RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9396
(1149 letters)
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 1441 bits (3734), Expect = 0.0
Identities = 518/1152 (44%), Positives = 741/1152 (64%), Gaps = 44/1152 (3%)
Query: 5 FIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPI 64
F+HL +HSEYS++DG +I +++ AA PA+A+TD NLFG ++FYK+A GIKPI
Sbjct: 2 FVHLHVHSEYSLLDGAAKIKPLVKKAAELGMPAVALTDHGNLFGAVEFYKAAKGAGIKPI 61
Query: 65 IGCDVWITNEIEN-----KKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEW 119
IGC+ ++ E ++ + L LL KN GY L +L S+AY+E + I EW
Sbjct: 62 IGCEAYVAPEKKDDVSGGGAYTHLTLLAKNETGYRNLFKLSSRAYLEGQYGYKPRIDREW 121
Query: 120 LEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNM 179
L + + +GLIALSG G++G A+ G+ D AE A + +IF D FY+E+ R P
Sbjct: 122 LAE--HSEGLIALSGCPSGEVGTALLAGQYDEAEEAAAEYQEIFGDRFYLELMRHGLPIE 179
Query: 180 NFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQ 239
+ +A + LP+VAT+ + +L + AHE CIAEG+ L + R + ++ EQ
Sbjct: 180 RRVEHALLELAKELGLPLVATNDVHYLTPEDAEAHEALLCIAEGKTLDDPDRFRFYSPEQ 239
Query: 240 NFKTQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKSK 299
K+ EM +LF D+P A+ NT+EIA+RCN+++ GKP LP+FPTP D+L ++K
Sbjct: 240 YLKSAEEMRELFADLPEALDNTVEIAERCNVEVRLGKPFLPRFPTPDGETEEDYLRKEAK 299
Query: 300 HGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIP 359
GL++RL L+ D E + Y +RL++E++ II+M F GYFLIV+DFIQWAK+N IP
Sbjct: 300 EGLEERLAFLFPDEERPE-----YVERLEYELDVIIQMGFPGYFLIVADFIQWAKDNGIP 354
Query: 360 VGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQY 419
VGPGRGSGA SLVAY+L ITD+DPL + LLFERFLNP R+SMPDFDIDFC + RD VI+Y
Sbjct: 355 VGPGRGSGAGSLVAYALGITDLDPLRFGLLFERFLNPERVSMPDFDIDFCQDRRDEVIRY 414
Query: 420 VKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAI 479
V ++YG+DAV+QI+TFGTM AK IRDVGRVL + Y F D I+KLIP PG ITL+ A
Sbjct: 415 VAEKYGRDAVAQIITFGTMKAKAVIRDVGRVLGMPYGFVDRITKLIPPDPG--ITLAKAY 472
Query: 480 KEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQEGMT 539
+EEP+L E +++ EV++LI++A+++EG+ RN G+HA GV+I+P+ L +F PLY+
Sbjct: 473 EEEPELRELYESDPEVKRLIDMARKLEGLTRNAGVHAAGVVISPTPLTDFVPLYRDPDSG 532
Query: 540 GIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDKDTY 599
++Q+D D+E GL+KFDFLGL TL+I+D + IKK L +PL+D TY
Sbjct: 533 MPVTQFDMKDVEAAGLVKFDFLGLRTLTIIDDALKLIKKRRGID--VDLEAIPLDDPKTY 590
Query: 600 NLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMD--LIKNFCRRKHG 657
LL++ T+ VFQLES+GM+++LK KPD FE+IIAL++LYRPGPM+ +I NF RKHG
Sbjct: 591 ELLQRGETLGVFQLESRGMRDLLKRLKPDCFEDIIALVALYRPGPMESGMIPNFIDRKHG 650
Query: 658 -EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTSEMIE 716
E YP P + +L ETYGI+VYQEQVMQIAQ+L GYSLG ADLLRRA+GKKK EM +
Sbjct: 651 REEIEYPHPELEPILKETYGIIVYQEQVMQIAQVLAGYSLGGADLLRRAMGKKKPEEMAK 710
Query: 717 HRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYSSFF 776
R+ F GA K G+ + A+ IF+ +EKFAGYGFNKSHA AYAL+SY TAYLK HY + F
Sbjct: 711 QREIFVEGAKKNGIDEEAADAIFDLLEKFAGYGFNKSHAAAYALVSYQTAYLKAHYPAEF 770
Query: 777 MAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIRYGLG 836
MAA L+ MD+T+K+ + + + + G+ +LPP++N S Y F IRYGLG
Sbjct: 771 MAALLTSDMDNTDKVAVYLDEC-RRMGIKVLPPDVNESLYDF----TVVD--GDIRYGLG 823
Query: 837 AIKGTGKSTIEAIVTERKFGF-FTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRY 895
AIKG G+ +EAIV R+ G F +LFDF R+D K +N+R++ SLI +GAFD R
Sbjct: 824 AIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKVNKRVLESLIKAGAFDSLGPNRA 883
Query: 896 MLVASIDVALKNAEKTKK--FINQLSLFKNDDNNNLKEYLNYVKVPSWSKKQELIEEKKV 953
L+AS++ A+ A++ KK Q LF ++ V W KK++L E++
Sbjct: 884 ALLASLEDAVDAADQHKKAEASGQFDLFGGLGEEPEDVEVSVPDVEEWDKKEKLAGERET 943
Query: 954 LGFCLSEHIFCIYETEIRQFIPIYLSELKPTY---SCTVSGIITELKLKTTYRG-KILII 1009
LG LS H YE E+R+ L++L+PT TV+G++ ++ + T RG K+ I+
Sbjct: 944 LGLYLSGHPLDGYEDELRRLRDTRLADLEPTEGGSVVTVAGLVVSVRRRVTKRGNKMAIV 1003
Query: 1010 VIDDNSNSVEVIINNQLYEKNKNILKENELLIVSGKV-LEDRFLKNIRINAEKIFDINVA 1068
++D S +EV++ ++ EK +++L+E+ +++V G+V +D +R+ A ++ D+ A
Sbjct: 1004 TLEDLSGRIEVMLFSEALEKYRDLLEEDRIVVVKGQVSFDDGG---LRLTAREVMDLEEA 1060
Query: 1069 RILYGKKFSVMFN----RTFNISILKKILLRFKCKNGLPFVLYYCINKSIKYEMKFPLNY 1124
R Y + + + LK++L + + P LY + + E++ +
Sbjct: 1061 RAKYARPLRISLPDRQLTPQLLERLKQVLEPHRGTS--PVHLYL-QDPDAEAELRLGDRW 1117
Query: 1125 KVQPIDDLKLAL 1136
+V P D L L
Sbjct: 1118 RVTPSDALLGDL 1129
>gnl|CDD|223660 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
recombination, and repair].
Length = 1139
Score = 1227 bits (3178), Expect = 0.0
Identities = 503/1149 (43%), Positives = 720/1149 (62%), Gaps = 34/1149 (2%)
Query: 3 PQFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIK 62
F+HL +HSEYS++DG +I ++++ A PALA+TD +NL+G ++FYK+A GIK
Sbjct: 2 MSFVHLHVHSEYSLLDGASKIEELVKKAKELGMPALALTDHNNLYGAVEFYKAAKKAGIK 61
Query: 63 PIIGCDVWITNEIEN--KKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWL 120
PIIGC+ ++ N ++ LLLL KNN GY L +L S AY+E G+ I + L
Sbjct: 62 PIIGCEAYVANGDGFRGRERPHLLLLAKNNEGYKNLVKLSSIAYLEGE-KGKPRIDKDLL 120
Query: 121 EKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMN 180
E +Y +GLIALS G++ + G D+AE + ++F D+FY+E+QR P
Sbjct: 121 EL-EYSEGLIALSACLGGEVPQLLLKGNEDLAEEALAWYKEVFGDDFYLELQRHGSPEDR 179
Query: 181 FQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQN 240
+ I +A + +P+VAT+ + ++ + AH+ CI G+ LS+ KR++ + EQ
Sbjct: 180 RRNDALIKLARELGIPLVATNDVHYINPEDREAHDALLCIRTGKTLSDDKRLRYSSAEQY 239
Query: 241 FKTQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKSKH 300
K+ EM +LF DIP A+ NT+EIA+RCN +L+ G P+LP FPTP + ++L ++
Sbjct: 240 LKSPEEMARLFADIPEALANTVEIAERCNFELDLG-PRLPNFPTPPGKSAAEYLRKLAEE 298
Query: 301 GLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIPV 360
GL++R E+ + + YK+RL++E++ I KM F GYFLIV DFI++A++N IPV
Sbjct: 299 GLEERYKERLAPEEVPE-KVREYKERLEYELDVINKMGFPGYFLIVWDFIKFARDNGIPV 357
Query: 361 GPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQYV 420
GPGRGS A SLVAY+L ITDIDPL Y+LLFERFLNP R+SMPD DIDFC E R+ VIQYV
Sbjct: 358 GPGRGSAAGSLVAYALGITDIDPLKYDLLFERFLNPERVSMPDIDIDFCDERREEVIQYV 417
Query: 421 KDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIK 480
++YG+D V+QI+TFGT+ AK AIRDVGRVL L Y D ++KLIPF PG +TL+ A +
Sbjct: 418 YEKYGRDRVAQIITFGTLRAKAAIRDVGRVLGLPYGEVDKLAKLIPFWPG--LTLAVAYE 475
Query: 481 EEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQEGMTG 540
EEP+L E + ++ EV++LIELA+++EG+ R++ HA GV+I+ L + PLYK +
Sbjct: 476 EEPELKELLDSDPEVKRLIELARKLEGLPRHLSTHAAGVVISDDPLTDLVPLYKDKN-RD 534
Query: 541 IISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDKDTYN 600
++QYD DD+E +GL+KFDFLGL TL+I+ + + IK+ + + L +PL+D TY
Sbjct: 535 GVTQYDMDDLEAVGLLKFDFLGLKTLTIIQRALDLIKE--KRGIDIDLASIPLDDPKTYE 592
Query: 601 LLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMD--LIKNFCRRKHG- 657
+L K +T+ VFQLES+GMK++LK KPD FE+I+AL++LYRPGPM +I F RKHG
Sbjct: 593 MLAKGDTLGVFQLESRGMKSLLKRLKPDNFEDIVALVALYRPGPMQGGMIPPFINRKHGR 652
Query: 658 EYFNYPDP-RTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTSEMIE 716
E YP P + +L ETYG++VYQEQVMQIAQ+L G+SLG+ADLLRRA+GKKK EM +
Sbjct: 653 EEIEYPHPEPLEPILKETYGVIVYQEQVMQIAQVLAGFSLGEADLLRRAMGKKKAEEMEK 712
Query: 717 HRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYSSFF 776
R+ F GA+K G K A +IF+ IEKFAGYGFNKSHA AYALLSY TAYLK HY + F
Sbjct: 713 QREKFIEGAVKNGYDKEFAEKIFDLIEKFAGYGFNKSHAAAYALLSYQTAYLKAHYPAEF 772
Query: 777 MAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIRYGLG 836
MAA L+ + +K+ +++A + G+ +LPP+IN S + F + K IR GLG
Sbjct: 773 MAALLTSEPMNFDKVAQYIQEARRM-GIEVLPPDINRSGWDFTV-----EEKKAIRLGLG 826
Query: 837 AIKGTGKSTIEAIVTERKFGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRYM 896
AIKG G+ IE IV RK F +L DF RID+K +N+R++ SLI +GAFD F + R
Sbjct: 827 AIKGVGEDAIEEIVEARKEKPFKSLEDFCDRIDRKGLNKRVLESLIKAGAFDSFGKNRAQ 886
Query: 897 LVASIDVALKNAEKTKKFINQLSLFKNDDNNNLKEYLNYVKVPSWSKKQELIEEKKVLGF 956
L+A++D L A T K QLSLF E ++YV +P WS+K++L EK+ LG
Sbjct: 887 LLAALDDLLDAASGTAKNSGQLSLF-GAAAAGESEQVSYVALPEWSEKEKLALEKETLGL 945
Query: 957 CLSEH-IFCIYETEIRQFIPIY-LSELKPT-YSCTVSGIITELKLK-TTYRGKILIIV-I 1011
LS H + +YE + + + L +L ++G I ++ + T +G + + +
Sbjct: 946 YLSGHPLDFLYEDLLARGLTPIRLLDLVEDGRRVVLAGGIVAVRQRPTKAKGNKMAFLTL 1005
Query: 1012 DDNSNSVEVIINNQLYEKNKNILKENELLIVSGKVLEDRFLKNIRINAEKIFDINVARIL 1071
+D + +EV++ YE+ + +L E LLIV GKV + E + + AR
Sbjct: 1006 EDETGILEVVVFPSEYERYRRLLLEGRLLIVKGKVQRREDGVGHALILEDLSPLEEARER 1065
Query: 1072 YGKKFSVMFN-RTFNISILK----KILLRFKCKNGLPFVLYYCINKSIKYEMKFPLNYKV 1126
++ T + LK K +LR K P +L Y N + ++
Sbjct: 1066 VADFLAIYLRLNTSQLDRLKLLKIKSILRQG-KGKTPVILIY-QNGDSRNFLRLGELRVS 1123
Query: 1127 QPIDDLKLA 1135
++ LK
Sbjct: 1124 TLVEALKDG 1132
>gnl|CDD|235868 PRK06826, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1151
Score = 1070 bits (2769), Expect = 0.0
Identities = 458/1180 (38%), Positives = 700/1180 (59%), Gaps = 79/1180 (6%)
Query: 1 MIPQFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKG 60
M F+HL +H+EYS++DG RI D+I+ A ++AITD ++G++ FYK+A +G
Sbjct: 1 MKMSFVHLHVHTEYSLLDGSARIKDLIKRAKELGMDSIAITDHGVMYGVVDFYKAAKKQG 60
Query: 61 IKPIIGCDVWI--------TNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGR 112
IKPIIGC+V++ +I+N+ L+LL KN GY L +++SKA+ E Y +
Sbjct: 61 IKPIIGCEVYVAPRSRFDKEPDIDNE-TYHLVLLAKNETGYKNLMKIVSKAFTEGFYY-K 118
Query: 113 AEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIF-PDNFYIEI 171
+ E L++ + +GLIALS G++ + G + A+ A + IF +NFY+E+
Sbjct: 119 PRVDHELLKE--HSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYKDIFGKENFYLEL 176
Query: 172 QRFKQPNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKR 231
Q P ++ I ++ + +P+VAT+ + +++K + AH+V CI G+ + + R
Sbjct: 177 QDHGIPEQRKVNEELIKLSKELGIPLVATNDVHYIRKEDAKAHDVLLCIQTGKTVDDENR 236
Query: 232 IKKFTKEQNFKTQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININ 291
++ + E K+ EM +LF +P A++NT++IA+RCN++ EFGK KLPKFP P+ +
Sbjct: 237 MRFPSDEFYLKSPEEMYELFSYVPEALENTVKIAERCNVEFEFGKSKLPKFPLPEGYDPY 296
