%)
Query: 198 STGFFELDKITSG-LQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGI 256
S+GF ELD++ G + PG LI++ G P +GK+ L + +A +N++ V S E S
Sbjct: 77 SSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLA-KNQMKVLYVSGEESLQ 135
Query: 257 QLAMRM--LGSVGKLDQHKLRTGRLSSDDWPRINDSIKKINKSQLYID 302
Q+ MR LG + LS +W +I +I++ N ID
Sbjct: 136 QIKMRAIRLGLPE--PNLYV----LSETNWEQICANIEEENPQACVID 177
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 41.1 bits (97), Expect = 0.001
Identities = 31/110 (28%), Positives = 51/110 (46%), Gaps = 12/110 (10%)
Query: 197 ISTGFFELDKIT-SGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSG 255
I TG ELD++ GL PG +I++ G P +GK+ L + +A + V S E S
Sbjct: 64 IPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA-KRGGKVLYVSGEESP 122
Query: 256 IQLAMRMLGSVGKLDQHKLRTGRL---SSDDWPRINDSIKKINKSQLYID 302
Q+ +R D+ + T L + + I SI+++ + ID
Sbjct: 123 EQIKLRA-------DRLGISTENLYLLAETNLEDILASIEELKPDLVIID 165
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 39.5 bits (93), Expect = 0.003
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 197 ISTGFFELDKITSG-LQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSG 255
ISTG ELD++ G L PG +I++ G P +GK+ L + +A + V S E S
Sbjct: 75 ISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA--KRGKVLYVSGEESL 132
Query: 256 IQLAMR 261
Q+ +R
Sbjct: 133 QQIKLR 138
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 36.2 bits (85), Expect = 0.035
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 197 ISTGFFELDKIT-SGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSG 255
ISTG ELD++ GL PG ++++ G P +GK+ L + +A V S E S
Sbjct: 62 ISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGG-KVLYVSGEESA 120
Query: 256 IQLAMR 261
Q+ +R
Sbjct: 121 SQIKLR 126
>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
Members of this protein family are archaeal
single-domain KaiC_related proteins, homologous to the
Cyanobacterial circadian clock cycle protein KaiC, an
autokinase/autophosphorylase that has two copies of the
domain.
Length = 229
Score = 33.2 bits (76), Expect = 0.20
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 197 ISTGFFELDKITSGLQP-GDLIIVAGRPSMGKTAFSL 232
+STG LDK+ G P G + V G P GKT F L
Sbjct: 2 LSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCL 38
>gnl|CDD|239776 cd04243, AAK_AK-HSDH-like, AAK_AK-HSDH-like: Amino Acid Kinase
Superfamily (AAK), AK-HSDH-like; this family includes
the N-terminal catalytic domain of aspartokinase (AK) of
the bifunctional enzyme AK- homoserine dehydrogenase
(HSDH). These aspartokinases are found in such bacteria
as E. coli (AKI-HSDHI, ThrA and AKII-HSDHII, MetL) and
in higher plants (Z. mays AK-HSDH). AK and HSDH are the
first and third enzymes in the biosynthetic pathway of
the aspartate family of amino acids. AK catalyzes the
phosphorylation of Asp to P-aspartyl phosphate. HSDH
catalyzes the NADPH-dependent conversion of Asp
3-semialdehyde to homoserine. ThrA and MetL are involved
in threonine and methionine biosynthesis, respectively.
In E. coli, ThrA is subject to allosteric regulation by
the end product L-threonine and the native enzyme is
reported to be tetrameric. As with bacteria, plant AK
and HSDH are feedback inhibited by pathway end products.
Maize AK-HSDH is a Thr-sensitive 180-kD enzyme.
