RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8865
(749 letters)
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 1478 bits (3829), Expect = 0.0
Identities = 515/758 (67%), Positives = 617/758 (81%), Gaps = 15/758 (1%)
Query: 1 MEKDPVYSQVTARLLMYCIQKEVFGK-----EIKQIDIPIKYKEYFSKFINKGIDNKLLN 55
+EK+P YS VTARLL+ +++E G E+ Q ++ +Y EYF FI KGI+ +LL+
Sbjct: 214 IEKEPNYSYVTARLLLDTLRREALGFLGVPEEVTQAEMATRYAEYFPAFIKKGIEAELLD 273
Query: 56 PKLAEFNLSLLSNALLPERDLQFNYLGLKILYDRYFLHIEGIRIEMPQFFFMRIAMGLSL 115
PKLA+F+L L AL PERDLQF YLGL+ LYDRYFLH++G RIE+PQ FFMR+AMGL+L
Sbjct: 274 PKLAQFDLERLGAALDPERDLQFTYLGLQTLYDRYFLHVDGTRIELPQAFFMRVAMGLAL 333
Query: 116 NESNREKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKEN 175
NE +RE AI+FYNLLSSF+FM STPTLFNSGT+R QLSSCYL+TVPDDL GI+E+IK+N
Sbjct: 334 NEIDREARAIEFYNLLSSFDFMSSTPTLFNSGTLRPQLSSCYLTTVPDDLDGIYEAIKDN 393
Query: 176 ALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICA 235
ALLSK+AGGLGNDWT VR+LGS IKGTNG+SQGV+PFLKVVND AVAVNQGGKRKGA+CA
Sbjct: 394 ALLSKFAGGLGNDWTPVRALGSHIKGTNGKSQGVVPFLKVVNDTAVAVNQGGKRKGAVCA 453
Query: 236 YLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDL 295
YLETWH+DIEEF+ELRKNTGDDRRRTHDMN A W+PDLFMKRV++ WTLFSP +VPDL
Sbjct: 454 YLETWHLDIEEFLELRKNTGDDRRRTHDMNTANWIPDLFMKRVMEDGEWTLFSPSEVPDL 513
Query: 296 HNKFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIR 355
H+ FGK FEE+Y YE + G+IKLFKKI A+ LWRK+LSMLFETGHPWITFKD CN+R
Sbjct: 514 HDLFGKAFEEAYTAYEAKAARGEIKLFKKIPAVDLWRKMLSMLFETGHPWITFKDPCNLR 573
Query: 356 SPQQHVGIIHSSNLCTEITLNTSKNEIGVCNLGSINLTLHMKNG-KLDPIKLKKTIRIAM 414
SPQQHVG++HSSNLCTEITLNTS +EI VCNLGS+NL H+K+G KLD KLK+T+ AM
Sbjct: 574 SPQQHVGVVHSSNLCTEITLNTSDDEIAVCNLGSVNLVAHIKDGAKLDHEKLKRTVSTAM 633
Query: 415 RMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEM 474
RMLDNVIDINYYAV KA+ SNLRHRPVGLGIMGFQD L++++IPY+S EA++FAD+SME
Sbjct: 634 RMLDNVIDINYYAVPKARNSNLRHRPVGLGIMGFQDALYLLRIPYASDEAVEFADRSMEA 693
Query: 475 ICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWK 534
+ YYA +ASTELAEE+GRYSSY+GSLW +GILP DSLKLL + RG YL+V+ S +L+W
Sbjct: 694 VSYYAIWASTELAEERGRYSSYEGSLWSRGILPIDSLKLLAEARG-GYLEVDRSSTLDWD 752
Query: 535 KLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLV 594
LR RIKK GMRNSNC+AIAPTATISNIIGVS SIEPTY+NL++KSNLSGEFT +N YLV
Sbjct: 753 ALRARIKKHGMRNSNCMAIAPTATISNIIGVSQSIEPTYQNLYVKSNLSGEFTVVNPYLV 812
Query: 595 KELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWI 654
++LK +GLWDE M+ +LKYFDG+L +I RIP DL+ +YATAFE+ P W++EA S RQKWI
Sbjct: 813 RDLKARGLWDEVMVNDLKYFDGSLQRIDRIPADLKALYATAFEVDPRWLVEAASRRQKWI 872
Query: 655 DQSQSLNIYISNKSGKKLDETYKLAWLRGLKTTYYLRSISANYAKKSNFEMG---IDSVN 711
DQ+QSLN+Y++ SGKKLDETYKLAWLRGLKTTYYLR++ A + +KS G S
Sbjct: 873 DQAQSLNLYMAGASGKKLDETYKLAWLRGLKTTYYLRTLGATHVEKSTVNTGALNAVSSG 932
Query: 712 LDEISIKGYNKNLQEIKNNKKCLINSEINDVNECESCQ 749
+ K C I D +CE+CQ
Sbjct: 933 GGGAGGAAAAAAAPPAADPKACSI-----DDPDCEACQ 965
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 943 bits (2440), Expect = 0.0