Query: 292 DFLISKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQ 351
++L GLKKR Y +P E+L +RL++E+ I +M + YFLIV DFI+
Sbjct: 297 EYLRELCYEGLKKR----YPNPS----EEL--IERLEYELSVIKQMGYVDYFLIVWDFIR 346
Query: 352 WAKNNSIPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPE 411
+A+ N I VGPGRGS A SLVAY+L IT IDP+ YNLLFERFLNP R+SMPD DIDFC E
Sbjct: 347 FARENGIMVGPGRGSAAGSLVAYTLGITKIDPIKYNLLFERFLNPERVSMPDIDIDFCYE 406
Query: 412 GRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGK 471
R VI YV ++YGKD V+QI+TFGTMAA+ AIRDVGR L+ Y+ D I+K+IP + G
Sbjct: 407 RRQEVIDYVVEKYGKDRVAQIITFGTMAARAAIRDVGRALNYPYAEVDRIAKMIPTELG- 465
Query: 472 LITLSNAIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCP 531
IT+ A++ P+L E +N+E VR+LI+ A+ +EG+ R+ HA GV+I+ L+ + P
Sbjct: 466 -ITIDKALELNPELKEAYENDERVRELIDTARALEGLPRHASTHAAGVVISSEPLVEYVP 524
Query: 532 LYKQEGMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKL 591
L K +G I++Q+ +EE+GL+K DFLGL TL+++ + IKK + L+K+
Sbjct: 525 LQKNDGS--IVTQFTMTTLEELGLLKMDFLGLRTLTVIRDAVDLIKK--NRGIEIDLDKI 580
Query: 592 PLNDKDTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDLIKNF 651
+DK Y ++ + TV VFQLES GM++ +KE KPD E+IIA ISLYRPGPMD I +
Sbjct: 581 DYDDKKVYKMIGEGKTVGVFQLESAGMRSFMKELKPDSLEDIIAGISLYRPGPMDSIPRY 640
Query: 652 CRRKHG-EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKK 710
+ K+ E Y P+ + +L TYG +VYQEQVMQI + L GYS+G++DL+RRA+ KKK
Sbjct: 641 IKNKNNPEKIEYLHPKLEPILKVTYGCIVYQEQVMQIVRDLAGYSMGRSDLVRRAMSKKK 700
Query: 711 TSEMIEHRKFFQNG--------AIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLS 762
M E RK F G I+ G+ + AN+IF+ + FA Y FNKSHA AYA+++
Sbjct: 701 HDVMEEERKNFIYGIVDEGGPGCIRNGIDEETANKIFDSMMDFASYAFNKSHAAAYAVVA 760
Query: 763 YYTAYLKTHYSSFFMAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPII 822
Y TAYLK +Y FMAA L+ M +++K+ +++ + G+ +LPP+IN S F
Sbjct: 761 YQTAYLKRYYPVEFMAALLNSVMGNSDKVAFYIEEC-RRLGIEVLPPDINESYSKFTV-- 817
Query: 823 ESDGKHKKIRYGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYINRRIINSL 881
+ KIR+GL A+K G++ I++IV ER K G F +L DF +R+D IN+R + SL
Sbjct: 818 ----EGDKIRFGLAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERVDTSQINKRAVESL 873
Query: 882 INSGAFDCFNEKRYMLVASIDVALKNAEKTKK--FINQLSLF---KNDDNNNLKEYLNYV 936
I +GAFD R L+A + L + K +K Q+SLF ++ ++L+ + Y
Sbjct: 874 IKAGAFDSLGVYRSQLLAVYEKILDSISKQRKKNIEGQISLFDLIGEEEESSLE--IKYP 931
Query: 937 KVPSWSKKQELIEEKKVLGFCLSEHIFCIYETEIRQFIPIYLSELKPTYSC--------- 987
+ + KK+ L EK++LG +S H YE +++ +S++
Sbjct: 932 DIKEFDKKELLAMEKEMLGLYISGHPLEEYEETLKKQTSATISDIISDEEEDGESKLKDG 991
Query: 988 ---TVSGIITELKLKTTYRGKIL-IIVIDDNSNSVEVIINNQLYEKNKNILKENELLIVS 1043
+ GIITE+K KTT +++ + ++D +VEVI+ ++YEK +++L E+ ++++
Sbjct: 992 DKVIIGGIITEVKRKTTRNNEMMAFLTLEDLYGTVEVIVFPKVYEKYRSLLNEDNIVLIK 1051
Query: 1044 GKVL--EDRFLKNIRINAEKI--FDINVARILYGKKFSVMFNRTFNISILKKILLRFKCK 1099
G+V ED + ++ E+I IN + LY + + + LK+IL ++
Sbjct: 1052 GRVSLRED---EEPKLICEEIEPLVINSEKKLY-LRVEDKKDIKLKLKELKEILKQYPGN 1107
Query: 1100 NGLPFVLYYCINKSIKYEMKFPLNYKVQPIDDLKLALINL 1139
P LY + K V +L L L
Sbjct: 1108 T--PVYLYTEKERKKF---KLDRELWVNLSPELINELKEL 1142
>gnl|CDD|233039 TIGR00594, polc, DNA-directed DNA polymerase III (polc). All
proteins in this family for which functions are known are
DNA polymerases. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1022
Score = 1045 bits (2705), Expect = 0.0
Identities = 465/1039 (44%), Positives = 663/1039 (63%), Gaps = 39/1039 (3%)
Query: 5 FIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPI 64
F+HL +HS+YS++DG +I +++ A PALA+TD N+FG ++FYK+ GIKPI
Sbjct: 1 FVHLHVHSDYSLLDGAAKIKPLVKKAKELGMPALALTDHGNMFGAVEFYKACKKAGIKPI 60
Query: 65 IGCDVWITNE-IENKKPSR-------LLLLVKNNNGYLQLCELLSKAYIENINYGRAEIR 116
IGC+ ++ +KK L+LL KNN GY L +L S AY+E Y + I
Sbjct: 61 IGCEAYVAPGSRFDKKRISKGKEAYHLILLAKNNTGYRNLMKLSSLAYLEGFYY-KPRID 119
Query: 117 IEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQ 176
E LE+ + +GLIALS G++ + G +AE A ++ +IF D++Y+E+Q
Sbjct: 120 KELLEE--HSEGLIALSACLSGEVPYLLLLGEERLAEEAALKYQEIFGDDYYLELQDHGI 177
Query: 177 PNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFT 236
P + + I+ + +P+VAT+ + ++ + AHE+ CI G+ LS+ KR+K ++
Sbjct: 178 PEQRVVNEALLEISEELGIPLVATNDVHYINPEDAHAHEILLCIQTGKTLSDPKRLKFYS 237
Query: 237 KEQNFKTQSEMIKLFYDIPSAIQNTIEIAKRCNL-KLEFGKPKLPK-FPTPKNININDFL 294
E K+ EM +LF DIP A+ NT+EIA+RCNL ++ G P+LP P + D+L
Sbjct: 238 DEFYLKSPEEMAELFADIPEALANTVEIAERCNLVDVKLGPPRLPSYQIPPDFTSQEDYL 297
Query: 295 ISKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAK 354
+ GL++RL P YK + +YK+RL++E++ I M F GYFLIV DFI+WAK
Sbjct: 298 RHLADEGLRERLAAG---PPGYK-RRAQYKERLEYELDVINSMGFPGYFLIVWDFIKWAK 353
Query: 355 NNSIPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRD 414
++ IPVGPGRGS A SLVAY+L ITDIDP+ + LLFERFLNP RISMPD DIDFC E RD
Sbjct: 354 DHGIPVGPGRGSAAGSLVAYALKITDIDPIKHGLLFERFLNPERISMPDIDIDFCDERRD 413
Query: 415 RVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLIT 474
VI+YV D+YG D V+QI+TFGTM AK A+RDV RVLD+ Y+ D I+KLIP +PGK T
Sbjct: 414 EVIEYVADKYGHDNVAQIITFGTMKAKAALRDVARVLDIPYAEADRIAKLIPPRPGK--T 471
Query: 475 LSNAIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYK 534
L A++ PQL + + + EV+QLI++A+++EG+ RN G+HA GV+I+ L ++ PLYK
Sbjct: 472 LKEALEASPQLRQLYEEDPEVKQLIDMARKLEGLNRNAGVHAAGVVISSEPLTDYVPLYK 531
Query: 535 QEGMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLN 594
+ I +QYD DD+E +GL+K DFLGL TL+++ I+K + + + +PL+
Sbjct: 532 DKEGGAISTQYDMDDLEAVGLLKMDFLGLKTLTLIQDATELIRK--RRGIDLDIASIPLD 589
Query: 595 DKDTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMD--LIKNFC 652
DK T++LL++ +T VFQLES+GM+++LK KPD FE+IIA+ +LYRPGPM+ +I +F
Sbjct: 590 DKKTFSLLQEGDTTGVFQLESRGMQDLLKRLKPDGFEDIIAVNALYRPGPMESGMIPDFI 649
Query: 653 RRKHG-EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKT 711
RKHG E YP P + +L ETYG++VYQEQVMQIAQ L G+SLG+ADLLRRA+GKKK
Sbjct: 650 DRKHGREPIEYPHPLLEPILKETYGVIVYQEQVMQIAQRLAGFSLGEADLLRRAMGKKKA 709
Query: 712 SEMIEHRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTH 771
EM + R+ F GA K G A +F+ IEKFAGYGFNKSHA AY ++SY TAYLK +
Sbjct: 710 EEMAKEREKFVEGAEKNGYDPEIAENLFDLIEKFAGYGFNKSHAAAYGMISYQTAYLKAN 769
Query: 772 YSSFFMAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKI 831
Y + FMAA L+ ++D K+ + + +A K G+ +LPP+IN S F +E G I
Sbjct: 770 YPAEFMAALLTSEINDIEKVAVYIAEA-KKMGIEVLPPDINESGQDF--AVEDKG----I 822
Query: 832 RYGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCF 890
RYGLGAIKG G+S +++I+ ER K G F +LFDF R+D K +N++++ +LI +GAFD
Sbjct: 823 RYGLGAIKGVGESVVKSIIEERNKNGPFKSLFDFINRVDFKKLNKKVLEALIKAGAFDSL 882
Query: 891 NEKRYMLVASIDVALKNAEKTKK--FINQLSLFKNDDNNNLKEYLNYVKVPSWSKKQELI 948
R L+AS+D AL + KK + Q SLF EY+ + W K+ L
Sbjct: 883 GPNRKTLLASLDDALDAVSRKKKAEALGQNSLFGALSEGTKPEYVFFPPDEEWPDKKLLA 942
Query: 949 EEKKVLGFCLSEHIFCIYETEI-RQFIPIYLSELKPTYSC---TVSGIITELKLKTTYRG 1004
EK+ LG +S H YE + P + +L+ T+ G+ + K TT G
Sbjct: 943 LEKETLGLYVSGHPLDAYEKALKNTATPAAIEDLEAPNDSQVRTLGGLNSVKKKITTKNG 1002
Query: 1005 K-ILIIVIDDNSNSVEVII 1022
K + + ++D + S+EV++
Sbjct: 1003 KPMAFLQLEDETGSIEVVV 1021
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 815 bits (2107), Expect = 0.0
Identities = 413/1088 (37%), Positives = 633/1088 (58%), Gaps = 65/1088 (5%)
Query: 4 QFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKP 63
F+ L HS+YS++DG ++ ++E A PA+A+TD ++G I+ K KGIKP
Sbjct: 2 AFVPLHNHSDYSLLDGASQLPKMVERAKELGMPAIALTDHGVMYGAIELLKLCKGKGIKP 61
Query: 64 IIGCDVWITN-EIENKKPSR-----LLLLVKNNNGYLQLCELLSKAYIENIN----YGRA 113
IIG ++++ N I++ +P + L++L KN GY L +L + +++ + + R
Sbjct: 62 IIGNEMYVINGSIDDPQPKKEKRYHLVVLAKNATGYKNLVKLTTISHLNGMRGRGIFSRP 121
Query: 114 EIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQR 173
I E L++ Y +GLI + G+I A+ GR D+A + A + ++F D+FY+EIQ
Sbjct: 122 CIDKELLKQ--YSEGLIVSTACLGGEIPQAILRGRPDVARDVAAWYKEVFGDDFYLEIQD 179
Query: 174 FKQPNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIK 233
+ + IA + + ++AT+ +L K + AH+ C+ G+++S+ KR++
Sbjct: 180 HGSIEDRIVNVELVRIAKELGIKLIATNDAHYLSKNDVEAHDALLCVLTGKLISDEKRLR 239
Query: 234 KFTKEQNFKTQSEMIKLFYD------IPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKN 287
+T + K++ EM++LF D I AI NT+E+A++ G ++P+FP P+
Sbjct: 240 -YTGTEYIKSEEEMLRLFRDHLDPEVIQEAIANTVEVAEKVEEYDILGTYRMPRFPIPEG 298
Query: 288 ININDFLISKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVS 347
+L ++ GL KRL L EI + YK+RL +E++ I +M F YFL+V
Sbjct: 299 HTAVSYLTEVTEQGLLKRL-KLNSLDEIDE----NYKERLSYELKIIEQMGFPTYFLVVW 353
Query: 348 DFIQWAKNNSIPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDID 407
D+I++A+ IPVGPGRGS A SLVAY+L IT+IDP+ LLFERFLNP R SMPD D D
Sbjct: 354 DYIRFAREQGIPVGPGRGSAAGSLVAYALGITNIDPVKNGLLFERFLNPERKSMPDIDTD 413
Query: 408 FCPEGRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPF 467
FC E R VI YV RYG+D V+QI+TF M +K ++DV RVLD+ Y D ++KLIP
Sbjct: 414 FCIERRGEVIDYVTRRYGEDKVAQIITFNRMTSKAVLKDVARVLDIPYGEADRLAKLIPV 473
Query: 468 KPGKLITLSNAIKEE---PQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPS 524
GK L I +E P+ E+ + + V++ +++A ++EG + G+HA GV+IA
Sbjct: 474 VRGKPAKLKAMIGKESPSPEFREKYEKDPRVKKWVDMAMRIEGTNKTFGVHAAGVVIASD 533
Query: 525 KLINFCPL-YKQEGMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKT 583
L PL +G +I+QY +DIE +GL+K DFLGL L++++KT+ +++ +
Sbjct: 534 PLDELVPLQRNNDGQ--VITQYFMEDIESLGLLKMDFLGLKNLTMIEKTLELVEQ--STG 589
Query: 584 TNFSLNKLPLNDKDTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPG 643
+ LPL+D+ T+ LL + + +FQLES GM+ ++++ KP E+I ++++LYRPG
Sbjct: 590 ERIDPDNLPLDDEKTFELLARGDLEGIFQLESSGMRQVVRDLKPSSLEDISSILALYRPG 649
Query: 644 PMD--LIKNFCRRKHG-EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQAD 700
P+D LI F RKHG E ++ P + +L+ETYGIMVYQEQ+M+IAQ L GYSLGQAD
Sbjct: 650 PLDAGLIPKFINRKHGREAIDFAHPLLEPILTETYGIMVYQEQIMKIAQDLAGYSLGQAD 709
Query: 701 LLRRAIGKKKTSEMIEHRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYAL 760
LLRRA+GKKK SEM +HR F GA K G+ + A+E+F+++ FA Y FNKSH+TAY