Arabidopsis AK-HSDH is an alanine-activated,
threonine-sensitive enzyme whose ACT domains, located
C-terminal to the AK catalytic domain, were shown to be
involved in allosteric activation. Also included in this
CD is the catalytic domain of the aspartokinase (AK) of
the lysine-sensitive aspartokinase isoenzyme AKIII, a
monofunctional class enzyme (LysC) found in some
bacteria such as E. coli. In E. coli, LysC is reported
to be a homodimer of 50 kD subunits. Also included in
this CD is the catalytic domain of aspartokinase (AK)
of the bifunctional enzyme AK - DAP decarboxylase
(DapDC) found in some bacteria. DapDC, which is the lysA
gene product, catalyzes the decarboxylation of DAP to
lysine.
Length = 293
Score = 32.5 bits (75), Expect = 0.43
Identities = 22/98 (22%), Positives = 42/98 (42%), Gaps = 15/98 (15%)
Query: 96 SLAQNIPSAANIRRYAEIVRDRGILRKLI------TVTD---EISSQAFISRGKEVKQIL 146
S+A SA IRR A+I++ R L+ VT+ ++ A S +L
Sbjct: 10 SVA----SAERIRRVADIIKSRASSPVLVVVSALGGVTNRLVALAELA-ASGDDAQAIVL 64
Query: 147 DEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKL 184
E + + KE+ + ++ L+ +++R+ L
Sbjct: 65 QEIRERHLDLI-KELLSGESAAELLAALDSLLERLKDL 101
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 31.7 bits (72), Expect = 0.71
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 197 ISTGFFELDKITSG-LQPGDLIIVAGRPSMGKTAFSLNI 234
I TG LD+I G L G ++++ G P GKT F+L
Sbjct: 5 IPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQF 43
>gnl|CDD|131935 TIGR02889, spore_YpeB, germination protein YpeB. Members of this
family are YpeB, a protein usually encoded with the
putative spore-cortex-lytic enzyme SleB and required,
together with SleB, for normal germination. This family
is retricted to endospore-forming species in the
Firmicutes lineage of bacteria, and found in all such
species to date except Clostridium perfringens. The
matching phenotypes of mutants in SleB (called a lytic
transglycosylase) and YpeB suggests that YpeB is
necessary to allow SleB to function [Cellular processes,
Sporulation and germination].
Length = 435
Score = 30.0 bits (68), Expect = 2.4
Identities = 22/100 (22%), Positives = 44/100 (44%), Gaps = 9/100 (9%)
Query: 87 EIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGILRKLITVTDEIS-SQAFISRGKEVKQI 145
++G + S QN P A++ R+A + L +L + + + F+S Q+
Sbjct: 54 QLGKTLAMGSQRQNTPVLADVWRHASAANES--LSQLPLTQESLEKTSKFLS------QV 105
Query: 146 LDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLH 185
D + AE + +K ++ + L N+ +K N+L
Sbjct: 106 GDFTYTLSVKDAEGKSLSDKEYKTLTTLYNQAVKLENQLR 145
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 29.9 bits (68), Expect = 2.7
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 7/62 (11%)
Query: 191 DNDVTGISTGFFELDKIT-SGLQPGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLP--VA 247
D+ ISTG LD+ GL G + + G S GKT +L + + P A
Sbjct: 36 REDIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLAL----QLVANAQKPGGKA 91
Query: 248 IF 249
F
Sbjct: 92 AF 93
>gnl|CDD|188631 cd00439, Transaldolase, Transaldolase. Transaldolase. Enzymes
found in the non-oxidative branch of the pentose
phosphate pathway, that catalyze the reversible transfer
of a dihydroxyacetone group from fructose-6-phosphate to
erythrose-4-phosphate yielding sedoheptulose-7-phosphate
and glyceraldehyde-3-phosphate. They are members of the
class I aldolases, who are characterized by using a
Schiff-base mechanism for stabilization of the reaction
intermediates.