Identities = 417/702 (59%), Positives = 534/702 (76%), Gaps = 2/702 (0%)
Query: 1 MEKDPVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFSKFINKGIDNKLLNPKLAE 60
+EK+P Y+ V A LL+ + KE GK D+ +K++F ++I +G D LNP+L
Sbjct: 302 IEKEPDYAFVAAELLLDVVYKEALGKSKYDEDLEEAHKDHFKRYILEG-DTYRLNPELKH 360
Query: 61 FNLSLLSNALLPERDLQFNYLGLKILYDRYFLHIEGIRIEMPQFFFMRIAMGLSLNES-N 119
++L L+ AL RDLQF+Y+G++ LYDRYF H EG R+E PQ F+MR++MGL+LNE +
Sbjct: 361 YDLDALAEALDLSRDLQFSYMGVQNLYDRYFNHHEGRRLETPQIFWMRVSMGLALNEGQD 420
Query: 120 REKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLS 179
+ AI FYNLLS+F + +TPTLFNSG SQLSSCYLSTV DDL I++ I +NA+LS
Sbjct: 421 KTSWAITFYNLLSTFRYTPATPTLFNSGMRHSQLSSCYLSTVQDDLVHIYKVISDNAMLS 480
Query: 180 KYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLET 239
K+AGG+GNDWT VR+ G+ IKGTNG+SQGVIPF+KV ND AVAVNQGGKRKGA+C YLE
Sbjct: 481 KWAGGIGNDWTAVRATGALIKGTNGKSQGVIPFIKVANDTAVAVNQGGKRKGAVCVYLEV 540
Query: 240 WHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKF 299
WH+D E+F+ELRKNTGD+RRRTHD+N A W+PDLF KR+ +K TWTLFSP DVP LH +
Sbjct: 541 WHLDYEDFLELRKNTGDERRRTHDINTASWIPDLFFKRLQQKGTWTLFSPDDVPGLHEAY 600
Query: 300 GKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQ 359
G+EFE+ Y YE + G+I+L+KK+ A LWRK+LSML+ETGHPW+TFKD NIRS Q
Sbjct: 601 GEEFEKLYEEYERKVDTGEIRLYKKVEAEDLWRKMLSMLYETGHPWMTFKDPSNIRSAQD 660
Query: 360 HVGIIHSSNLCTEITLNTSKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDN 419
H G++ SNLCTEI LN S+ E VCNLGSINL H+ N LD KL +TI IA+R+LDN
Sbjct: 661 HKGVVRCSNLCTEILLNCSETETAVCNLGSINLVEHIVNDGLDEEKLSETISIAIRILDN 720
Query: 420 VIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYA 479
VIDIN+Y K+AK +NL HR +GLG+MGFQD L+ + I Y+S+EA++FAD S E+I YYA
Sbjct: 721 VIDINFYPTKEAKEANLAHRAIGLGVMGFQDALYKLNISYASQEAVEFADYSSELIAYYA 780
Query: 480 YYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNR 539
AS+ LA+E+G YSSY GS WD+G LP D+++LL++ RG L ++ S +W+ +R+
Sbjct: 781 ILASSLLAKERGTYSSYKGSKWDRGYLPIDTIELLKEYRGEANLLMDTSSRKDWEPVRSL 840
Query: 540 IKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKK 599
IK++GMRNS +AIAPTATISNIIGV+ SIEPTY++L +KSNLSGEFT N YL+++LKK
Sbjct: 841 IKEYGMRNSQLMAIAPTATISNIIGVTQSIEPTYKHLFVKSNLSGEFTIPNVYLIEKLKK 900
Query: 600 KGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQS 659
G+WD M+ +LKYFDG+L +I RIPD L+KI+ TAFEI P WIIE S RQKWID QS
Sbjct: 901 LGIWDADMLDDLKYFDGSLLEIERIPDHLKKIFLTAFEIEPEWIIECASRRQKWIDMGQS 960
Query: 660 LNIYISNKSGKKLDETYKLAWLRGLKTTYYLRSISANYAKKS 701
LN+Y++ GKKL Y AW +GLKTTYYLRS +A +KS
Sbjct: 961 LNLYLAEPDGKKLSNMYLTAWKKGLKTTYYLRSSAATSVEKS 1002
>gnl|CDD|233902 TIGR02506, NrdE_NrdA, ribonucleoside-diphosphate reductase, alpha
subunit. This model represents the alpha (large) chain
of the class I ribonucleotide reductase (RNR). RNR's are
responsible for the conversion of the ribose sugar of
RNA into the deoxyribose sugar of DNA. This is the
rate-limiting step of DNA biosynthesis. Class I RNR's
generate the required radical (on tyrosine) via a
"non-heme" iron cofactor which resides in the beta