Sbjct: 710 LLRRAMGKKKVSEMQKHRGIFVEGASKRGVDEKVADELFDQMVLFAEYCFNKSHSTAYGA 769
Query: 761 LSYYTAYLKTHYSSFFMAANLSLSMDDTNKIKILVKDAIKTC---GLSILPPNINLSKYY 817
++Y TAYLK HY +MAA L+++ ++K V+ I C G+ ++PP+IN S
Sbjct: 770 VTYQTAYLKAHYPVAYMAALLTVNAGSSDK----VQRYISNCNSMGIEVMPPDINRSGID 825
Query: 818 FFPIIESDGKHKKIRYGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYINRR 876
F P K +I +GL A+K G I I+ R G F +L D R+ +NRR
Sbjct: 826 FTP------KGNRILFGLSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRLPSNVLNRR 879
Query: 877 IINSLINSGAFDCFNEK--RYMLVASIDVALKNAEKTKK--FINQLSLF------KNDDN 926
+ SLI+ GA D F+ R L+A +D+ L A + Q +LF + + +
Sbjct: 880 SLESLIHCGALDAFSPNANRAQLIADLDLVLDWASSRARDRASGQGNLFDLLAGSEEEAS 939
Query: 927 NNLKEYLNYVKVPSWSKKQELIEEKKVLGFCLSEHIFCIYETEIRQFIPIYLSELKPTYS 986
N+L VP + ++L EK++LGF LS+H + PI LS L+
Sbjct: 940 NDLSSAPKAAPVPDYPPTEKLKLEKELLGFYLSDHPLKQLTEPAKLLAPISLSSLEEQPD 999
Query: 987 -CTVSGI--ITELKLKTTYRG-KILIIVIDDNSNSVEVIINNQLYEKNKNILKENELLIV 1042
VS I I E+K TT +G ++ I+ ++D + S E ++ + YE+ + L + L+V
Sbjct: 1000 KAKVSAIAMIPEMKQVTTRKGDRMAILQLEDLTGSCEAVVFPKSYERLSDHLMTDTRLLV 1059
Query: 1043 SGKVLEDR 1050
KV DR
Sbjct: 1060 WAKV--DR 1065
>gnl|CDD|180749 PRK06920, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1107
Score = 790 bits (2042), Expect = 0.0
Identities = 386/1053 (36%), Positives = 594/1053 (56%), Gaps = 60/1053 (5%)
Query: 5 FIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPI 64
F+HL+ + +S++ +I++++ A +LAITD + ++G+I FYK+ GI PI
Sbjct: 3 FVHLQCQTVFSLLKSACKIDELVVRAKELGYSSLAITDENVMYGVIPFYKACKKHGIHPI 62
Query: 65 IGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCE----LLSKAYIENINYGRAEIRIEWL 120
IG I +E E +K L+LL +N GY L + +++K+ + I +WL
Sbjct: 63 IGLTASIFSE-EEEKSYPLVLLAENEIGYQNLLKISSSIMTKS--------KEGIPKKWL 113
Query: 121 EKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPD-NFYIEIQRFKQ-PN 178
Y GLIA+S G+I + + AE AR + +F + ++ +
Sbjct: 114 AH--YAKGLIAISPGKDGEIEQLLLEDKESQAEEVARAYQNMFGNFYMSLQHHAIQDELL 171
Query: 179 MNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKE 238
+ ++ +F N +N+P+VAT+ ++++ +++ L HE + G +++ R + T +
Sbjct: 172 LQEKLPEFSN---RVNIPVVATNDVRYINQSDALVHECLLSVESGTKMTDPDRPRLKTDQ 228
Query: 239 QNFKTQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKS 298
K+ EM LF +P AI NT+EIA+RC +++ F +LPKFP P N + +L
Sbjct: 229 YYLKSSDEMEALFSHVPEAIYNTVEIAERCRVEIPFHVNQLPKFPVPSNETADMYLRRVC 288
Query: 299 KHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSI 358
+ GL+KR Y K + RL E+ I +M FS YFLIV DF+++A N I
Sbjct: 289 EEGLQKR----------YGTPKEVHINRLNHELNVISRMGFSDYFLIVWDFMKYAHENHI 338
Query: 359 PVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQ 418
GPGRGS A SLV+Y L ITDIDP+ Y+LLFERFLNP R+++PD DIDF RD +I+
Sbjct: 339 LTGPGRGSAAGSLVSYVLEITDIDPIEYDLLFERFLNPERVTLPDIDIDFPDTRRDEMIR 398
Query: 419 YVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNA 478
YVKD+YG+ V+QIVTFGT+AAK AIRD+ RV+ L D SKLIP K G ITL +A
Sbjct: 399 YVKDKYGQLRVAQIVTFGTLAAKAAIRDIARVMGLPPRDIDIFSKLIPSKLG--ITLKDA 456
Query: 479 IKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQEGM 538
+E L E I+ ++ E+AK+VEG+ R+ +HA GV+++ L + QEG
Sbjct: 457 YEESQSLREFIQGNLLHERVFEIAKRVEGLPRHTSIHAAGVIMSQEPLTGSVAI--QEGH 514
Query: 539 TGI-ISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDKD 597
+ ++QY D +EE+GL+K DFLGL L++L+ I FI++ K + LPL D+
Sbjct: 515 NDVYVTQYPADALEELGLLKMDFLGLRNLTLLENIIKFIEQKTGKEIDIR--NLPLQDEK 572
Query: 598 TYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDLIKNFCRRKHG 657
T+ LL + +T VFQLES GM+N+L+ KP+ FE+I+A+ SLYRPGPM+ I F KHG
Sbjct: 573 TFQLLGRGDTTGVFQLESSGMRNVLRGLKPNEFEDIVAVNSLYRPGPMEQIPTFIESKHG 632
Query: 658 EY-FNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTSEMIE 716
+ Y P K +L TYG++VYQEQ+MQIA L G+SLG+ADLLRRA+ KK + +
Sbjct: 633 KRKIEYLHPDLKPILERTYGVIVYQEQIMQIASKLAGFSLGEADLLRRAVSKKNRDILDQ 692
Query: 717 HRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYSSFF 776
RK F G ++ G + A +I++ I +FA YGFN+SHA AY+++ Y AYLK +Y+ F
Sbjct: 693 ERKHFVQGCLQNGYDETSAEKIYDLIVRFANYGFNRSHAVAYSMIGYQLAYLKANYTLEF 752
Query: 777 MAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIRYGLG 836
M A LS ++ + +KI +++ K G +LPP++ S Y F + IRY L
Sbjct: 753 MTALLSSAIGNEDKIVQYIRET-KRKGFHVLPPSLQRSGYNFQI------EGNAIRYSLL 805
Query: 837 AIKGTGKSTIEAIVTERKFGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRYM 896
+I+ G +T+ A+ ER+ F +LF+F R+ K++ R + + + SG FD F R
Sbjct: 806 SIRNIGMATVTALYEEREKKMFEDLFEFCLRMPSKFVTERNLEAFVWSGCFDDFGVSRTN 865
Query: 897 LVASIDVALKNAEKTKKFINQLSLFKNDDNNNLKEYLNYVKVPSWSKKQELIEEKKVLGF 956
L S+ AL+ A L ++ + K YV+ S ++L +EK+VLGF
Sbjct: 866 LWKSLKGALEYAN----------LARDLGDAVPKS--KYVQGEELSFIEQLNKEKEVLGF 913
Query: 957 CLSEHIFCIYETEIRQF--IPIYLSELKPTYSCTVSGIITELKLKTTYRG-KILIIVIDD 1013
LS + Y ++ + + IT +K+ T +G K+ I D
Sbjct: 914 YLSSYPTAQYVKLAKELEIPSLAQAMRHKKKVQRAIVYITSVKVIRTKKGQKMAFITFCD 973
Query: 1014 NSNSVEVIINNQLYEKNKNILKENELLIVSGKV 1046
++ +E ++ + Y + L+E +++V G +
Sbjct: 974 QNDEMEAVVFPETYIHFSDKLQEGAIVLVDGTI 1006
>gnl|CDD|181933 PRK09532, PRK09532, DNA polymerase III subunit alpha; Reviewed.
Length = 874
Score = 599 bits (1546), Expect = 0.0
Identities = 314/808 (38%), Positives = 483/808 (59%), Gaps = 63/808 (7%)
Query: 5 FIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPI 64
F+ L +HS+YS++DG ++ +++ A PA+A+TD ++G I+ K NKGIKPI
Sbjct: 3 FVGLHIHSDYSLLDGASQLPALVDRAIELGMPAIALTDHGVMYGAIELLKVCRNKGIKPI 62
Query: 65 IGCDVWITN-EIENKKPSR---LLLLVKNNNGYLQLCELLSKAYIENIN----YGRAEIR 116
IG ++++ N +IE +K R ++L KN GY L +L + ++++ + + R I
Sbjct: 63 IGNEMYVINGDIEKQKRRRKYHQVVLAKNTQGYKNLVKLTTISHLQGVQGKGIFARPCIN 122
Query: 117 IEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQ 176
E LE+ Y +GLI S G+I A+ +GR D A A+ + K+F D+FY+EIQ
Sbjct: 123 KELLEQ--YHEGLIVTSACLGGEIPQAILSGRPDAARKVAKWYKKLFGDDFYLEIQDHGS 180
Query: 177 PNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFT 236
+ + IA + + I+AT+ F+ + AH+ CI G++++ KR++ ++
Sbjct: 181 QEDRIVNVEIVKIARELGIKIIATNDSHFISCYDVEAHDALLCIQTGKLITEDKRLR-YS 239
Query: 237 KEQNFKTQSEMIKLFYD------IPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNINI 290
+ K+ EM LF D I AI NT+E+A + G+P++P +P P
Sbjct: 240 GTEYLKSAEEMRLLFRDHLPDDVIAEAIANTLEVADKIEPYNILGEPRIPNYPVPSGHTP 299
Query: 291 NDFLISKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFI 350
+ ++ + GL +RL + E + YK+RL++E++ + +M FS YFL+V D+I
Sbjct: 300 DTYVEEVAWQGLLERL----NCKSRSEVEPV-YKERLEYELKMLQQMGFSTYFLVVWDYI 354
Query: 351 QWAKNNSIPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCP 410
++A++N+IPVGPGRGS A SLVAY L IT+IDP+ + LLFERFLNP R SMPD D DFC
Sbjct: 355 KYARDNNIPVGPGRGSAAGSLVAYCLKITNIDPVHHGLLFERFLNPERKSMPDIDTDFCI 414
Query: 411 EGRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPF--- 467
E RD +I+YV ++YG+D V+QI+TF M +K ++DV RVLD+ Y D ++KLIP
Sbjct: 415 ERRDEMIKYVTEKYGEDRVAQIITFNRMTSKAVLKDVARVLDIPYGEADKMAKLIPVSRG 474
Query: 468 KPGKLITLSNAIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLI 527
KP KL + + EP+ E+ N+ VR+ +++A ++EG + G+HA GV+I+ L
Sbjct: 475 KPTKLKVMISDETPEPEFKEKYDNDPRVRRWLDMAIRIEGTNKTFGVHAAGVVISSEPLD 534
Query: 528 NFCPLYK-QEGMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNF 586
PL K +G +I+QY +D+E +GL+K DFLGL L+ + KT IK+ +
Sbjct: 535 EIVPLQKNNDG--AVITQYFMEDLESLGLLKMDFLGLRNLTTIQKTADLIKE--NRGVEI 590
Query: 587 SLNKLPLNDKD-------------------TYNLLKKANTVAVFQLESQGMKNMLKEAKP 627
L++LPL+++ T+ LL++ + +FQLES GMK ++++ KP
Sbjct: 591 DLDQLPLDERKALKILAKGEAKKLPKDVQKTHKLLERGDLEGIFQLESSGMKQIVRDLKP 650
Query: 628 DYFEEIIALISLYRPGPMD--LIKNFCRRKHG-EYFNYPDPRTKDVLSETYGIMVYQEQV 684
E+I ++++LYRPGP+D LI F RKHG E +Y + +L+ETYG++VYQEQ+
Sbjct: 651 SNIEDISSILALYRPGPLDAGLIPKFINRKHGREPIDYEHQLLEPILNETYGVLVYQEQI 710
Query: 685 MQIAQILGGYSLGQADLLRRAIGKKKTSEMIEHRKFFQNGAIKYGLSKHKANEIFNEIEK 744
M++AQ L GYSLG+ADLLRRA+GKKK SEM +HR+ F +GA K G+SK A +F+++ K
Sbjct: 711 MKMAQDLAGYSLGEADLLRRAMGKKKISEMQKHREKFIDGAAKNGVSKKVAENLFDQMVK 770
Query: 745 FAGYGFNKSHATAYALLSYYTAYLKTHY 772
FA Y LSY T L Y
Sbjct: 771 FAEY-----------CLSYDTEVLTVEY 787
>gnl|CDD|219543 pfam07733, DNA_pol3_alpha, Bacterial DNA polymerase III alpha
subunit.
Length = 384
Score = 560 bits (1445), Expect = 0.0
Identities = 213/441 (48%), Positives = 283/441 (64%), Gaps = 60/441 (13%)
Query: 292 DFLISKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQ 351
++L + GLK+R + +Y++RL+ E+ IIKM F+GYFLIV D ++
Sbjct: 1 EYLRKLCEEGLKERYGDGVPK---------KYQERLEKELNVIIKMGFAGYFLIVWDLVK 51
Query: 352 WAKNNSIPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPE 411
WAK+N IPVGPGRGS A SLVAY L IT++DPL ++LLFERFLNP R SMPD DIDF E
Sbjct: 52 WAKDNGIPVGPGRGSAAGSLVAYLLGITEVDPLKHDLLFERFLNPERDSMPDIDIDFEDE 111
Query: 412 GRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGK 471
R+ VI YVK++YG+D V+QI TFGT+AAK AIRDVGR
Sbjct: 112 RREEVIDYVKEKYGEDRVAQIATFGTLAAKSAIRDVGRA--------------------- 150
Query: 472 LITLSNAIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCP 531
+LIELAK++EG+ R+ G HAGGV+I+ L +F P
Sbjct: 151 -------------------------ELIELAKKLEGLPRHTGQHAGGVVISDDPLTDFVP 185
Query: 532 LYKQEGMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKL 591
L K ++Q+DKDD+E++GL+KFDFLGL TL+I+ + IK+ + + L +
Sbjct: 186 LQKPADDDRPVTQFDKDDLEDLGLLKFDFLGLRTLTIIRDALDLIKE--NRGIDIDLATI 243
Query: 592 PLNDKDTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDL--IK 649
PL+D TY LL +T+ VFQ ES+GM++MLK KPD FE+++AL +LYRPGPM +
Sbjct: 244 PLDDPKTYKLLSSGDTLGVFQFESRGMRSMLKRLKPDTFEDLVALSALYRPGPMQGGNVD 303
Query: 650 NFCRRKHG-EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGK 708
++ +RKHG E YP P + +L ETYG++VYQEQVMQIAQIL G+SLG+ADLLRRA+GK
Sbjct: 304 DYIKRKHGKEKIEYPHPDLEPILKETYGVIVYQEQVMQIAQILAGFSLGEADLLRRAMGK 363
Query: 709 KKTSEMIEHRKFFQNGAIKYG 729
KK EM + R+ F GA + G
Sbjct: 364 KKPEEMEKLREKFIEGAKENG 384
>gnl|CDD|235944 PRK07135, dnaE, DNA polymerase III DnaE; Validated.