Length = 252
Score = 29.6 bits (66), Expect = 3.4
Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 108 RRYAEIVRDRGILRKLITVTDEISSQAFISRGKEVKQI-LDEAESKIFSIAEKEICINKG 166
+ +++V R I K+ + I + K++ + + IFSIA+ E + G
Sbjct: 107 KYLSKVVNRRNIYIKIPATAEGIPA------IKDLIAAGISVNVTLIFSIAQYEAVADAG 160
Query: 167 FQQIQPLLNRV 177
P ++R+
Sbjct: 161 TSVASPFVSRI 171
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 29.8 bits (67), Expect = 3.4
Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 16/99 (16%)
Query: 147 DEAESKI---FSIAEKEICINKGFQQIQPLLNRVI-------------KRINKLHNRGTN 190
DEA+SK+ S A+ ++ L+ +I + L +
Sbjct: 192 DEADSKVTSFLSAADGVTTLDNSDLDFDETLDLLIGLVEDAIEEQEYDQYAANLEGYELD 251
Query: 191 DNDVTGISTGFFELDKITSGLQPGDLIIVAGRPSMGKTA 229
+ D + F +G + ++ + GRP++GK+
Sbjct: 252 EGDEDLLEGSGFVAGDEKAGPKAVGVVAIVGRPNVGKST 290
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 30.1 bits (68), Expect = 3.4
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 211 LQPGDLIIVAGRPSMGKTAFSLNI-----GEHIAIENK 243
++PG+L +V GRP G + I G HI +E
Sbjct: 84 IKPGELTVVLGRPGSGCSTLLKTIASNTDGFHIGVEGV 121
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 29.2 bits (66), Expect = 3.8
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 216 LIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGI 256
LII+ G PS GK+ + + +++ E V + S E GI
Sbjct: 1 LIILTGLPSSGKSTRAKELAKYLE-EKGYDVIVISDESLGI 40
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 29.0 bits (65), Expect = 4.0
Identities = 32/159 (20%), Positives = 52/159 (32%), Gaps = 21/159 (13%)
Query: 217 IIVAGRPSMGKT-AFSLNIGEHIAIENKLPVAIFSMEMSGIQLAMRMLGSVGKL--DQHK 273
+I+A GKT A L E + V + LA + + KL
Sbjct: 27 VILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRE---LAEQWAEELKKLGPSLGL 83
Query: 274 LRTGRLSSDDWPRINDSIKKINKSQLYIDETPSLNVIELRANSRRLSRQCGKIGVIIIDY 333
G D ++ L TP + L + LS + ++I+D
Sbjct: 84 KVVGLYGGDSKREQLRKLESGKTDILVT--TPGRLLDLLENDKLSLS----NVDLVILDE 137
Query: 334 LQLMSANSRGENRATEISEISRNLKGLAKEINCPILALS 372
+ G+ ++ + LK L K N +L LS
Sbjct: 138 AHRLLDGGFGD-------QLEKLLKLLPK--NVQLLLLS 167
>gnl|CDD|214640 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 = 28.5 bits (63), Expect = 4.0
Identities = 22/136 (16%), Positives = 47/136 (34%), Gaps = 11/136 (8%)
Query: 213 PGDLIIVAGRPSMGKTAFSLNIGEHIAIENKLPVAIFSMEMSGIQLAMRMLGSVGKLDQH 272
PG++I++ G P GKT + + + V E ++ ++L + +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGG-GVIYIDGEDILEEVLDQLLLIIVGGKKA 59
Query: 273 KLRTGRLSSDDWPRINDSIKKINKSQ---LYIDETPSLNVIELRANSRRLSRQCGKIGVI 329
R+ ++ K + L +DE SL E A L + +
Sbjct: 60 SGSGEL-------RLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLK 112
Query: 330 IIDYLQLMSANSRGEN 345
L ++ + ++
Sbjct: 113 SEKNLTVILTTNDEKD 128
>gnl|CDD|221355 pfam11981, DUF3482, Domain of unknown function (DUF3482). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and eukaryotes. This domain
is typically between 289 to 301 amino acids in length.
This domain is found associated with pfam01926. THe
central region of these proteins contains a hydrophobic
region that is similar to pfam05433.