(small) subunit. The alpha subunit contains the
catalytic and allosteric regulatory sites. The mechanism
of this enzyme requires molecular oxygen. E. Coli
contains two versions of this enzyme which are regulated
independently (NrdAB and NrdEF, where NrdA and NrdE are
the large chains ). Most organisms contain only one, but
the application of the gene symbols NrdA and NrdE are
somewhat arbitrary. This model identifies RNR's in
diverse clades of bacteria, eukaryotes as well as
numerous DNA viruses and phage [Purines, pyrimidines,
nucleosides, and nucleotides, 2'-Deoxyribonucleotide
metabolism].
Length = 617
Score = 694 bits (1792), Expect = 0.0
Identities = 283/623 (45%), Positives = 386/623 (61%), Gaps = 17/623 (2%)
Query: 80 YLGLKILYDRYFL--HIEGIRIEMPQFFFMRIAMGLSLNE--SNREKCAIKFYNLLSSFN 135
Y+GLK LY+RY L G E PQ +MR+AMGL+ E R AI+FY+LLS
Sbjct: 1 YMGLKELYNRYLLRNAATGAIYESPQEAYMRVAMGLASLEPKDTRLADAIRFYDLLSRLK 60
Query: 136 FMCSTPTLFNSGTIRSQLSSCYLSTVPDD-LYGIFESIKENALLSKYAGGLGNDWTQVRS 194
+TPTLFN+GT R QLSSC+L V DD L I+++I + A LSK+ GG+G + T++R+
Sbjct: 61 ISPATPTLFNAGTPRGQLSSCFLLDVTDDTLESIYKAIDDVAQLSKHGGGIGLNLTKLRA 120
Query: 195 LGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRKNT 254
+GSPI+GTN S+G+IPFLK+++ AVNQGGKR GA YLE WH DIEEF++L+KN
Sbjct: 121 IGSPIRGTNNASKGIIPFLKLLDSSVEAVNQGGKRPGAAAVYLEVWHPDIEEFLDLKKNN 180
Query: 255 GDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEESYILYENQT 314
GD+RRR ++ +W+PDLFMKRV + W LFSPYDVP L+ +G+EFEE Y E
Sbjct: 181 GDERRRCDNLFYGLWIPDLFMKRVEEDKDWYLFSPYDVPGLYGLYGEEFEEEYERLEKDV 240
Query: 315 KLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSP-QQHVGIIHSSNLCTEI 373
+ K +K+SA L + IL ETG P+I FKDA N +P + G I SNLCTEI
Sbjct: 241 EARKKI--RKVSARDLMKDILRTRVETGRPYILFKDAVNKHNPFKTGGGAIKMSNLCTEI 298
Query: 374 TLNTSKN---EIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKK 430
T T + E VCNL S+NL + K D +L+ +RIA+R LDNVID+ Y
Sbjct: 299 TQPTDDSHKGETAVCNLASVNLANFVMEDKFDFSELEDAVRIAVRFLDNVIDLQNYPTAP 358
Query: 431 AKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEK 490
A SN R R +G+G+MG D L + +PY S+EA D+ E I YYA AS ELA+EK
Sbjct: 359 AAKSNQRRRSIGIGVMGLHDVLAKLGLPYDSEEARDLNDRIFEAIYYYAIKASAELAKEK 418
Query: 491 GRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNC 550
G + + GS + +G L D+ + + S +W+ LR RIK++G+RNS
Sbjct: 419 GPFPGFSGSKYAKGWLHPDTWEKTIDPKTSMAP-----TEEDWEALRERIKEYGLRNSQL 473
Query: 551 VAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIAN 610
A+ PTA+ S + GV+ SIEP + N+ K LSGEF N+YL+KEL++ GLWD +
Sbjct: 474 TALMPTASSSQLTGVTESIEPVFSNIFTKKTLSGEFLIPNKYLMKELEELGLWDADRRGD 533
Query: 611 LKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYI-SNKSG 669
+ G+ I+ IP+ L+ Y TA+E+ +I+ + RQK++DQS SLN+++ +
Sbjct: 534 IVENVGSPQPIAAIPETLKYKYKTAYELDQEALIDMAADRQKFVDQSISLNLFLTEEVTA 593
Query: 670 KKLDETYKLAWLRGLKTTYYLRS 692
K L + LAW +GLKT YY RS
Sbjct: 594 KDLLKLLLLAWKKGLKTMYYCRS 616
>gnl|CDD|217257 pfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel
domain.