Length = 973
Score = 539 bits (1390), Expect = e-175
Identities = 330/1038 (31%), Positives = 512/1038 (49%), Gaps = 97/1038 (9%)
Query: 4 QFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKP 63
+ I+L ++EYS + ++++ +I+ A + L +TD +N+FG+ KFYK IKP
Sbjct: 2 KLINLHTNTEYSFLSSTIKLDSLIKYAKENNLKTLVLTDHNNMFGVPKFYKLCKKNNIKP 61
Query: 64 IIGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEKN 123
IIG D+ E+EN R +LL KN +GY L EL SK EI + L+
Sbjct: 62 IIGLDL----EVENF---RFILLAKNYSGYKLLNELSSK------KSKNKEIELNDLDS- 107
Query: 124 KYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMNF-Q 182
D +I + G +A+ ++ N+YI K N + Q
Sbjct: 108 ---DNIIIIDHPKNG---------------FYAKNKEQLELKNYYINSNDPKIENAVYVQ 149
Query: 183 IQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQNFK 242
++ + N L I+ I + ++ + F K
Sbjct: 150 ERKLLFAEDNEYLKILNK-------------------IGNNKEENSNFKFFDFEKW---- 186
Query: 243 TQSEMIKLFYDIPSAI-QNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKSKHG 301
F DI I + T + + N++ + LP F + + FL K
Sbjct: 187 --------FEDIDEKILKRTNYLVENINIEFPKKEFNLPDFDNNLGLESDLFLKKILKES 238
Query: 302 LKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIPVG 361
+ + L P + K+R+ +E I K+ FS YFLI+ DFI+WA+ N I +G
Sbjct: 239 VINKKAELKYYPNV--------KERINYEYSVIKKLKFSNYFLIIWDFIKWARKNKISIG 290
Query: 362 PGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQYVK 421
PGRGS + SLV+Y L+IT ++PL Y+LLFERFLNP+RI+MPD DID + RD VI Y+
Sbjct: 291 PGRGSASGSLVSYLLNITSVNPLKYDLLFERFLNPDRITMPDIDIDIQDDRRDEVIDYIF 350
Query: 422 DRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKE 481
++YG + + I TF T+ AK AIRDVGR+L + S ++ISKLIP +L A +
Sbjct: 351 EKYGYEHCATISTFQTLGAKSAIRDVGRMLGIPESDVNAISKLIPNN----QSLEEAYDK 406
Query: 482 EPQLAERIKNEEEV--RQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQEGMT 539
+ ++ + ++L ++AK++EG+ R G HA G++I+ + N+ P ++ +
Sbjct: 407 NKSFFRELISKGDPIYKKLYKIAKKLEGLPRQSGTHAAGIIISNKPITNYVPTFESK-DN 465
Query: 540 GIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDKDTY 599
QY + +E+ GL+K D LGL L+I+ I K + N LP+ DK T
Sbjct: 466 YNQVQYSMEFLEDFGLLKIDLLGLKNLTIIKNIEEKINKELLFDHLINFNDLPIIDKKTN 525
Query: 600 NLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDLIKNFCRRKHGEY 659
NLL T +FQLES GMK+ +K+ D FE+I+A+ISLYRPGP+ I + + K
Sbjct: 526 NLLSNGKTEGIFQLESPGMKSTIKKVGIDSFEDIVAIISLYRPGPIQYIPIYAKNKKNPK 585
Query: 660 -FNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTSEMIEHR 718
P ++++ TYGI++YQEQ+MQIAQ + G+S QADLLRRAI KK +++ + +
Sbjct: 586 NIEKIHPEYDEIVAPTYGIIIYQEQIMQIAQKVAGFSFAQADLLRRAISKKDETKLDKIK 645
Query: 719 KFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYSSFFMA 778
F G IK G SK +I++ IEKFA YGFNKSHA AYA L+Y AY K +Y F +
Sbjct: 646 DKFIEGGIKNGYSKKVLEKIYSLIEKFADYGFNKSHAVAYATLAYKMAYYKANYPLVFYS 705
Query: 779 ANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIRYGLGAI 838
A +S S IK VK+A K G+ + P+IN S + +G KI L I
Sbjct: 706 ALISNSNGSQENIKKYVKEA-KNNGIKVYSPDINFS---TENAVFDNG---KIFLPLIMI 758
Query: 839 KGTGKSTIEAIVTERK-FGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRYML 897
KG G I+ I+ ER G + N FDF R+ I++ II LI + F + L
Sbjct: 759 KGLGSVAIKKIIDERNKNGKYKNFFDFILRLKFIGISKSIIEKLIKANTLRSFGNQD-TL 817
Query: 898 VASIDVALKNAEKTKKFINQLSLFKNDDNNNLKEYLNYVKVPSWSKKQELIEEKKVLGFC 957
+ ++++A AE + + +D N + ++ ++E E + LG
Sbjct: 818 LNNLELAKNYAETILSKVAK--NLYDDYKNFGLDLEFILEEIERDLEEESKNEIEYLGMS 875
Query: 958 LSEHIFCIYETEIRQFIPIYLSELKPTYSCTVSGIITELKLKTTYRGKILIIVIDDNSNS 1017
+ E I L +L+ ++ + +K + +++ D+S
Sbjct: 876 FNAFDTNKLEKN-----QIRLKDLRINTEYRLAIEVKNVKRLRKANKEYKKVILSDDSVE 930
Query: 1018 VEVIINNQLYEKNKNILK 1035
+ + +N+ Y + + K
Sbjct: 931 ITIFVNDNDYLLFETLKK 948
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 529 bits (1364), Expect = e-170
Identities = 348/1149 (30%), Positives = 561/1149 (48%), Gaps = 143/1149 (12%)
Query: 5 FIHLRLHSEYSIIDGLLRINDVIEAAAN-DYQPALAITDLSNLFGIIKFYKSAYNKGIKP 63
F L + YS +D L+ + +E A YQ + I D NL+G F + A G++P
Sbjct: 2 FAQLDTKTVYSFMDSLIDLEKYVERAKELGYQ-TIGIMDKDNLYGAYHFIEGAQKNGLQP 60
Query: 64 IIGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEKN 123
I+G ++ I E ++ L L+ KN GY L ++ + G+ ++ + +
Sbjct: 61 ILGLELNIFVE---EQEVTLRLIAKNTQGYKNLLKISTA-----KMSGK----KQFSDLS 108
Query: 124 KYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMNFQI 183
+Y +G IAV I F + P ++YI + + P +F
Sbjct: 109 QYLEG-------------IAV------IVPYFDWSETLELPFDYYIGV-DQETPGSDF-- 146
Query: 184 QQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQNFKT 243
PI+ +++ + + ++ I + L + + +Q +
Sbjct: 147 ----------KRPILPLRTVRYFESADRETLQMLHAIRDNLSLREVPLV---SSDQELIS 193
Query: 244 QSEMIKLFYD-IPSAIQN----TIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKS 298
+ LF + P A+ N I+ + L KLP+F ++ + L +
Sbjct: 194 CQSLETLFQERFPQALDNLEKLVSGISYDFDTDL-----KLPRFN--RDRPAVEELRELA 246
Query: 299 KHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSI 358
+ GLK++ L+ P Y++RL E+ I M F YFLIV D +++ ++
Sbjct: 247 ELGLKEK--GLWSSP---------YQERLDKELSVIHDMGFDDYFLIVWDLLRFGRSQGY 295
Query: 359 PVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQ 418
+G GRGS A SLVAY+L IT IDP+ +NLLFERFLN R SMPD DID R ++
Sbjct: 296 YMGMGRGSAAGSLVAYALDITGIDPVKHNLLFERFLNKERYSMPDIDIDLPDIYRSEFLR 355
Query: 419 YVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNA 478
YV++RYG D +QIVTF T AK AIRDV + + +++K I F+ +L++
Sbjct: 356 YVRNRYGSDHSAQIVTFSTFGAKQAIRDVFKRFGVPEYELSNLTKKISFRD----SLASV 411
Query: 479 IKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQEGM 538
++ + I ++ E ++ E+AK++EG R +HA GV+++ L N PL + M
Sbjct: 412 YEKNISFRQIINSKLEYQKAFEIAKRIEGNPRQTSIHAAGVVMSDDDLTNHIPLKYGDDM 471
Query: 539 TGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDKDT 598
+I+QYD +E GL+K DFLGL L+ + K + K + + + L DK+T
Sbjct: 472 --MITQYDAHAVEANGLLKMDFLGLRNLTFVQKMQEKVAK--DYGIHIDIEAIDLEDKET 527
Query: 599 YNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDLIKNFCRRKHG- 657
L +T +FQ E G N+LK KP FE+I+A SL RPG D NF +R+HG
Sbjct: 528 LALFAAGDTKGIFQFEQPGAINLLKRIKPVCFEDIVATTSLNRPGASDYTDNFVKRRHGQ 587
Query: 658 EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTSEMIEH 717
E + DP +L TYGIM+YQEQVMQIAQ+ G+SLG+ADLLRRA+ KK SEM +
Sbjct: 588 EKVDLIDPVIAPILEPTYGIMLYQEQVMQIAQVFAGFSLGKADLLRRAMSKKNASEMQKM 647
Query: 718 RKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYSSFFM 777
+ F GA++ G S+ KA E+F+ +EKFAGYGFN+SHA AY+ L++ AY K HY + F
Sbjct: 648 EEDFLQGALELGHSEEKARELFDRMEKFAGYGFNRSHAFAYSALAFQLAYFKAHYPAVFY 707
Query: 778 AANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIRYGLGA 837
L+ S D + DA++ G + +IN Y+ ++KKI GL
Sbjct: 708 DIMLNYSSSD------YITDALEF-GFEVAKLSINTIPYHDKI------ENKKIYLGLKN 754
Query: 838 IKGTGKSTIEAIVTERKFGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRYML 897
IKG + I+ R F+++ DF R+ + Y + + LI G FD F + R +
Sbjct: 755 IKGLPRDLAYWIIENRP---FSSIEDFLTRLPENYQKKEFLEPLIKIGLFDSFEKNRQKI 811
Query: 898 VASIDVALKNAEKTKKFINQL-SLFKNDDNNNLKEYLNYVKVPSWSKKQELIEEKKVLGF 956
+ N + F+N+L SLF + ++V+ +S+ ++ E+++LG
Sbjct: 812 IN-------NLDNLFVFVNELGSLFAD-------SSYSWVEAEDYSETEKYSLEQELLGV 857
Query: 957 CLSEH-IFCIYETEIRQFIPIYLSELKPTYSCTVSGIITELKL-KTTYRGK-ILIIVIDD 1013
+S+H + I E R F PI S+L T+ I +++ +T +G+ + + + D
Sbjct: 858 GVSKHPLQAIAEKSSRPFTPI--SQLVKNSEATILVQIQSIRVIRTKTKGQQMAFLSVTD 915
Query: 1014 NSNSVEVIINNQLYEKNKNILKENELLIVSGKVLE--DRF---LKNIRINAEKIFDINVA 1068
++V + + Y + K+ LKE + + GK+ E R L+ I+ + + F I +
Sbjct: 916 TKKKLDVTLFPETYRQYKDELKEGKFYYLKGKIQERDGRLQMVLQQIQEASSERFWILLE 975
Query: 1069 RILYGKKFSVMFNRTFNISILKKILLRFKCKNGLPFVLYYCINK-SIKYEMKFPLNYKVQ 1127
N + I +IL F +P +++Y K +I+ + V
Sbjct: 976 ------------NHEHDQEI-SEILGAFPGS--IPVIIHYQEEKETIQST-----HIFVA 1015
Query: 1128 PIDDLKLAL 1136
++L+ L
Sbjct: 1016 KSEELEEKL 1024
>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
Length = 971
Score = 522 bits (1345), Expect = e-168
Identities = 316/921 (34%), Positives = 456/921 (49%), Gaps = 100/921 (10%)
Query: 5 FIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPI 64
FI+L HS YS++ L I+D+I+ A ++ QP + +TDL+NL+G I+FY A + PI
Sbjct: 2 FINLNTHSHYSLLSSTLSIDDIIKFALDNNQPYVCLTDLNNLYGCIEFYDKAKAHNLIPI 61
Query: 65 IGCDVWITNEIENKKP-SRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEKN 123
IG EIE + + L+L KN NGYL L ++ S ++ N
Sbjct: 62 IGL------EIEYQSTNATLVLYAKNYNGYLNLIKISS-----------------FIMTN 98
Query: 124 K---YQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMN 180
K QD +L D+ I + G NFY Q Q N
Sbjct: 99 KEFEIQD--------YLDDLFIVCKKGTFVFKS-----------PNFY---QTHNQNAPN 136
Query: 181 FQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQN 240
+ A N N K F A + N +I + Q+
Sbjct: 137 AIAFNSVFYA-NKN------------DKIVFNAMLA---------IKNDLKIDELKNCQD 174
Query: 241 FK-----TQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLI 295
F +E LF I + N ++ +++ + K+ +I ++ L
Sbjct: 175 FDNNHFLNDNEAQSLFSPI--QLDNLNKVLNELKVEIHDLPINIIKYDKQNSIISSEILK 232
Query: 296 SKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKN 355
GL KRL K Y KRL++E++ I + F YFLIV DFI +AK+
Sbjct: 233 QLCISGLNKRL------NANDGQVKKIYVKRLKYELDIINEKQFDDYFLIVYDFINFAKS 286
Query: 356 NSIPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDR 415
N I +GPGRGS A SL+AY L ITDIDP+ YNL+FERFLNP R SMPD D D E RD
Sbjct: 287 NGIIIGPGRGSAAGSLIAYLLHITDIDPIKYNLIFERFLNPTRKSMPDIDTDIMDERRDE 346
Query: 416 VIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITL 475
V++Y+ ++YG D V+ I+TF + AK AIRDVGR+L + D I K I KP L
Sbjct: 347 VVEYLFEKYGNDHVAHIITFQRIKAKMAIRDVGRILGIDLKVIDKICKNI--KPDYEEDL 404
Query: 476 SNAIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQ 535
AIK+ L E +E L +LAK++ R +G HA GV+++ S L N P+ Q
Sbjct: 405 DLAIKKNTILKEMYVLHKE---LFDLAKKIINAPRQIGTHAAGVVLSNSLLTNIIPI--Q 459
Query: 536 EGMTG-IISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLN 594
G+ +SQY + +E GLIK D LGL L+I+D + IK+ + L + LN
Sbjct: 460 LGINDRPLSQYSMEYLERFGLIKMDLLGLKNLTIIDNVLKLIKE--NQNKKIDLFNINLN 517
Query: 595 DKDTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDLIKNFCRR 654
DK+ + L K T +FQLES GMK +LK+ KP E+I + +L+RPGP IK F R
Sbjct: 518 DKNVFEDLAKGRTNGIFQLESPGMKKVLKKVKPQNIEDISIVSALFRPGPQQNIKTFVER 577
Query: 655 KHG-EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTSE 713
+ E F+Y + TK +L T+GI+VYQEQV+ + + + + + AD RRAI KK
Sbjct: 578 RFKREEFSYWNEATKKILEPTHGIIVYQEQVINLVKTIANFDIATADNFRRAISKKDEKI 637
Query: 714 MIEHRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYS 773
+I+ +K F GA+K + N+IF I FA YGFN SH+ AY+ +SY+ AYLK +Y
Sbjct: 638 LIQLKKDFIEGALKNNYKQPLVNQIFEYIFSFADYGFNHSHSLAYSYISYWMAYLKHYYP 697
Query: 774 SFFMAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIRY 833
F++ LS + +K+ + + K +SI P+IN S F D + + IR+
Sbjct: 698 LEFLSILLSHTSASKDKLLSYL-NEAKEFNISIKKPDINYSSNSF----VLDTQKQIIRF 752
Query: 834 GLGAIKGTGKSTIEAIVTERKFGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEK 893
G IKG G ++ I + + F++ + + K ++ I LIN G FD F
Sbjct: 753 GFNTIKGFGDELLKKIKSALQNKTFSDFISYIDALKKNNVSLSNIEILINVGTFDSFKLS 812
Query: 894 RYMLVASIDVALKNAEKTKKF 914
R L+ ++ + F
Sbjct: 813 RLFLLNNLPEIFEKTSLNGHF 833
>gnl|CDD|235553 PRK05672, dnaE2, error-prone DNA polymerase; Validated.