Length = 293
Score = 29.2 bits (66), Expect = 4.7
Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 142 VKQILDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHNRG 188
++ D K+ E+E+C++ ++ L R ++ + L NRG
Sbjct: 189 ARRYGDRILGKL--KGERELCVDDATLRL--LALRQLQLLAALANRG 231
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC transporters
are a large family of proteins involved in the transport
of a wide variety of different compounds including
sugars, ions, peptides, and more complex organic
molecules. The nucleotide-binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 202
Score = 28.8 bits (65), Expect = 5.0
Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 200 GFFELDKITSGLQPGDLIIVAGRPSMGKT----AFSLNIGEHIAIENKL 244
L + ++PG++++V GRP G + A + ++++E +
Sbjct: 19 KIPILKDFSGVVKPGEMVLVLGRPGSGCSTLLKALANRTEGNVSVEGDI 67
>gnl|CDD|137559 PRK09859, PRK09859, multidrug efflux system protein MdtE;
Provisional.
Length = 385
Score = 28.9 bits (64), Expect = 5.5
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 207 ITSGLQPGDLIIVAG----RPSMGKTAFS 231
+TSGLQ GD +IV+G RP + A S
Sbjct: 345 VTSGLQAGDRVIVSGLQRIRPGIKARAIS 373
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 28.6 bits (65), Expect = 5.5
Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 8/52 (15%)
Query: 68 HPADVITVFDSLSNTGNAEEIGGLSYLNSLAQNIPSAANIRRYAEIVRDRGI 119
D + +FDS S T + + + S +++ N E ++ G+
Sbjct: 86 AGVDEVRIFDSASETHSRKNLN-----KSREEDL---ENAEEAIEAAKEAGL 129
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 28.4 bits (64), Expect = 6.1
Identities = 37/164 (22%), Positives = 55/164 (33%), Gaps = 34/164 (20%)
Query: 197 ISTGFFELDKITSGLQP-GDLIIVAGRPSMGKTAFSLNIGEHIAIENKL----PVAIFSM 251
+ TG LD+I G P G ++++ G P GKT F L L P ++
Sbjct: 1 VPTGIPGLDEILKGGIPRGRVVLITGGPGTGKTIFGL----QFLYNGALEYGEPGVYVTL 56
Query: 252 E--MSGIQLAMRMLG-------SVGKLDQHKLRTGRLSSDDWPRINDS-----------I 291
E ++ + G GKL T + I
Sbjct: 57 EEPPEDLRENAKSFGWDLEKLEEEGKLAIIDASTSG-IGIAEVKGRFDLEELIERLREAI 115
Query: 292 KKINKSQLYIDETPSL----NVIELRANSRRLSRQCGKIGVIII 331
++I ++ ID +L R RRL R K+GV I
Sbjct: 116 REIGAKRVVIDSITTLYLLLKPAMAREILRRLKRVLKKLGVTAI 159
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 29.0 bits (64), Expect = 6.3
Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 4/102 (3%)
Query: 115 RDRGILRKLITVTDEISSQAFISRGKEVKQILDEAESKIFSIAEKEICINKGFQQIQPLL 174
RDRG L + I T + + + G+ +DE + + I G+ ++ L+
Sbjct: 1891 RDRGALPRDILSTGSLRLKDIVEPGRLGALPIDELRKRDMDTDGDDAFIYAGYPKLAALI 1950
Query: 175 NRVIKRINKLHNRGTNDNDVTGISTGFFELDKITSGLQPGDL 216
+RV+ R +L + + T +D ++ QPG L
Sbjct: 1951 SRVMDRKARLGRQKSFKPPKTATPA----IDPVSGHYQPGRL 1988
>gnl|CDD|238025 cd00070, GLECT, Galectin/galactose-binding lectin. This domain
exclusively binds beta-galactosides, such as lactose,
and does not require metal ions for activity. GLECT
domains occur as homodimers or tandemly repeated
domains. They are developmentally regulated and may be
involved in differentiation, cell-cell interaction and
cellular regulation.