Length = 516
Score = 686 bits (1772), Expect = 0.0
Identities = 250/542 (46%), Positives = 345/542 (63%), Gaps = 30/542 (5%)
Query: 153 LSSCYL-STVPDDLYGIFESIKENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIP 211
LSSC+L +V D L I++++KE ALLSK GG+G + +++R+ GSPI+GT G S GV+P
Sbjct: 1 LSSCFLLPSVDDSLDSIYDTLKEAALLSKSGGGIGINLSKIRAKGSPIRGTGGVSSGVVP 60
Query: 212 FLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVP 271
FLKV +D A VNQGGKR+GA+ YLE WH DIEEF++L+KN GD+ RR ++N+ +WVP
Sbjct: 61 FLKVFDDTARYVNQGGKRRGAVAVYLEVWHPDIEEFLDLKKNNGDEERRARNLNLGVWVP 120
Query: 272 DLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEESYILYENQTKLGKIKLFKKISALYLW 331
DLFMKRV WTLFSP + P L + +G+EFEE Y E GK+K K + A LW
Sbjct: 121 DLFMKRVENDEDWTLFSPREAPGLEDLYGEEFEEEYEKLEAN---GKVK--KTVKARELW 175
Query: 332 RKILSMLFETGHPWITFKDACNIRSPQQHVGIIHSSNLCTEITLNTSKNEIGVCNLGSIN 391
KI+ +ETG P+I FKDA N +PQ+H+G I SSNLCTEI TS E VCNL SIN
Sbjct: 176 FKIVESAWETGEPYILFKDAVNRHNPQKHLGTIKSSNLCTEIVQPTSPGEDAVCNLASIN 235
Query: 392 LTLHMKNGK-LDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQD 450
L ++N D +L++ +R+A+R LDNVID+N Y V +A+ SN RHR +GLG+MG D
Sbjct: 236 LAKFVENDFTFDFEELREVVRLAVRALDNVIDLNDYPVPEARKSNKRHRSIGLGVMGLAD 295
Query: 451 CLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDS 510
L + IPY S+EA + AD+ E I YYA AS ELA+EKG + ++GS + +G
Sbjct: 296 ALAKLGIPYDSEEARELADEIFETIYYYALKASNELAKEKGPFPGFEGSKYAKGEFHAIP 355
Query: 511 LKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIE 570
L+ +W++LR IKK G+RNS AIAPT +IS I G + IE
Sbjct: 356 LR------------------EDWEELREDIKKHGLRNSQLTAIAPTGSISQIAGTTEGIE 397
Query: 571 PTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRK 630
P + N++ + + SGEF +N YL+++L++ LW E M L Y +G++ I IP++++
Sbjct: 398 PIFSNVYSRRSKSGEFLVVNPYLLRDLRE--LWSEEMKNELAY-NGSVQPIPEIPEEIKA 454
Query: 631 IYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYISNK-SGKKLDETYKLAWLRGLKT-TY 688
+Y TAF+I P I+ + RQ ++DQS S +++ + L Y AW GLKT TY
Sbjct: 455 LYKTAFDIDPKGHIDMAAARQPFVDQSISKTLFLPEDATASDLKSLYLYAWKLGLKTGTY 514
Query: 689 YL 690
Y
Sbjct: 515 YR 516
>gnl|CDD|153088 cd01679, RNR_I, Class I ribonucleotide reductase. Ribonucleotide
reductase (RNR) catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and many viruses, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophages, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class I RNR is oxygen-dependent and can
be subdivided into classes Ia (eukaryotes, prokaryotes,
viruses and phages) and Ib (which is found in
prokaryotes only). It is a tetrameric enzyme of two
alpha and two beta subunits; this model covers the major
part of the alpha or large subunit, called R1 in class
Ia and R1E in class Ib.