Length = 1046
Score = 490 bits (1263), Expect = e-155
Identities = 275/922 (29%), Positives = 457/922 (49%), Gaps = 84/922 (9%)
Query: 1 MIPQFIHLRLHSEYSIIDG------LLRINDVIEAAANDYQPALAITDLSNLFGIIKFYK 54
M+P + L HS +S +DG L V AA + ALAITD L G+++ +
Sbjct: 1 MLPPYAELHCHSNFSFLDGASHPEEL-----VERAARLGLR-ALAITDECGLAGVVRAAE 54
Query: 55 SAYNKGIKPIIGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAE 114
+A G++ +IG ++ + + + P LL+L ++ GY +L L+++A + RA
Sbjct: 55 AAKELGLRLVIGAELSLGPDPDPGGP-HLLVLARDREGYGRLSRLITRARL------RAG 107
Query: 115 IRIEWLEKNKYQ---DGLIALSGAHLGDI-----GIAVQN----GRNDIAENFARRWSKI 162
K +Y+ D L +G H + G + G A
Sbjct: 108 -------KGEYRLDLDDLAEPAGGHWAILTGCRKGFVILALPYGGDAAALAALAALLDAF 160
Query: 163 FPDNFYIEIQRFKQPNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAE 222
F D ++E+ +P+ + + + +A+ +P+VAT + ++ + T I
Sbjct: 161 FADRVWLELTLHGRPDDDRRNARLAALAARAGVPLVATGDVHMHHRSRRRLQDAMTAIRA 220
Query: 223 GEILSNTKRIKKFTKEQNFKTQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKF 282
L+ E++ ++ +EM +LF D P A+ T+E+A+RC L+ + P
Sbjct: 221 RRSLAEAGGWLAPNGERHLRSGAEMARLFPDYPEALAETVELAERCAFDLDLLAYEYPDE 280
Query: 283 PTPKNININDFLISKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGY 342
P P +L ++ G +R Y K R +++ E+ I ++ + GY
Sbjct: 281 PVPAGHTPASWLRQLTEAGAARR----YGPG---IPPKAR--AQIEHELALIAELGYEGY 331
Query: 343 FLIVSDFIQWAKNNSIPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMP 402
FL V D +++A++ I + GRGS A+S V Y+L IT++DP+ LLFERFL+P R P
Sbjct: 332 FLTVHDIVRFARSQGI-LCQGRGSAANSAVCYALGITEVDPVQSGLLFERFLSPERDEPP 390
Query: 403 DFDIDFCPEGRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSIS 462
D D+DF + R+ VIQYV RYG+D +Q+ T + A+RDV + L L D+ +
Sbjct: 391 DIDVDFEHDRREEVIQYVYRRYGRDRAAQVANVITYRPRSAVRDVAKALGLSPGQVDAWA 450
Query: 463 KLIPFKPGKLITLSNAIKEEPQLAERIKNEEE--VRQLIELAKQVEGIIRNVGMHAGGVL 520
K + G L +L + + E R+++ELA Q+ G R++ H+GG +
Sbjct: 451 KQVSRWSGSADDL-------QRLRQAGLDPESPIPRRVVELAAQLIGFPRHLSQHSGGFV 503
Query: 521 IAPSKLINFCPL--YKQEGMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKK 578
I L P+ EG + I Q+DKDD +GL+K D L L LS L + I
Sbjct: 504 ICDRPLARLVPVENAAMEGRSVI--QWDKDDCAAVGLVKVDVLALGMLSALHRAFDLIA- 560
Query: 579 INTKTTNFSLNKLPLNDKDTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALIS 638
+ +L +PL+D Y++L +A++V VFQ+ES+ ML +P F +++ ++
Sbjct: 561 -EHRGRRLTLASIPLDDPAVYDMLCRADSVGVFQVESRAQMAMLPRLRPRTFYDLVVEVA 619
Query: 639 LYRPGPM--DLIKNFCRRKHG-EYFNYPDPRTKDVLSETYGIMVYQEQVMQIAQILGGYS 695
+ RPGP+ ++ + RR++G E YP P + VL T G+ ++QEQVMQIA G++
Sbjct: 620 IVRPGPIQGGMVHPYLRRRNGQEPVTYPHPELEKVLERTLGVPLFQEQVMQIAIDAAGFT 679
Query: 696 LGQADLLRRAIGKKKTSEMIE-HRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSH 754
G+AD LRRA+ + +E R+ +G + G + A+ IF +I+ F YGF +SH
Sbjct: 680 PGEADQLRRAMAAWRRKGRLERLRERLYDGMLARGYTGEFADRIFEQIKGFGEYGFPESH 739
Query: 755 ATAYALLSYYTAYLKTHYSSFFMAANL-SLSMD----DTNKIKILVKDAIKTCGLSILPP 809
A ++A L Y +++LK H+ + F AA L S M LV+DA + G+ +LP
Sbjct: 740 AASFAKLVYASSWLKCHHPAAFCAALLNSQPMGFYSPQQ-----LVQDA-RRHGVEVLPV 793
Query: 810 NINLSKYYFFPIIES-DGKHKKIRYGLGAIKGTGKSTIEAIVTERKFGFFTNLFDFTKRI 868
++N S + +E +R GL ++G G+ E IV R G FT++ D +R
Sbjct: 794 DVNASGWD--ATLEPLPDGGPAVRLGLRLVRGLGEEAAERIVAARARGPFTSVEDLARRA 851
Query: 869 DKKYINRRIINSLINSGAFDCF 890
++RR + +L ++GA
Sbjct: 852 G---LDRRQLEALADAGALRSL 870
>gnl|CDD|213988 cd07433, PHP_PolIIIA_DnaE1, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III
DnaE1. PolIIIAs that contain an N-terminal PHP domain
have been classified into four basic groups based on
genome composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that are responsible for the replication
of the DNA duplex. PolIIIA core enzyme catalyzes the
reaction for polymerizing both DNA strands. dnaE1 is the
longest compared to dnaE2 and dnaE3. A unique motif was
also identified in dnaE1 and dnaE3 genes.
Length = 277
Score = 414 bits (1067), Expect = e-136
Identities = 138/279 (49%), Positives = 189/279 (67%), Gaps = 2/279 (0%)
Query: 4 QFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKP 63
F+HLR+HSEYS++DG +RI +++ A D PALAITDLSNLFG +KFYK+A GIKP
Sbjct: 1 SFVHLRVHSEYSLLDGAVRIKKLVKLAKEDGMPALAITDLSNLFGAVKFYKAASKAGIKP 60
Query: 64 IIGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEKN 123
IIG D+ + N + +P RL LL +N GY L EL+S+AY+E G I++EWL +
Sbjct: 61 IIGADLNVANPDDADEPFRLTLLAQNEQGYKNLTELISRAYLEGQRNGGPHIKLEWLAE- 119
Query: 124 KYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMNFQI 183
Y +GLIALSG GDIG + G D+AE + KIFPD FY+E+QR +P
Sbjct: 120 -YSEGLIALSGGRDGDIGQLLLEGNPDLAEALLQFLKKIFPDRFYLELQRHGRPEEEAYE 178
Query: 184 QQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQNFKT 243
I++A + LP+VAT+ ++FLK +F AHE R CIAEG L + +R ++++ +Q FK+
Sbjct: 179 HALIDLAYELGLPLVATNDVRFLKPEDFEAHEARVCIAEGRTLDDPRRPRRYSPQQYFKS 238
Query: 244 QSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKF 282
EM +LF D+P AI+NT+EIAKRCN+++E GKP LP F
Sbjct: 239 AEEMAELFADLPEAIENTVEIAKRCNVRIELGKPFLPDF 277
>gnl|CDD|213997 cd12113, PHP_PolIIIA_DnaE3, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III
DnaE3. PolIIIAs that contain an N-terminal PHP domain
have been classified into four basic groups based on
genome composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that is responsible for the replication
of the DNA duplex. The alpha subunit of DNA polymerase
III core enzyme catalyzes the reaction for polymerizing
both DNA strands. The PolIIIA PHP domain has four
conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination,
and like other PHP structures, the PolIIIA PHP exhibits
a distorted (beta/alpha) 7 barrel and coordinates up to
3 metals. Initially, it was proposed that PHP region
might be involved in pyrophosphate hydrolysis, but such
an activity has not been found. It has been shown that
the PHP of PolIIIA has a trinuclear metal complex and is
capable of proofreading activity. Bacterial genome
replication and DNA repair mechanisms is related to the
GC content of its genomes. There is a correlation
between GC content variations and the dimeric
combinations of PolIIIA subunits. Eubacteria can be
grouped into different GC variable groups: the
full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1
group, and the low GC or polC-dnaE3 group.
Length = 283
Score = 248 bits (636), Expect = 1e-74
Identities = 118/286 (41%), Positives = 171/286 (59%), Gaps = 12/286 (4%)
Query: 4 QFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKP 63
F+HL +H+EYS++DG +RI D+++ A PALAITD N+FG I+FYK+A GIKP
Sbjct: 1 DFVHLHVHTEYSLLDGAIRIKDLVKRAKELGMPALAITDHGNMFGAIEFYKAAKKAGIKP 60
Query: 64 IIGCDVWITNE--------IENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEI 115
IIGC+V++ +K+ L+LL KN GY L +L+S AY+E Y + I
Sbjct: 61 IIGCEVYVAPGSRFDKKDKKGDKRYYHLVLLAKNEEGYRNLMKLVSLAYLEGF-YYKPRI 119
Query: 116 RIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIF-PDNFYIEIQRF 174
E L KY +GLIALS G+I + NG + A A + IF DNFY+E+Q
Sbjct: 120 DKELLA--KYSEGLIALSACLAGEIPQLLLNGDEEEAREAALEYRDIFGKDNFYLELQDH 177
Query: 175 KQPNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKK 234
P + I +A + +P+VAT+ + +L K + AH+V CI G+ L + R++
Sbjct: 178 GLPEQKKVNEGLIELAKELGIPLVATNDVHYLNKEDAEAHDVLLCIQTGKTLDDPNRMRF 237
Query: 235 FTKEQNFKTQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLP 280
T E K+ EM +LF D+P A++NT+EIA+RCN++L+FGK LP
Sbjct: 238 DTDEFYLKSPEEMRELFPDVPEALENTLEIAERCNVELDFGKLHLP 283
>gnl|CDD|236003 PRK07373, PRK07373, DNA polymerase III subunit alpha; Reviewed.
Length = 449
Score = 175 bits (446), Expect = 3e-47
Identities = 102/317 (32%), Positives = 167/317 (52%), Gaps = 31/317 (9%)
Query: 750 FNKSHATAYALLSYYTAYLKTHYSSFFMAANLSLSMDDTNKIKILVKDAIKTC---GLSI 806
FNKSH+TAYA ++Y TAYLK +Y +MAA L+ + + +K V+ + C G+ +
Sbjct: 38 FNKSHSTAYAYVTYQTAYLKANYPVEYMAALLTANSGNQDK----VQKYRENCQKMGIEV 93
Query: 807 LPPNINLSKYYFFPIIESDGKHKKIRYGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFT 865
PP+IN S F P+ +KI +GL A++ G+ IE+I+ R + G F +L DF
Sbjct: 94 EPPDINRSGKDFTPV------GEKILFGLSAVRNLGEGAIESILKAREEGGEFKSLADFC 147
Query: 866 KRIDKKYINRRIINSLINSGAFDCFNEKRYMLVASIDVALKNAEK--TKKFINQLSLF-- 921
R+D + +NRR + +LI GAFD R L+ +++ + A+K +K Q +LF
Sbjct: 148 DRVDLRVVNRRALETLIYCGAFDKIEPNRQQLINDLELVIDWAQKRAKEKASGQGNLFDL 207
Query: 922 -------KNDDNNNLKEYLNYVKVPSWSKKQELIEEKKVLGFCLSEHIFCIYETEIRQFI 974
+ NN ++ + V +S +++L EK++LGF +SEH R
Sbjct: 208 LGGNTSNSSAANNAFEQAPSAPPVADFSLQEKLKLEKELLGFYVSEHPLKSIRRPARLLS 267
Query: 975 PIYLSELKP----TYSCTVSGIITELKLKTTYRGK-ILIIVIDDNSNSVEVIINNQLYEK 1029
PI LSEL+ T V ++ E+K T +G + + ++D S E ++ + YE+
Sbjct: 268 PINLSELEEQKEKTKVSAVV-MLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYER 326
Query: 1030 NKNILKENELLIVSGKV 1046
+L+ + LI+ GKV
Sbjct: 327 ISELLQVDARLIIWGKV 343
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of this
protein are restricted to the Gram-positive lineages,
including the Mycoplasmas. This protein is designated
alpha chain and given the gene symbol polC, but is not a
full-length homolog of other polC genes. The N-terminal
region of about 200 amino acids is rich in low-complexity
sequence, poorly alignable, and not included n this model
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1213
Score = 139 bits (351), Expect = 4e-33
Identities = 213/980 (21%), Positives = 369/980 (37%), Gaps = 245/980 (25%)
Query: 43 LSNLFGIIKFYKSAYNKGIKPIIGCDVWITNEIENKK--PSRLLLLVKNNNGYLQLCELL 100
+ +F + KGI + + +++E K+ P+ +++ KN G L +L+
Sbjct: 344 TAKVF--KVMVEQLKEKGITNLEELNNKLSSEELYKRLRPNHIIIYAKNQAGLKNLYKLV 401
Query: 101 SKAYIENINYGRAEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWS 160
S + + Y R RI KY++GL+ S G++ A+ + +D E A+R+
Sbjct: 402 SISLTKY-FYTRP--RILRSLLKKYREGLLIGSACSEGELFDALLSKPDDELEEIAKRYD 458
Query: 161 KIF---PDNFYIEIQRFKQPNM---NFQIQQFINIASNINLPIVATHPIQFLKKTEFLAH 214
I P N+ I+R + + I++ I +A +N P+VAT + +++ + +
Sbjct: 459 FIEIQPPGNYAHLIEREQVKDKEALKEIIKKLIELAKELNKPVVATGDVHYIEPEDKIYR 518
Query: 215 EVRTCIAEGEILSNTKRIKKFTKEQNFKTQSEMIKLF--------YDIPSAIQNTIEIAK 266
++ N K E +F+T +EM+ F Y+I ++NT +IA
Sbjct: 519 KILVASQGLGNPLNRHFNPKEVPELHFRTTNEMLDEFSFLGEEKAYEI--VVENTNKIAD 576
Query: 267 RCNLKLEFGKPKLPKFPTPKNININDFLISKSKHGLKKRLLNLYKD--PEIYKCEKLRYK 324
+ E +P K TPK ++ + + KK +Y D PEI +
Sbjct: 577 QI----EEIQPIKDKLYTPKIEGADEKIRDLTYENAKK----IYGDPLPEI-------VE 621
Query: 325 KRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIPVGPGRGSGASSLVAYSLSITDIDPL 384
+R++ E+++II F+ +LI +Q + + VG RGS SSLVA IT+++PL
Sbjct: 622 QRIEKELKSIIGNGFAVIYLISQLLVQKSLQDGYLVGS-RGSVGSSLVATMTGITEVNPL 680
Query: 385 S-----------------------------------------YNLLFERFLNPNRISMPD 403
++ FE FL +PD
Sbjct: 681 PPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLKKDGQDIPFETFLGFKGDKVPD 740
Query: 404 FDIDFCPEGRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISK 463
D++F E + + YVK+ +G+D + T GT+A K A
Sbjct: 741 IDLNFSGEYQAKAHNYVKELFGEDHTFRAGTIGTVAEKTAY------------------- 781
Query: 464 LIPFKPGKLITLSNAIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAP 523
+K+ + + + E+ L + G+ R G H GG++I P
Sbjct: 782 -------------GYVKKYFEDQGKHYRDAEI---ERLVQGCTGVKRTTGQHPGGIIIVP 825
Query: 524 S--KLINFCPLYKQEGMTGIISQYDKDDIEE-----------IG--LIKFDFLGLTTLSI 568
+ +F P+ QY DD I L+K D LG
Sbjct: 826 KYMDVYDFTPV-----------QYPADDTNSDWKTTHFDFHSIHDNLLKLDILGHD---- 870
Query: 569 LDKTIYFIKKINTKTTNFSLNKLPLNDKDT--------------YNLLKKANTVAVFQLE 614
D T IK + T +P++DK+ +L+K T+ + +
Sbjct: 871 -DPT--MIKMLQ-DLTGIDPKTIPMDDKEVMSIFSSPKALGVTPEEILEKTGTLGIPEFG 926
Query: 615 SQGMKNMLKEAKPDYFEEIIALISL------YRPGPMDLIKNFCRRKHGEYFNYPDPRTK 668
++ ++ ML+E KP F +++ + L + DLIK+ +
Sbjct: 927 TKFVRGMLEETKPKTFADLVRISGLSHGTDVWLGNAQDLIKSGIK------------TLS 974
Query: 669 DVLSETYGIMVY-QEQVMQIAQILGGYSLGQADLLRRAIGKKKTSEMIEHRKFFQNGAIK 727
DV+ IMVY + ++ + + +R+ GK +E IE K
Sbjct: 975 DVIGCRDDIMVYLIHKGLEPKL-----AFKIMEKVRK--GKGLKAEYIELMK-------- 1019
Query: 728 YGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYSSFFMAANLSLSMDD 787
++K E + E Y F K+HA AY L+++ AY K HY + AA S+
Sbjct: 1020 ----ENKVPEWYIESCLKIKYMFPKAHAAAYVLMAWRIAYFKVHYPLEYYAAYFSIRAKA 1075
Query: 788 -----TNKIKILVKDAIKTC-----------------------------GLSILPPNINL 813
K K +K ++ G P ++
Sbjct: 1076 FDLETMIKGKEFIKQKLEEINTRRKINKASPKEKDLLTVLEIVLEMMARGFKFQPIDLYK 1135
Query: 814 SKYYFFPIIESDGKHKKIRYGLGAIKGTGKSTIEAIVTERKFGFFTNLFDFTKRIDKKYI 873
S+ F +IE + + AI G G++ +IV R F + D KR I
Sbjct: 1136 SQATEF-LIEGNT----LIPPFNAIPGLGENVANSIVEARNEKPFLSKEDLKKRTK---I 1187
Query: 874 NRRIINSLINSGAFDCFNEK 893
++ I L + G D E
Sbjct: 1188 SKTHIEKLDSMGVLDNLPET 1207
Score = 46.6 bits (111), Expect = 9e-05
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 6 IHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPII 65
+ L H++ S +D + + + ++ A A+AITD + + YK+A GIK I
Sbjct: 105 VELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDGIKIIY 164
Query: 66 GCDVWITNEIENKKPS 81
G + N ++++ P
Sbjct: 165 GME---ANLVDDRVPI 177
Score = 31.6 bits (72), Expect = 3.2
Identities = 17/85 (20%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 988 TVSGIITELKLKTTYRGKILI-IVIDDNSNSVEVIINNQLYEKNKNI--LKENELLIVSG 1044
+ G I ++++K G+ L+ I + D ++S+ + + E + +K + + G
Sbjct: 11 KIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARG 70
Query: 1045 KVLEDRFLKNIRINAEKIFDINVAR 1069
K+ D F +++++ + I +I A
Sbjct: 71 KIELDNFSRDLQMIIKDIEEIPYAE 95
>gnl|CDD|213986 cd07431, PHP_PolIIIA, Polymerase and Histidinol Phosphatase domain
of alpha-subunit of bacterial polymerase III. PolIIIAs
that contain an N-terminal PHP domain have been
classified into four basic groups based on genome
composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that is responsible for the replication
of the DNA duplex. The alpha subunit of DNA polymerase
III core enzyme catalyzes the reaction for polymerizing
both DNA strands. The PolIIIA PHP domain has four
conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination,
and like other PHP structures, exhibits a distorted
(beta/alpha) 7 barrel and coordinates up to 3 metals.