Length = 127
Score = 27.6 bits (62), Expect = 6.6
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 206 KITSGLQPGDLIIVAGRPSMGKTAFSLNIG 235
+ GL+PG + V GR FS+N+G
Sbjct: 5 PLPGGLKPGSTLTVKGRVLPNAKRFSINLG 34
>gnl|CDD|233547 TIGR01730, RND_mfp, RND family efflux transporter, MFP subunit.
This model represents the MFP (membrane fusion protein)
component of the RND family of transporters. RND refers
to Resistance, Nodulation, and cell Division. It is, in
part, a subfamily of pfam00529 (Pfam release 7.5) but
hits substantial numbers of proteins missed by that
model. The related HlyD secretion protein, for which
pfam00529 is named, is outside the scope of this model.
Attributed functions imply outward transport. These
functions include nodulation, acriflavin resistance,
heavy metal efflux, and multidrug resistance proteins.
Most members of this family are found in Gram-negative
bacteria. The proposed function of MFP proteins is to
bring the inner and outer membranes together and enable
transport to the outside of the outer membrane. Note,
however, that a few members of this family are found in
Gram-positive bacteria, where there is no outer membrane
[Transport and binding proteins, Unknown substrate].
Length = 322
Score = 28.4 bits (64), Expect = 7.2
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 197 ISTGFFELDK--ITSGLQPGDLIIVAG 221
+ G I SGL+ GD I+ AG
Sbjct: 283 VEVGLRNGGYVEIESGLKAGDQIVTAG 309
>gnl|CDD|181856 PRK09436, thrA, bifunctional aspartokinase I/homoserine
dehydrogenase I; Provisional.
Length = 819
Score = 29.0 bits (66), Expect = 7.5
Identities = 17/101 (16%), Positives = 37/101 (36%), Gaps = 17/101 (16%)
Query: 96 SLAQNIPSAANIRRYAEIVRDRGILRKLITV-------TD---EISSQAFISRGKEVKQI 145
S+A +A R A+I+ ++ V T+ + +A ++G +
Sbjct: 10 SVA----NAERFLRVADIIESNARQEQVAVVLSAPAKVTNHLVAMIEKA--AKGDDAYPE 63
Query: 146 LDEAESKIFSIAEKEICINKGFQQIQPLLNRVIKRINKLHN 186
+ +AE + + GF L +V + +L +
Sbjct: 64 ILDAERIFHELLDGLAAALPGFDL-AQLKAKVDQEFAQLKD 103
>gnl|CDD|181283 PRK08197, PRK08197, threonine synthase; Validated.
Length = 394
Score = 28.4 bits (64), Expect = 7.7
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 390 DLRESGAIEQDADVILF 406
LRESG ++ D V+LF
Sbjct: 359 QLRESGWLKGDERVVLF 375
>gnl|CDD|100033 cd02197, HypE, HypE (Hydrogenase expression/formation protein).
HypE is involved in Ni-Fe hydrogenase biosynthesis.
HypE dehydrates its own carbamoyl moiety in an
ATP-dependent process to yield the enzyme thiocyanate.
The N-terminal domain of HypE is related to the
ATP-binding domains of the AIR synthases,
selenophosphate synthetase (SelD), and FGAM synthase and
is thought to bind ATP.
Length = 293
Score = 28.2 bits (64), Expect = 8.1
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 16/49 (32%)
Query: 195 TGISTGFFELDKITSG--LQPGDLIIVAGRPSMGKTAFSLNIGEH-IAI 240
TGI G I S ++PGD IIV+G IG+H AI
Sbjct: 134 TGI--GVIPRGVIISPSNIRPGDKIIVSG-----------TIGDHGAAI 169
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.136 0.379
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,065,488
Number of extensions: 2309170
Number of successful extensions: 2515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2440
Number of HSP's successfully gapped: 89
Length of query: 452
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 352
Effective length of database: 6,502,202
Effective search space: 2288775104
Effective search space used: 2288775104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.5 bits)