Length = 460
Score = 665 bits (1718), Expect = 0.0
Identities = 247/597 (41%), Positives = 330/597 (55%), Gaps = 143/597 (23%)
Query: 102 PQFFFMRIAMGLSLNESNREKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTV 161
PQ MR+A+GL+ S + A +FY+LLS F +TPTLFN+GT R QLSSC+L TV
Sbjct: 1 PQDRLMRVALGLA---SGDLEWAKEFYDLLSKQRFTPATPTLFNAGTPRGQLSSCFLLTV 57
Query: 162 PDDLYGIFESIKENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAV 221
D L I+++IKE A LSK GG+G + + +R+ GSPI+GTNG S GVIPFLK++ND A
Sbjct: 58 DDSLESIYDTIKECAQLSKIGGGIGLNLSNIRATGSPIRGTNGASNGVIPFLKLLNDTAR 117
Query: 222 AVNQGGKRKGAICAYLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKK 281
V+QGG+RKGA YLE WH DIEEF++L+KN GD+RRR D+ +W+PDLFM+RV +
Sbjct: 118 YVDQGGQRKGAGAVYLEIWHPDIEEFLDLKKNNGDERRRARDLFYGVWIPDLFMERVERD 177
Query: 282 STWTLFSPYDVPDLHNKFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFET 341
LWRKIL FET
Sbjct: 178 ------------------------------------------------LWRKILESQFET 189
Query: 342 GHPWITFKDACNIRSPQQHVGIIHSSNLCTEITLNTSKN-----EIGVCNLGSINLTLHM 396
G+P+I FKD CN ++PQ+H+G I SSNLCTEI TS + E VCNL SINL +
Sbjct: 190 GYPYILFKDTCNRKNPQKHLGTIKSSNLCTEILQPTSPSEDEPGEDAVCNLASINLGNFV 249
Query: 397 KNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMK 456
KL++ +++A+R LDNVID+NYY V +AK SN+RHR +GLG+MG D L +++
Sbjct: 250 TFE-----KLEEVVKLAVRALDNVIDLNYYPVPEAKRSNMRHRAIGLGVMGLHDYLALLR 304
Query: 457 IPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEK 516
IPY S+EA+ D+ E I YYA AS ELA+E+G
Sbjct: 305 IPYESEEALDLNDRIFETINYYALKASCELAKERG------------------------- 339
Query: 517 ERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNL 576
G+RNS +AIAPTA+IS I+G + SIEP N+
Sbjct: 340 ---------------------------GLRNSLLLAIAPTASISQILGATPSIEPITSNI 372
Query: 577 HIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAF 636
+++ LSGEF +N +L K+L + GL Y TA+
Sbjct: 373 YVRRVLSGEFPVVNPHLEKDLWEYGL-----------------------------YKTAY 403
Query: 637 EISPNWIIEAGSVRQKWIDQSQSLNIYI-SNKSGKKLDETYKLAWLRGLKTTYYLRS 692
EI W+I+ + RQK IDQ QSLN+++ + + L+ Y AW +GLKT YYLR+
Sbjct: 404 EIDQRWLIDLAADRQKHIDQGQSLNLFLTPPATTRDLNSLYFYAWKKGLKTLYYLRT 460
>gnl|CDD|180610 PRK06539, PRK06539, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 822
Score = 643 bits (1659), Expect = 0.0
Identities = 284/700 (40%), Positives = 439/700 (62%), Gaps = 5/700 (0%)
Query: 4 DPVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFSKFINKGIDNKLLNPKLAE-FN 62