Initially, it was proposed that PHP region might be
involved in pyrophosphate hydrolysis, but such activity
has not been found. It has been shown that the PHP
domain of PolIIIA has a trinuclear metal complex and is
capable of proofreading activity.
Length = 179
Score = 119 bits (301), Expect = 6e-31
Identities = 61/227 (26%), Positives = 93/227 (40%), Gaps = 58/227 (25%)
Query: 7 HLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPIIG 66
HL +HS YS++D +R D++ A ALA+TD + L+G ++FYK+ GIKPIIG
Sbjct: 2 HLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIG 61
Query: 67 CDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLE-KNKY 125
++ + + E P LLLL KNN GY L L + A + G ++ E
Sbjct: 62 LELTVEGDGE---PYPLLLLAKNNEGYQNLLRLSTAAMLGEEKDG--VPYLDLEELAEAA 116
Query: 126 QDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMNFQIQQ 185
L+ L G L
Sbjct: 117 SGLLVVLLGPLL------------------------------------------------ 128
Query: 186 FINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRI 232
+ +A+ LP+VAT+ + +L + A +V T ++NT RI
Sbjct: 129 -LLLAAEQGLPLVATNDVHYLNPEDAFAADVLTA---FLAVANTVRI 171
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type)
[DNA replication, recombination, and repair].
Length = 1444
Score = 130 bits (329), Expect = 2e-30
Identities = 220/1013 (21%), Positives = 368/1013 (36%), Gaps = 277/1013 (27%)
Query: 43 LSNLFGIIKFYKSAYNKGIKPIIGCDVWITNEIENKK--PSRLLLLVKNNNGYLQLCELL 100
+ +F F K KGI + + +++E K+ P + VKN G L +L+
Sbjct: 575 TAKVF--FVFLKDLKEKGITNLSELNDKLSSEDLYKRLRPKHATIYVKNQVGLKNLYKLV 632
Query: 101 SKAYIENINYGRAEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWS 160
S ++ + YGR RI K ++GL+ S G++ A ++ E A+ +
Sbjct: 633 SISHTKY-FYGRP--RIPRSVLKKNREGLLIGSACSEGELFDAALQKPDEEVEEIAKFYD 689
Query: 161 --KIFPDNFY---IEIQRFK-QPNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAH 214
+I P Y IE + K + + I++ I + +N P+VAT + +L + +
Sbjct: 690 FIEIQPPANYAHLIEREGLKDKEALKEIIKKLIKLGKKLNKPVVATGNVHYLDPEDKIYR 749
Query: 215 EVRTCIAEGEILSNTKRIKKFTKEQNFKTQSEMIKLF--------YDIPSAIQNTIEIAK 266
++ N ++ E +F+T EM++ F Y+I ++NT +IA
Sbjct: 750 KILVASQGLGNPLNRTFNEQTLPEVHFRTTDEMLQEFSFLGEEKAYEI--VVENTNKIAD 807
Query: 267 RCNLKLEFGKPKLPKFPTPKNININDFLISKSKHGLKKRLLNLYKD--PEIYKCEKLRYK 324
E +P K TPK + + + K +Y D PEI +
Sbjct: 808 MI----EDIQPIKDKLYTPKIEGAEEKVRDLTYEKAHK----IYGDPLPEIVE------- 852
Query: 325 KRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIPVGPGRGSGASSLVAYSLSITDIDPL 384
+R++ E+ +II F+ +LI ++ + ++ VG RGS SSLVA + IT+++PL
Sbjct: 853 QRIEKELNSIIGNGFAVIYLISQKLVKKSLDDGYLVGS-RGSVGSSLVATMIGITEVNPL 911
Query: 385 S-----------------------------------------YNLLFERFLNPNRISMPD 403
+++ FE FL +PD
Sbjct: 912 PPHYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTPLKKDGHDIPFETFLGFKGDKVPD 971
Query: 404 FDIDFCPEGRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISK 463
D++F E + + YVK+ +G+D V + T GT+A K A V + +
Sbjct: 972 IDLNFSGEYQPKAHNYVKELFGEDYVFRAGTIGTVAEKTAYGYVKKYFE----------- 1020
Query: 464 LIPFKPGKLITLSNAIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAP 523
K E + L + G+ R G H GG++I P
Sbjct: 1021 ----DYNKFYR---------------DAE-----IDRLVQGCTGVKRTTGQHPGGIIIVP 1056
Query: 524 S--KLINFCPLYKQEGMTGIISQYDKDDIEE-----------IG--LIKFDFLGL---TT 565
+ +F P+ Q+ DD I L+K D LG T
Sbjct: 1057 KYMDVYDFTPV-----------QFPADDTNSEWKTTHFDFHAIHDNLLKLDILGHDDPTM 1105
Query: 566 LSILDKTIYFIKKINTKTTNFSLNKLPLNDKDTYNLLKKANTVAVF--QLESQ-GM---- 618
+ +L + I+ KT +P++D + + ++ V Q+ + G
Sbjct: 1106 IKMLQD----LTGIDPKT-------IPMDDPEVMKIFSSTESLGVTPEQIGEKTGTLGIP 1154
Query: 619 -------KNMLKEAKPDYFEEIIALISL------YRPGPMDLIKNFCRRKHGEYFNYPDP 665
+ ML+E KP F E++ + L + DLIK+
Sbjct: 1155 EFGTRFVRQMLEETKPKTFAELVRISGLSHGTDVWLGNAQDLIKS----------GIAT- 1203
Query: 666 RTKDVLSETYGIMVYQEQVMQIAQILGGYSLGQA----DLLRRAIGKKKTSEMIEHRKFF 721
DV+ IMVY I G A + +R+ G K +E E K
Sbjct: 1204 -LSDVIGCRDDIMVY--------LIHKGLEPSLAFKIMEFVRKGKG-LKPAEYEELMK-- 1251
Query: 722 QNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHATAYALLSYYTAYLKTHYSSFFMAANL 781
++K E + E Y F K+HA AY L+++ AY K H+ + AA
Sbjct: 1252 ----------ENKVPEWYIESCLKIKYMFPKAHAAAYVLMAWRIAYFKVHHPLEYYAAYF 1301
Query: 782 SLSMDD-----TNKIKILVKDAIK-------------------TC---------GLSILP 808
S+ DD +K K +K ++ G
Sbjct: 1302 SIRADDFDIETMSKGKEAIKAKMEEINKRKGNKASPKEKNLLTVLEIVLEMLARGFKFQK 1361
Query: 809 PNINLSKYYFFPIIESDGKHKKIRYGLGAIKGTGKSTIEAIVTERKFGFFTNLFDFTKRI 868
++ S F +I+ D + AI G G++ ++IV R+ F + D KR
Sbjct: 1362 IDLYKSDATEF-VIDGD----TLIPPFIAIPGLGENVAKSIVEAREEKEFLSKEDLKKRT 1416
Query: 869 DKKYINRRIINSLINSGAFDCFNEKRYMLVASIDVALKNAEKTKKFINQLSLF 921
I++ I L G + E NQLSLF
Sbjct: 1417 K---ISKTHIEKLDEMGCLEGLPET----------------------NQLSLF 1444
Score = 49.2 bits (118), Expect = 1e-05
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 6 IHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPII 65
+ L H++ S +D + + ++++ A A+AITD + + YK+A GIK I
Sbjct: 337 VELHFHTKMSQMDAITSVEELVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKYGIKAIY 396
Query: 66 GCDVWITNEIENKKP 80
G + N +++ P
Sbjct: 397 GLE---ANLVDDGVP 408
Score = 35.8 bits (83), Expect = 0.18
Identities = 43/221 (19%), Positives = 83/221 (37%), Gaps = 22/221 (9%)
Query: 858 FTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRYMLVASIDVALK---NAEKTKKF 914
F +L + K K N +I ++N+ FD F K L + E
Sbjct: 112 FKSLLNKLKLKVKG--NNILIEQVLNNPEFDHFKNKSPELQKKLQSFGFPQLLIEFEVND 169
Query: 915 INQLSLFKN-------DDNNNLKEYLNYVKVPSWSKKQELIEEKKVLGFCLSEHIFCIYE 967
I++ F+ + +E L K ++ ++ + K + I
Sbjct: 170 ISEEQEFEKFEEAINEEVEKAAQEALEAEKKLK-AESPKVEKPKPLFDGQKGRKIK--ST 226
Query: 968 TEIRQFIPIYLSELKPTYSCTVSGIITELKLKTTYRGKILI-IVIDDNSNSVEVIINNQL 1026
EI+ I I E + V G I ++++K G+ L+ I + D ++S+ + +
Sbjct: 227 EEIKPLIKINEEETR----VKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRD 282
Query: 1027 YEKNKNI--LKENELLIVSGKVLEDRFLKNIRINAEKIFDI 1065
E K +K+ + G V D F +++ + I +I
Sbjct: 283 EEDEKKFDGIKKGMWVKARGNVQLDTFTRDLTMIINDINEI 323
>gnl|CDD|213989 cd07434, PHP_PolIIIA_DnaE2, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III at
DnaE2 gene. PolIIIA DnaE2 plays a role in SOS
mutagenesis/translesion synthesis and has dominant
effects in determining GC variability in the bacterial
genome. PolIIIAs that contain an N-terminal PHP domain
have been classified into four basic groups based on
genome composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that are responsible for the replication
of the DNA duplex. PolIIIA core enzyme catalyzes the
reaction for polymerizing both DNA strands. PolC PHP is
located in a different location compared to dnaE1, 2,
and 3. dnaE1 is the longest compared to dnaE2 and dnaE3.
A unique motif was also identified in dnaE1 and dnaE3
genes. The PHP domain has four conserved sequence motifs
and contains an invariant histidine that is involved in
metal ion coordination. PHP domains found in DnaEs of
thermophilic origin exhibit 3'-5' exonuclease activity.
Length = 260
Score = 96.8 bits (242), Expect = 5e-22
Identities = 67/269 (24%), Positives = 119/269 (44%), Gaps = 59/269 (21%)
Query: 26 VIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPIIGCDVWITNEIENKKPSRLLL 85
V AA Y+ ALAITD +L G+++ + +A G+K I+G ++ + + +RL+L
Sbjct: 23 VARAAELGYR-ALAITDECSLAGVVRAHAAAKELGLKLIVGSELVLADG------TRLVL 75
Query: 86 LVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQ 145
L ++ GY +LC L++ RAE K +Y+ L L G + I +
Sbjct: 76 LARDRAGYGRLCRLITLGR------RRAE-------KGEYRLTLADLLAHAEGLLLILLP 122
Query: 146 NGRNDIAENF---ARRWSKIFPDNFYIEIQRFKQPNMNFQIQQFINIASNINLPIVAT-- 200
R A R ++ FP ++ ++ + ++ + +A+ + LP+VAT
Sbjct: 123 PDRLPAAAALLAQLRWLARAFPGRLWLALELHLGGDDARRLARLAALAAALGLPLVATGD 182
Query: 201 ---H-----PIQFLKKTEFLAHEVRTCIAEG--------EILSNTKRIKKFTKEQNFKTQ 244
H P+Q +V T I G + +N E++ ++
Sbjct: 183 VLMHSPSRRPLQ----------DVLTAIRLGTTVAEAGRRLAANA--------ERHLRSP 224
Query: 245 SEMIKLFYDIPSAIQNTIEIAKRCNLKLE 273
+E+ +LF P A+ T+EIA RC L+
Sbjct: 225 AELARLFLYPPEALAETLEIAARCTFSLD 253
>gnl|CDD|217238 pfam02811, PHP, PHP domain. The PHP (Polymerase and Histidinol
Phosphatase) domain is a putative phosphoesterase
domain.
Length = 174
Score = 92.2 bits (229), Expect = 2e-21
Identities = 56/178 (31%), Positives = 87/178 (48%), Gaps = 25/178 (14%)
Query: 6 IHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSA--YNKGIKP 63
+ L +H+++S++DG L I ++++AA A+AITD NLFG +FY++A G+KP
Sbjct: 1 VDLHVHTDFSLLDGALSIEELVKAAKELGLEAIAITDHDNLFGAPEFYEAAKKKRAGLKP 60
Query: 64 IIGCDVWITNEI--------ENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEI 115
IIG ++ I ++ + K L+LL +GY L EL S AY E+
Sbjct: 61 IIGVEINIVDDEDEKDLDEDDLNKSLDLVLLSV--HGYRNLPELSSAAYTED-------- 110
Query: 116 RIEWLEKNKYQDGLIALSGAHL-GDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQ 172
E LE ++GLI + AH G +G A+ G + AE + I
Sbjct: 111 --ELLEAVL-EEGLIIIL-AHPEGYVGTALLLGPLEEAEKLLEEYFGEDGFYLEINNS 164
>gnl|CDD|213990 cd07435, PHP_PolIIIA_POLC, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III at
PolC gene. DNA polymerase III alphas (PolIIIAs) that
contain a PHP domain have been classified into four
basic groups based on phylogenetic and domain structural
analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group
is distinct from the other three and is clustered
together. The PHP (also called histidinol
phosphatase-2/HIS2) domain is associated with several
types of DNA polymerases, such as PolIIIA and family X
DNA polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. DNA polymerase III
holoenzyme is one of the five eubacterial DNA
polymerases that are responsible for the replication of
the DNA duplex. The alpha subunit of DNA polymerase III
core enzyme catalyzes the reaction for polymerizing both
DNA strands. PolC PHP is located in different location
compare to dnaE1, 2, and 3. The PHP domain has four
conserved sequence motifs and and contains an invariant
histidine that is involved in metal ion coordination.The
PHP domain of PolC is structurally homologous to other
members of the PHP family that have a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel. PHP domains found
in dnaEs of thermophilic origin exhibit 3'-5'
exonuclease activity. In contrast, PolC PHP lacks
detectable nuclease activity.