DP + V ARLL+ I K V G ++ + +F + I KG+ LL+ +L F+
Sbjct: 73 DPAFDTVAARLLLKKIYKRVLGDYDSPEELQDLHANHFRRTIEKGVAEGLLDSRLGGLFD 132
Query: 63 LSLLSNALLPERDLQFNYLGLKILYDRYFLHI-EGIRIEMPQFFFMRIAMGLSLNESNRE 121
L L+ AL P RD Y+G+ L +RY + G +E+PQ+F+MRIAMGLSLNE +
Sbjct: 133 LERLAAALDPTRDELLKYIGVVTLNNRYGIRARNGDALEVPQYFWMRIAMGLSLNEDDPT 192
Query: 122 KCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLSKY 181
A+ FY +S ++ + TL N+GT QLS+C++ + DD+ I ++ ++ L+K
Sbjct: 193 SSALAFYEKMSKLEYLAAGSTLVNAGTPYPQLSNCFVMEMQDDIEHIAKTTRDVMWLTKG 252
Query: 182 AGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWH 241
GG+G +++R+ GSPI+ N S G IPF+ ++ V AV++GGK+ GA+C Y+E WH
Sbjct: 253 TGGIGLSVSKLRAQGSPIRSNNTTSTGPIPFMHTIDSVLRAVSRGGKKFGALCFYMENWH 312
Query: 242 MDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGK 301
MD EF++LR+N+GD RRT N A+W+ D FMKRV W LF P + PDL+ +GK
Sbjct: 313 MDFPEFLDLRQNSGDPYRRTRTANTAVWISDEFMKRVQNDEDWYLFDPLETPDLNELYGK 372
Query: 302 EFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHV 361
F + Y Y Q + G+I++FK+I+A +R IL L T HPW+T+KD N R+ +
Sbjct: 373 AFSKRYAQYVEQAEAGRIRMFKRITAREQFRAILMSLQTTSHPWLTWKDTINNRALNNNT 432
Query: 362 GIIHSSNLCTEITLNTSKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVI 421
G IH SNLCTEI L ++ + VCNL SINL+ H+ +G+LD +L+++ R+A+R LDN+I
Sbjct: 433 GTIHLSNLCTEICLPQDRDNVSVCNLASINLSRHLADGELDWAQLEESTRLAVRQLDNLI 492
Query: 422 DINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYY 481
DI +VK+A +SN ++R +GLG+MGF D + + Y S+EA D+ ME I Y A
Sbjct: 493 DITASSVKEADFSNQQNRAIGLGVMGFTDMVERLGYSYESEEAYDLIDRIMEHISYAAID 552
Query: 482 ASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIK 541
S +LA E+G Y +++GS W +G++P DS+ LLE +RG + VN + L+W LR +++
Sbjct: 553 ESADLAAERGAYPNFEGSRWSRGMVPVDSIALLEADRGVP-VDVNRTTRLDWDALRAKVR 611
Query: 542 KFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKG 601
GMRN+ +AIAPTA+I + G + ++P + + +S SG+F E+NR LV +LK+ G
Sbjct: 612 G-GMRNATLMAIAPTASIGLVAGTTPGLDPQFSQIFSRSTSSGKFLEVNRNLVADLKELG 670
Query: 602 LWDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLN 661
LW E++ + G++ +I+ IPD+++ +Y T+F++SP +E + QKW+DQ+ S N
Sbjct: 671 LW-ETVREEILRSQGDIQEIAAIPDEIKALYRTSFQLSPYAFLEVAARAQKWVDQAISRN 729
Query: 662 IYISNKSGKKLDETYKLAWLRGLKTTYYLRSISANYAKKS 701
+Y+ ++ + + Y AW G+KTTYYL + A++S
Sbjct: 730 MYLESRDIGDMMDIYTAAWEMGVKTTYYLHMKPRHTAEQS 769
>gnl|CDD|223287 COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide
transport and metabolism].
Length = 651
Score = 626 bits (1616), Expect = 0.0
Identities = 258/707 (36%), Positives = 363/707 (51%), Gaps = 111/707 (15%)
Query: 2 EKDPVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFSKFINKGIDNKLLNPKLAEF 61
E DP ++ ARL ++KE + + + ++ F+ N D +LL E
Sbjct: 29 EDDPDVQRLAARLAGSDLRKEAVRQFGRFDVL---DEKVFALVANGYYDQRLLRLYSRED 85
Query: 62 NLSLLSNALLPERDLQFNYLGLKILYDRYFLHIE--GIRIEMPQFFFMRIAMGLSLNESN 119
L L+ +L ERD QF+Y K+LY RY L E +E+PQ FMR+A+ L+ NE+
Sbjct: 86 -LDDLNKKILLERDRQFSYAAAKVLYSRYLLKDEDGSEILELPQDLFMRVALLLAQNEAP 144
Query: 120 --REKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENAL 177
R + A +FY+L+SS FM +TPTL N GT R QLSSC++ V DD
Sbjct: 145 ERRLEWAKEFYDLMSSLRFMPATPTLLNGGTPRGQLSSCFVLPVEDD------------- 191
Query: 178 LSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYL 237
S GV+PF+K+++D A+NQGG R+GA YL
Sbjct: 192 ----------------------------SSGVVPFMKLLDDAFDAINQGGVRRGAQAVYL 223
Query: 238 ETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHN 297
+ WH DIEEF++ ++N GD+ R D+++ +W+PDLFMKR + WTLFSP D + +
Sbjct: 224 DIWHPDIEEFLDAKRNNGDEILRAFDISVGVWIPDLFMKRAKEGEDWTLFSPRDGYEAPD 283
Query: 298 KFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSP 357
+G EFEE Y YE K+I A L+ K+ FETG P++ F D N R+P
Sbjct: 284 VYGAEFEE-YAEYEADPG----IRKKRIKARELFDKLAEAAFETGDPYLIFVDTLNRRNP 338
Query: 358 Q-QHVGIIHSSNLCTEITLNTS-------KNEIGVCNLGSINLTLHMKNGKLDPIKLKKT 409
+ G I +SNLC+EI T E CNLGSINL +K G L +
Sbjct: 339 NAEGGGAIRASNLCSEILQRTKPLSLEQPLGEDASCNLGSINLAKFVKYGD----GLAEL 394
Query: 410 IRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFAD 469
+ +A+R LDNVID+N Y V +A+ +N R +GLG+MG D L + IPY S+EA+KF D
Sbjct: 395 VAVAVRALDNVIDLNPYPVPEAERANAESRAIGLGVMGLADLLAQLGIPYGSEEALKFND 454
Query: 470 QSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSE 529
+ E I YYA AS ELA+E+G Y ++GS W +GILP D +L
Sbjct: 455 RLFEYIAYYALKASAELAKERGPYPYFEGSRWARGILPIDYPRLFGI------------- 501
Query: 530 SLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEFTEI 589
+ +W+KLR IKK G+RNS AIAPT +IS I G ++ IEP + ++ + G F +
Sbjct: 502 TEDWEKLREDIKKHGLRNSYLTAIAPTGSISYIAGTTSGIEPIFALVYFRETKGGRFYYV 561
Query: 590 NRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSV 649
L ++L A+EI P W I+ +
Sbjct: 562 VPPLFEDLLAYYGL-------------------------------AYEIDPLWHIDMQAA 590
Query: 650 RQKWIDQSQSLNIYI-SNKSGKKLDETYKLAWLRGLKTTYYLRSISA 695
Q+WIDQ S + + + + K L++ Y AW GLKTTYY R+ A
Sbjct: 591 AQRWIDQGISKTLNLPNTATTKDLNKAYLYAWKLGLKTTYYRRTSQA 637
>gnl|CDD|236266 PRK08447, PRK08447, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 789
Score = 627 bits (1619), Expect = 0.0
Identities = 320/750 (42%), Positives = 435/750 (58%), Gaps = 111/750 (14%)
Query: 5 PVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFSKFINKGIDNKLLNPKLAE-FNL 63
P ++ V ARL +Y + +V G KEYF K +G ++L L E ++L
Sbjct: 72 PNWTFVAARLFLYDLYHKVSGFTGYN-----HLKEYFEKGEKEG---RIL-LGLKEKYDL 122
Query: 64 SLLSNALLPERDLQFNYLGLKILYDRYFLH-IEGIRIEMPQFFFMRIAMGLSLNESNREK 122
L+ + PERDLQFNYLG+K LYDRY + IE+PQ FM IAM L+ NE + +K
Sbjct: 123 DDLNAYIKPERDLQFNYLGIKTLYDRYLIKDRNNNPIELPQHMFMAIAMFLAQNELDPQK 182
Query: 123 CAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLSKYA 182
A KFY+++S F M +TPTL N+ T R QLSSCY+ + PD++ GIF+S KE ALLSKY