Length = 268
Score = 91.0 bits (227), Expect = 5e-20
Identities = 73/292 (25%), Positives = 122/292 (41%), Gaps = 63/292 (21%)
Query: 6 IHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPII 65
+ L H++ S +DG+ + ++++ AA A+AITD + + Y++A GIK I
Sbjct: 2 VELHAHTKMSAMDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPEAYEAAKKNGIKVIY 61
Query: 66 GCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEKNKY 125
G + ++ + P + +LVKN G L +L+S + + Y RI E KY
Sbjct: 62 GVEAYLVD------PYHITILVKNQTGLKNLYKLVSLS---HTKYFYRVPRIPKSELEKY 112
Query: 126 QDGLIALSGAHLGDIGIAVQNGRNDI-AENFARRWSKIFPDNFYIEIQRFKQPNMNFQ-- 182
++GL+ S G++ A N ++D E A F D YIEI QP N+Q
Sbjct: 113 REGLLIGSACENGELFEAALNKKSDEELEEIAS-----FYD--YIEI----QPLDNYQFL 161
Query: 183 ---------------IQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILS 227
++ I + +N P+VAT + +L + R EIL
Sbjct: 162 IEKGLIKSEEELKEINKRIIKLGKKLNKPVVATGDVHYLDPED---KIYR------EILL 212
Query: 228 NTKRIKKFTKE----QNFKTQSEMIKLF--------YDI----PSAIQNTIE 263
+ + F+T EM+ F Y++ + I + IE
Sbjct: 213 AGQGGGDGRADEQPDLYFRTTDEMLDEFSYLGEEKAYEVVVTNTNKIADMIE 264
>gnl|CDD|197753 smart00481, POLIIIAc, DNA polymerase alpha chain like domain.
DNA polymerase alpha chain like domain, incl. family of
hypothetical proteins.
Length = 67
Score = 79.2 bits (196), Expect = 4e-18
Identities = 30/65 (46%), Positives = 43/65 (66%)
Query: 7 HLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPIIG 66
L +HS+YS++DG L ++++ A A+AITD NLFG ++FYK+A GIKPIIG
Sbjct: 1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIG 60
Query: 67 CDVWI 71
+ I
Sbjct: 61 LEANI 65
>gnl|CDD|239931 cd04485, DnaE_OBF, DnaE_OBF: A subfamily of OB folds corresponding to
the C-terminal OB-fold nucleic acid binding domain of
Thermus aquaticus and Escherichia coli type C replicative
DNA polymerase III alpha subunit (DnaE). The DNA
polymerase holoenzyme of E. coli contains two copies of
this replicative polymerase, each of which copies a
different DNA strand. This group also contains Bacillus
subtilis DnaE. Replication in B. subtilis and
Staphylococcus aureus requires two different type C
polymerases, polC and DnaE, both of which are thought to
be included in the DNA polymerase holoenzyme. At the B.
subtilis replication fork, polC appears to be involved in
leading strand synthesis and DnaE in lagging strand
synthesis.
Length = 84
Score = 65.2 bits (160), Expect = 6e-13
Identities = 30/83 (36%), Positives = 55/83 (66%), Gaps = 3/83 (3%)
Query: 988 TVSGIITELKLKTTYRGK-ILIIVIDDNSNSVEVIINNQLYEKNKNILKENELLIVSGKV 1046
TV+G++T ++ + T +GK + + ++D + S+EV++ + YEK +++LKE+ LL+V GKV
Sbjct: 1 TVAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKV 60
Query: 1047 LEDRFLKNIRINAEKIFDINVAR 1069
+R+ AE+I D+ AR
Sbjct: 61 ERRD--GGLRLIAERIEDLEDAR 81
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 71.4 bits (176), Expect = 2e-12
Identities = 138/612 (22%), Positives = 223/612 (36%), Gaps = 183/612 (29%)
Query: 43 LSNLFGIIKFYKSAYNKGIKPI--IGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELL 100
+ L IKF K KGI + + + + + +P +LVKN G L +L+
Sbjct: 573 TAYLL--IKFLKDLKEKGITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLV 630
Query: 101 SKAYIENINYGRAEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWS 160
S + + Y RI +KY++GL+ S G++ AV ++ E A+
Sbjct: 631 SLSNTKY-FYRVP--RIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAK--- 684
Query: 161 KIFPDNFYIEIQRFKQPNMNFQ-----------------IQQFINIASNINLPIVATHPI 203
F D YIEIQ P N+Q I+ I + +N P+VAT +
Sbjct: 685 --FYD--YIEIQ----PPANYQHLIERELVKDEEELKEIIKNLIELGKKLNKPVVATGDV 736
Query: 204 QFLKKTEFLAHEVRTCIAEGEILSNTKRIK-----KFTKEQNFKTQSEMIKLF------- 251
+L + + + IL ++ E +F+T EM+ F
Sbjct: 737 HYLDPEDKIYRK---------ILVASQGGGNPLNRHPLPELHFRTTDEMLDEFAFLGEEL 787
Query: 252 -YDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKSKHGLKKRLLNLY 310
+I ++NT +IA E +P K TPK + + + + +Y
Sbjct: 788 AKEI--VVENTNKIADLI----EEIEPIKDKLYTPKIEGAEEEIRELTYKKAHE----IY 837
Query: 311 KD--PEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIPVGPGRGSGA 368
+ PEI + KR++ E+ +II F+ +LI ++ + + VG RGS
Sbjct: 838 GEPLPEIVE-------KRIEKELNSIIGNGFAVIYLISQKLVKKSLEDGYLVGS-RGSVG 889
Query: 369 SSLVAYSLSITDIDPL------------------SY-----------------------N 387
SS VA + IT+++PL S +
Sbjct: 890 SSFVATMIGITEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLKKDGHD 949
Query: 388 LLFERFLNPNRISMPDFDIDFCPEGRDRVIQYVKDRYGKDAVSQIVTFGTMAAKGAIRDV 447
+ FE FL +PD D++F E + Y K +G+D V + T GT+A K A
Sbjct: 950 IPFETFLGFKGDKVPDIDLNFSGEYQPVAHNYTKVLFGEDHVFRAGTIGTVAEKTA---- 1005
Query: 448 GRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKEEPQLAERIKNEEEVRQL-IE-LAKQV 505
Y + E + R I+ LA+
Sbjct: 1006 -------YGYVKK-------------------------YEEDTG-KFYRNAEIDRLAQGC 1032
Query: 506 EGIIRNVGMHAGGVLIAPSKL--INFCPLYKQEGMTGIISQYDKDDIEE----------- 552
G+ R G H GG+++ P + +F P+ QY DD+
Sbjct: 1033 TGVKRTTGQHPGGIIVVPKYMDIYDFTPI-----------QYPADDVNSEWKTTHFDFHS 1081
Query: 553 IG--LIKFDFLG 562
I L+K D LG
Sbjct: 1082 IHDNLLKLDILG 1093
Score = 52.9 bits (128), Expect = 9e-07
Identities = 51/206 (24%), Positives = 74/206 (35%), Gaps = 62/206 (30%)
Query: 748 YGFNKSHATAYALLSYYTAYLKTHYSSFFMAANLSLSMDDTN-KIKILVKDAIKTC---- 802
Y F K+HA AY L+++ AY K HY + AA S+ DD + + K+AIK
Sbjct: 1261 YMFPKAHAAAYVLMAWRIAYFKVHYPLAYYAAYFSVRADDFDLETMSKGKEAIKAKMKEI 1320
Query: 803 ---------------------------GLSILPPNINLSKYYFFPIIESDGKHKKIRYGL 835
G ++ S F IIE D +
Sbjct: 1321 KSKGNDASNKEKDLLTVLEIALEMLERGFKFQKVDLYKSDATEF-IIEGDS----LIPPF 1375
Query: 836 GAIKGTGKSTIEAIVTERKFGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRY 895
A+ G G++ ++IV R+ G F + D KR +++ +I L G D E
Sbjct: 1376 NALPGLGENVAKSIVEAREEGEFLSKEDLRKRTK---VSKTLIEKLDELGVLDDLPET-- 1430
Query: 896 MLVASIDVALKNAEKTKKFINQLSLF 921
NQLSLF
Sbjct: 1431 --------------------NQLSLF 1436
Score = 50.2 bits (121), Expect = 7e-06
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 8 LRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPIIG 66
L LH++ S +D + ++++++ AA A+AITD + + Y +A GIK I G
Sbjct: 337 LHLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYG 395
Score = 46.0 bits (110), Expect = 1e-04
Identities = 35/214 (16%), Positives = 80/214 (37%), Gaps = 18/214 (8%)
Query: 861 LFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRYMLVASIDVALKNAEKTKKFINQLSL 920
K+ + ++I + N D +K + +K EK I ++
Sbjct: 110 FKSLLKKQKVEVEGNKLIIKVNNEIERDHLKKKH------LPKLIKQYEKFGFGILKIDF 163
Query: 921 FKNDDNNNLKEYLNYVKVPSWSKKQELIEE--------KKVLGFCLSEHIFCIYETEIRQ 972
+D L+++ + +E +E KK + +I +
Sbjct: 164 EIDDSKEELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDK 223
Query: 973 FIPIYLSELKPT-YSCTVSGIITELKLKTTYRGKILIIV-IDDNSNSVEVII--NNQLYE 1028
+ E+ V G + ++++K G+ ++ I D ++S+ V ++
Sbjct: 224 EEITPMKEINEEERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDL 283
Query: 1029 KNKNILKENELLIVSGKVLEDRFLKNIRINAEKI 1062
K + +K+ + + V G V D F +++ +NA+ I
Sbjct: 284 KKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQDI 317
>gnl|CDD|213985 cd07309, PHP, Polymerase and Histidinol Phosphatase domain. The
PHP (also called histidinol phosphatase-2/HIS2) domain
is associated with several types of DNA polymerases,
such as PolIIIA and family X DNA polymerases, stand
alone histidinol phosphate phosphatases (HisPPases),
and a number of uncharacterized protein families. The
PHP domain has four conserved sequence motifs and
contains an invariant histidine that is involved in
metal ion coordination. PHP in polymerases has
trinuclear zinc/magnesium dependent proofreading
activity. It has also been shown that the PHP domain
functions in DNA repair. The PHP structures have a
distorted (beta/alpha)7 barrel fold with a trinuclear
metal site on the C-terminal side of the barrel.
Length = 88
Score = 53.6 bits (129), Expect = 7e-09
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 6 IHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKF--------YKSAY 57
+ L H+ +S D ++ ++++ A ALAITD NL G+ +F K+A
Sbjct: 1 VDLHTHTVFSDGD-HAKLTELVDKAKELGPDALAITDHGNLRGLAEFNTAGKXNHIKAAE 59
Query: 58 NKGIKPIIGCDVWIT 72
GIK IIG +V +T
Sbjct: 60 AAGIKIIIGSEVNLT 74
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding domain
of lysyl, aspartyl, and asparaginyl -tRNA synthetases
(See pfam00152). Aminoacyl-tRNA synthetases catalyze the
addition of an amino acid to the appropriate tRNA
molecule EC:6.1.1.-. This family also includes part of
RecG helicase involved in DNA repair. Replication factor
A is a heterotrimeric complex, that contains a subunit in
this family. This domain is also found at the C-terminus
of bacterial DNA polymerase III alpha chain.
Length = 75
Score = 47.3 bits (113), Expect = 7e-07
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 988 TVSGIITELKLKTTYRGKILIIVIDDNSNSVEVIINNQLYEKNKNILKENELLIVSGKVL 1047
TV+G +T GK+ + + D + S++V++ + EK LKE ++++V+GKV
Sbjct: 2 TVAGRVTS---VRRSGGKVAFLTLRDGTGSIQVVLFKEEAEKLAKKLKEGDVVLVTGKVK 58
Query: 1048 EDRFLKNIRINAEKIFDI 1065
+ + + E+I +
Sbjct: 59 KRPG-GELELVVEEIEVL 75
>gnl|CDD|239934 cd04488, RecG_wedge_OBF, RecG_wedge_OBF: A subfamily of OB folds
corresponding to the OB fold found in the N-terminal
(wedge) domain of Escherichia coli RecG. RecG is a
branched-DNA-specific helicase, which catalyzes the
interconversion of a DNA replication fork to a
four-stranded (Holliday) junction in vivo and in vitro.
This interconversion provides a route to repair stalled
forks. The RecG monomer contains three domains. The
N-terminal domain is named for its wedge structure, and
may provide the specificity of RecG for binding
branched-DNA structures. During the reversal of fork to
Holliday junction, the wedge domain is fixed at the
junction of the fork where the leading and lagging strand
duplex arms meet, and is thought to promote the unwinding
of the nascent leading and lagging strands. In order to
form the Holliday junction, these nascent strands would
be annealed, and the parental strands reannealed. The
wedge domain may also be a processivity factor of RecG on
these branched chain substrates.
Length = 75
Score = 44.1 bits (105), Expect = 1e-05
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 988 TVSGIITELKLKTTYRGKILIIVIDDNSNSVEVII-NNQLYEKNKNILKENELLIVSGKV 1046
TV G + +++ + L + + D + ++ ++ N Q Y K + L + VSGKV
Sbjct: 1 TVEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQPYLKKQ--LPPGTRVRVSGKV 58
>gnl|CDD|239601 cd03524, RPA2_OBF_family, RPA2_OBF_family: A family of
oligonucleotide binding (OB) folds with similarity to the
OB fold of the single strand (ss) DNA-binding domain
(DBD)-D of human RPA2 (also called RPA32). RPA2 is a
subunit of Replication protein A (RPA). RPA is a nuclear
ssDNA-binding protein (SSB) which appears to be involved
in all aspects of DNA metabolism including replication,
recombination, and repair. RPA also mediates specific
interactions of various nuclear proteins. In animals,
plants, and fungi, RPA is a heterotrimer with subunits of
70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA
contains six OB folds, which are involved in ssDNA
binding and in trimerization. The ssDNA binding mechanism
is believed to be multistep and to involve conformational
change. This family also includes OB folds similar to
those found in Escherichia coli SSB, the wedge domain of
E. coli RecG (a branched-DNA-specific helicase), E. coli
ssDNA specific exodeoxyribonuclease VII large subunit,
Pyrococcus abyssi DNA polymerase II (Pol II) small
subunit, Sulfolobus solfataricus SSB, and Bacillus
subtilis YhaM (a 3'-to-5'exoribonuclease). It also
includes the OB folds of breast cancer susceptibility
gene 2 protein (BRCA2), Oxytricha nova telomere end
binding protein (TEBP), Saccharomyces cerevisiae
telomere-binding protein (Cdc13), and human protection of
telomeres 1 protein (POT1).
Length = 75
Score = 39.7 bits (93), Expect = 4e-04
Identities = 16/71 (22%), Positives = 37/71 (52%)
Query: 988 TVSGIITELKLKTTYRGKILIIVIDDNSNSVEVIINNQLYEKNKNILKENELLIVSGKVL 1047
T+ GI+ ++ T ++ + D ++ V + +L E+ +N+LKE +++ + GKV
Sbjct: 1 TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVK 60
Query: 1048 EDRFLKNIRIN 1058
+ R + +
Sbjct: 61 KFRGRLQLIVE 71
>gnl|CDD|239930 cd04484, polC_OBF, polC_OBF: A subfamily of OB folds corresponding to
the N-terminal OB-fold nucleic acid binding domain of
Bacillus subtilis type C replicative DNA polymerase III
alpha subunit (polC). Replication in B. subtilis and
Staphylococcus aureus requires two different polymerases,
polC and DnaE. The holoenzyme is thought to include the
two different polymerases. At the B. subtilis replication
fork, polC appears to be involved in leading strand
synthesis and DnaE in lagging strand synthesis.
Length = 82
Score = 39.1 bits (92), Expect = 8e-04
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 987 CTVSGIITELKLKTTYRGK-ILIIVIDDNSNSVEVIINNQLYEKNK-NILKENELLIVSG 1044
V G + +L+++ G+ IL + D ++S+ V + EK+K + + + + V G
Sbjct: 2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDEKDKEELKSKGDWVRVRG 61
Query: 1045 KVLEDRFLKNIRINAEKI 1062
KV D F K + + I
Sbjct: 62 KVQYDTFSKELVLMINDI 79
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 40.5 bits (96), Expect = 0.006
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 7/87 (8%)
Query: 978 LSELKPTYSCTVSGIITELKLKTTYRGKILIIVIDDNSNSVEVII--NNQLYEKNKNILK 1035
++EL+P TV G + + + + L + + D + ++ + NQ Y K + LK
Sbjct: 53 IAELRPGEKVTVEGEVLSAE-VVFGKRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQ--LK 109
Query: 1036 ENELLIVSGKVLEDRFLKNIRINAEKI 1062
+ + V GKV R + + +
Sbjct: 110 VGKRVAVYGKV--KRGKYGLEMVHPEY 134
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 38.0 bits (89), Expect = 0.034
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 978 LSELKPTYSCTVSGIITELKLKTTYRGKILIIVIDDNSNSVEVIINNQLYEKNKNILKEN 1037
++E +P T+ G + + + K+L + + D + + ++ N K LK
Sbjct: 54 IAEARPGEIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNF-PAYLKKKLKVG 112
Query: 1038 ELLIVSGKV 1046
E +IV GKV
Sbjct: 113 ERVIVYGKV 121
>gnl|CDD|162728 TIGR02146, LysS_fung_arch, homocitrate synthase. This model
includes the yeast LYS21 gene which carries out the
first step of the alpha-aminoadipate (AAA) lysine
biosynthesis pathway. A related pathway is found in
Thermus thermophilus. This enzyme is closely related to
2-isopropylmalate synthase (LeuA) and citramalate
synthase (CimA), both of which are present in the
euryarchaeota. Some archaea have a separate homocitrate
synthase (AksA) which also synthesizes longer
homocitrate analogs.
Length = 344
Score = 35.9 bits (83), Expect = 0.11
Identities = 29/123 (23%), Positives = 42/123 (34%), Gaps = 20/123 (16%)
Query: 170 EIQRFKQPNMNFQIQQFINIASNINLP----IVATHPI---QFLKKTEFLAH-------- 214
E ++F P NF +Q I IA ++ I THP Q E +A
Sbjct: 8 EGEQF--PGANFSTEQKIEIAKALDEFGIDYIEVTHPAASKQSRIDIEIIASLGLKANIV 65
Query: 215 ---EVRTCIAEGEILSNTKRIKKFTKEQNFKTQSEMIKLFYDIPSAIQNTIEIAKRCNLK 271
R A+ + I F +E I + + TIE AK L+
Sbjct: 66 THIRCRLDDAKVAVELGVDGIDIFFGTSKLLRIAEHRSDAKSILESARETIEYAKSAGLE 125
Query: 272 LEF 274
+ F
Sbjct: 126 VRF 128
>gnl|CDD|214846 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.
Length = 122
Score = 33.3 bits (77), Expect = 0.17
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 17/77 (22%)
Query: 13 EYSIIDGLLRINDVIEAAANDYQPALAIT---DLSNLFGIIKFYKSAYNKGIKPIIGCDV 69
E++++ L R +V+EAAA +P DL+ F S YN+ ++G +
Sbjct: 38 EWALLLKLARFPEVLEAAAEQLEPHRLANYLYDLAAAFH------SFYNR--VRVLGEE- 88
Query: 70 WITNEIENKKPSRLLLL 86
+ +RL LL
Sbjct: 89 -----NPELRKARLALL 100
>gnl|CDD|224408 COG1491, COG1491, Predicted RNA-binding protein [Translation,
ribosomal structure and biogenesis].
Length = 202
Score = 33.9 bits (78), Expect = 0.33
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 11/71 (15%)
Query: 835 LGAIKGTGKSTIEAIVTERKFGFFTNLFDFTKRIDK-----KYINRRIINSLINSGAFDC 889
L + G GK T+ AI+ ERK F + D +R+ K I RI++ L +
Sbjct: 132 LELLPGIGKKTMWAILEERKKKPFESFEDIKERVKGLHDPAKMIAERILDELKDED---- 187
Query: 890 FNEKRYMLVAS 900
+K Y+ VA
Sbjct: 188 --DKYYLFVAP 196
>gnl|CDD|224472 COG1555, ComEA, DNA uptake protein and related DNA-binding proteins
[DNA replication, recombination, and repair].
Length = 149
Score = 32.8 bits (75), Expect = 0.42
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 835 LGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYINRRIINSLIN 883
L A+ G G +AI+ R + G F ++ D K K I + + L +
Sbjct: 99 LQALPGIGPKKAQAIIDYREENGPFKSVDDLAK---VKGIGPKTLEKLKD 145
>gnl|CDD|213987 cd07432, PHP_HisPPase, Polymerase and Histidinol Phosphatase
domain of Histidinol phosphate phosphatase. HisPPase
catalyzes the eighth step of histidine biosynthesis, in
which L-histidinol phosphate undergoes
dephosphorylation to produce histidinol. HisPPase can
be classified into two types: the bifunctional HisPPase
found in proteobacteria that belongs to the DDDD
superfamily and the monofunctional Bacillus subtilis
type that is a member of the PHP family. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. The PHP
domain has four conserved sequence motifs and contains
an invariant histidine that is involved in metal ion
coordination. The PHP domain of HisPPase is
structurally homologous to other members of the PHP
family that have a distorted (beta/alpha)7 barrel fold
with a trinuclear metal site on the C-terminal side of
the barrel.
Length = 129
Score = 31.8 bits (73), Expect = 0.69
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 10 LHSEYSIIDGLLRINDVIEAAAN---DYQPALAITDLSNLFGIIKFYKSAYNKGIKPIIG 66
+HS +S D + +++E A D +AITD + + G + K AY G+ I G
Sbjct: 5 IHSVFSP-DSDMTPEEIVERAIELGLD---GIAITDHNTIDGAEEALKEAYKDGLLVIPG 60
Query: 67 C 67
Sbjct: 61 V 61
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 33.1 bits (76), Expect = 0.87
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 438 MAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKEEPQLAER-IKNEEEVR 496
A G + VG LD + D+++ + KPG L + +++ E L ER + EEE++
Sbjct: 281 EARPGGLVGVGTKLDPALTKADALAGQVVGKPGTLPPVWESLELEVHLLERVVGTEEELK 340
Query: 497 QLIELAKQVEGIIRNVG 513
+E K E ++ NVG
Sbjct: 341 --VEPIKTGEVLMLNVG 355
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 32.3 bits (74), Expect = 1.7
Identities = 24/111 (21%), Positives = 46/111 (41%), Gaps = 6/111 (5%)
Query: 978 LSELKPTYSCTVSGIITELKLKTTYRGKILIIVI-DDNSNSVEVIINNQLYEKNKNILKE 1036
+ EL P T+ G + + R K+L + + D +E+ N+ + K K K
Sbjct: 26 IGELLPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRAFLKKK--FKV 83
Query: 1037 NELLIVSGKVLEDRFLKNIRINAEKIFDINVARILYGKKFSVMFNRTFNIS 1087
++V GKV +F + I+ E F + + K ++ T ++
Sbjct: 84 GSKVVVYGKVKSSKFKAYL-IHPE--FISEKDGVEFELKILPVYPLTEGLT 131
>gnl|CDD|224434 COG1517, COG1517, CRISPR system related protein [Defense mechanisms].
Length = 406
Score = 31.6 bits (72), Expect = 2.3
Identities = 10/65 (15%), Positives = 21/65 (32%)
Query: 990 SGIITELKLKTTYRGKILIIVIDDNSNSVEVIINNQLYEKNKNILKENELLIVSGKVLED 1049
++ E T G +I + + QL E+ + E + + +
Sbjct: 301 KEVLLEDIKLLTEIGVNSDPIIKRRISKILNSYKLQLEERKIKLEGTIEDSEIRKMNIFE 360
Query: 1050 RFLKN 1054
R +N
Sbjct: 361 REERN 365
>gnl|CDD|226044 COG3513, COG3513, Predicted CRISPR-associated nuclease, contains
McrA/HNH-nuclease and RuvC-like nuclease domain [Defense
mechanisms].
Length = 1088
Score = 31.8 bits (72), Expect = 2.8
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 2/87 (2%)
Query: 854 KFGFFTNLFDFTKRIDKKYINRRIINSLINSGAFDCFNEKRYMLVASIDVALKNAEKTKK 913
F NL D K + K+ + +I L+ +FD F + + + ++ +
Sbjct: 389 DFSLLKNLEDIVKAL-TKFEDNEMIEELLKKLSFDDFVNISLKALRRLSPLMLQGKRYDQ 447
Query: 914 FINQLSLF-KNDDNNNLKEYLNYVKVP 939
N++ + K D N N K+ L K
Sbjct: 448 ACNEILDYLKGDANRNKKQLLPAFKET 474
>gnl|CDD|113683 pfam04919, DUF655, Protein of unknown function, DUF655. This
family includes several uncharacterized archaeal
proteins.
Length = 181
Score = 30.5 bits (69), Expect = 3.7
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 835 LGAIKGTGKSTIEAIVTERKFGFFTNLFDFTKRID-----KKYINRRIINSL 881
L + G GK + AI+ ERK F + D +R+ K I RII +
Sbjct: 118 LELLPGIGKKMMWAILEERKKKPFESFEDIKERVKGLHDPVKLIVERIIEEI 169
>gnl|CDD|200570 cd10946, CE4_Mll8295_like, Putative catalytic NodB homology domain
of uncharacterized Mll8295 protein encoded from
Rhizobium loti and its bacterial homologs. This family
is represented by a putative polysaccharide deacetylase
Mll8295 encoded from Rhizobium loti. Although its
biological function still remains unknown, Mll8295 shows
high sequence homology to the catalytic domain of
Streptococcus pneumoniae polysaccharide deacetylase PgdA
(SpPgdA), which is an extracellular metal-dependent
polysaccharide deacetylase with de-N-acetylase activity
toward a hexamer of chitooligosaccharide
N-acetylglucosamine, but not shorter
chitooligosaccharides or a synthetic peptidoglycan
tetrasaccharide. Both Mll8295 and SpPgdA belong to the
carbohydrate esterase 4 (CE4) superfamily. This family
also includes many uncharacterized bacterial
polysaccharide deacetylases.
Length = 217
Score = 30.1 bits (68), Expect = 5.7
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 455 YSFCDSISKLI-PFKPGKLITLSNAIKEEPQLAERIKNEEEVRQLIELAKQ 504
D + F GK+I L++ + + N ++++ I L K+
Sbjct: 161 VKKIDHLLNTNNTFTKGKVILLTH-----DFMFQDGWNLTKLKEFIRLLKK 206
>gnl|CDD|227461 COG5132, BUD31, Cell cycle control protein, G10 family
[Transcription / Cell division and chromosome
partitioning].
Length = 146
Score = 29.5 bits (66), Expect = 5.9
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 104 YIENINYGRAEIRIE---WLEKNKYQDGLIA 131
YI N+ Y R I + WL KN+Y D +
Sbjct: 59 YIYNLYYKRGAISTKLYGWLSKNRYADHELI 89
>gnl|CDD|218729 pfam05746, DALR_1, DALR anticodon binding domain. This all alpha
helical domain is the anticodon binding domain in
Arginyl and glycyl tRNA synthetase. This domain is
known as the DALR domain after characteristic conserved
amino acids.
Length = 117
Score = 28.8 bits (65), Expect = 5.9
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 18/88 (20%)
Query: 2 IPQFIHLRLHSEYSIIDGLLRINDVIEAAANDYQP---ALAITDLSNLFGIIKFYKSAYN 58
L E ++ LL+ +V+E AA + +P A + +L++ F FY
Sbjct: 23 DIDADLLTEEEEKELLKALLQFPEVLEEAAEELEPHRLANYLYELASAFH--SFYN---- 76
Query: 59 KGIKPIIGCDVWITNEIENKKPSRLLLL 86
+ + +E ++ +RL LL
Sbjct: 77 ---------NCRVLDEDNEERNARLALL 95
>gnl|CDD|224297 COG1379, COG1379, PHP family phosphoesterase with a Zn ribbon
[General function prediction only].
Length = 403
Score = 30.1 bits (68), Expect = 8.1
Identities = 31/129 (24%), Positives = 50/129 (38%), Gaps = 6/129 (4%)
Query: 8 LRLHSEYSI-IDGLLRINDVIEAAANDYQPALAITDLSN--LFGIIKFYKSAYNKGIKPI 64
L +HS YS L+ + ++ E A + D + IK + G +
Sbjct: 7 LHIHSHYSGATSKLMVLPNIAEYAKLKGLDLVGTGDCLHPEWLEEIKKSIESDEDGTFEV 66
Query: 65 IGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIR---IEWLE 121
G +T E+E+ + LL++ + + +L E LSK GR + E E
Sbjct: 67 KGVRFILTAEVEDSRRVHHLLILPSLSAAEELSEWLSKYSKNIETEGRPRVYLTGAELAE 126
Query: 122 KNKYQDGLI 130
K GLI
Sbjct: 127 IVKDLGGLI 135
>gnl|CDD|132768 cd06093, PX_domain, The Phox Homology domain, a phosphoinositide
binding module. The PX domain is a phosphoinositide
(PI) binding module involved in targeting proteins to
membranes. Proteins containing PX domains interact with
PIs and have been implicated in highly diverse functions
such as cell signaling, vesicular trafficking, protein
sorting, lipid modification, cell polarity and division,
activation of T and B cells, and cell survival. Many
members of this superfamily bind
phosphatidylinositol-3-phosphate (PI3P) but in some
cases, other PIs such as PI4P or PI(3,4)P2, among
others, are the preferred substrates. In addition to
protein-lipid interaction, the PX domain may also be
involved in protein-protein interaction, as in the cases
of p40phox, p47phox, and some sorting nexins (SNXs). The
PX domain is conserved from yeast to humans and is found
in more than 100 proteins. The majority of PX
domain-containing proteins are SNXs, which play
important roles in endosomal sorting.
Length = 106
Score = 28.1 bits (63), Expect = 8.3
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 270 LKLEFGKPKLPKFPTPKNININDF-LISKSKHGLKKRLLNLYKDPEIYKCEKLRY 323
LK +F LP P K D I + + L++ L +L PE+ E+L+
Sbjct: 48 LKKKFPGVILPPLPPKKLFGNLDPEFIEERRKQLEQYLQSLLNHPELRNSEELKE 102
>gnl|CDD|233017 TIGR00549, mevalon_kin, mevalonate kinase. This model represents
mevalonate kinase, the third step in the mevalonate
pathway of isopentanyl pyrophosphate (IPP) biosynthesis.
IPP is a common intermediate for a number of pathways
including cholesterol biosynthesis. This model covers
enzymes from eukaryotes, archaea and bacteria. The
related enzyme from the same pathway, phosphmevalonate
kinase, serves as an outgroup for this clade. Paracoccus
exhibits two genes within the
phosphomevalonate/mevalonate kinase family, one of which
falls between trusted and noise cutoffs of this model.
The degree of divergence is high, but if the trees
created from this model are correct, the proper names of
these genes have been swapped [Central intermediary
metabolism, Other].
Length = 274
Score = 29.6 bits (67), Expect = 8.4
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 355 NNSIPVGPGRGSGASSLVAYSLSITD--IDPLSYNLLFER 392
++ IP G G GS A+ VA ++ D LS L E
Sbjct: 85 DSEIPPGRGLGSSAAVAVALIRALADYFGSELSKEELAEL 124
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 28.6 bits (65), Expect = 9.2
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 825 DGKHKKIRYGLGAIKGTGKSTIEAIV 850
DG K + Y L IKG G+ T AI
Sbjct: 18 DG-TKPVEYALTGIKGIGRRTARAIA 42
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 29.9 bits (68), Expect = 9.8
Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 19/86 (22%)
Query: 5 FIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAIT----DLSNLFGIIKFYKSAYNKG 60
L E ++ LL +V+E AA + +P + DL+ F FY +
Sbjct: 485 DALLTELEERELVKKLLEFPEVLEEAAEELEPHR-LANYLYDLAGSFN--SFYNAC---- 537
Query: 61 IKPIIGCDVWITNEIENKKPSRLLLL 86
P++G E E + +RL L+
Sbjct: 538 --PVLG------AENEELRAARLALV 555
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
0.322 0.140 0.402
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 60,235,798
Number of extensions: 6265524
Number of successful extensions: 6388
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6191
Number of HSP's successfully gapped: 121
Length of query: 1149
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 1042
Effective length of database: 6,191,724
Effective search space: 6451776408
Effective search space used: 6451776408
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 (21.9 bits)
S2: 65 (29.0 bits)