Sbjct: 183 WAKKFYDVISKFEVMLATPTLSNARTTRHQLSSCYIGSTPDNIEGIFDSYKEMALLSKYG 242
Query: 183 GGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHM 242
GG+G DW++VR++GS I G + G+IPFLK+ ND+A+AV+Q G RKGAI YLE WHM
Sbjct: 243 GGIGWDWSKVRAMGSYIDGHKNAAGGIIPFLKITNDIAIAVDQLGTRKGAIAVYLEPWHM 302
Query: 243 DIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKE 302
DI +FI+LRKN+G++RRR HD+ A+W+ DLFMKRV + + WTLF PY+ DL +G+E
Sbjct: 303 DISDFIDLRKNSGEERRRAHDLFPALWINDLFMKRVEEDAMWTLFDPYECKDLTELYGEE 362
Query: 303 FEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVG 362
FE+ Y+ YE K+ K + I+A LW+KIL+ FETG P++ FKD N +P H G
Sbjct: 363 FEKRYLEYEKDEKIIK----EYINAKELWKKILTNYFETGLPFLCFKDNANRANPNAHAG 418
Query: 363 IIHSSNLCTEITLNTSKN------------------------EIGVCN-------LGSIN 391
II SSNLCTEI NT+ N + G+ L S+
Sbjct: 419 IIRSSNLCTEIFQNTAPNHYKIKIEFEDGSIEFFEEEELVTVDSGITKKAKKITSLDSLK 478
Query: 392 ------LTLHMKNGK----------LDPIKLKKTIR----IAMRMLDNVIDINYYAVKKA 431
+ K+GK L I K+ I IA+RMLDNVID+N+Y +K
Sbjct: 479 GKKIYIVEKEKKDGKTAVCNLASINLSKINTKEDIERVVPIAIRMLDNVIDLNFYPNRKV 538
Query: 432 KYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKG 491
K +NL+ R +GLG+MG L KI + SKE ++ D+ ME I Y A AS+ LA EKG
Sbjct: 539 KATNLKSRAIGLGVMGEAQMLAEHKIAWGSKEHLEKIDEIMEQISYNAIDASSNLALEKG 598
Query: 492 RYSSYDGSLWDQGILPQDS-----LKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMR 546
Y ++GS W +GI P D KL+ ERG + + +W+ LR ++KK GMR
Sbjct: 599 VYPDFEGSNWSKGIFPIDKANEEAKKLV--ERGGLF-----DSACDWEGLREKVKKDGMR 651
Query: 547 NSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDES 606
N +AIAPT++IS ++G + +IEP Y+ + NLSG
Sbjct: 652 NGYLMAIAPTSSISILVGTTQTIEPVYKRKWFEENLSG---------------------- 689
Query: 607 MIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYIS- 665
+I + NLS + + Y A+++ +I+A +VRQKWIDQ QSLNI++S
Sbjct: 690 LIPVVV---PNLSP------ETWQYYTPAYDLDQKDLIKAAAVRQKWIDQGQSLNIFLSL 740
Query: 666 -NKSGKKLDETYKLAWLRGLKTTYYLRSIS 694
SGK L+E Y LAW GLK+TYYLRS S
Sbjct: 741 DKASGKYLNEIYTLAWKLGLKSTYYLRSES 770
>gnl|CDD|178056 PLN02437, PLN02437, ribonucleoside--diphosphate reductase large
subunit.
Length = 813
Score = 557 bits (1437), Expect = 0.0
Identities = 282/725 (38%), Positives = 408/725 (56%), Gaps = 57/725 (7%)
Query: 5 PVYSQVTARLLMYCIQKEV---FGKEIKQIDIPIKYKEYFSKFINKGIDNKLLNPKLAEF 61
P Y+ + AR+ + + K F + +K + Y G+ L+ + +
Sbjct: 72 PDYAILAARIAVSNLHKNTKKSFSETVKDM--------YNHVNERSGLKAPLIADDVYDI 123
Query: 62 ---NLSLLSNALLPERDLQFNYLGLKILYDRYFLHIEGIRIEMPQFFFMRIAMGLSLNES 118
N + L + ++ +RD ++Y G K L Y L + G +E PQ MR+++G+ ++
Sbjct: 124 IMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVNGKVVERPQHMLMRVSVGIHKDDI 183
Query: 119 NREKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDD-LYGIFESIKENAL 177
AIK Y+L+S F ++PTLFN+GT R QLSSC+L + DD + GI++++KE A+
Sbjct: 184 ES---AIKTYHLMSQRWFTHASPTLFNAGTPRPQLSSCFLICMKDDSIEGIYDTLKECAV 240
Query: 178 LSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGG-KRKGAICAY 236
+SK AGG+G +R+ GS I+GTNG S G++P L+V ND A V+QGG KRKGA Y
Sbjct: 241 ISKSAGGIGLSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAIY 300
Query: 237 LETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLH 296
LE WH DI EF++LRKN G + R D+ A+W+PDLFM+RV W+LF P + P L
Sbjct: 301 LEPWHADIFEFLDLRKNHGKEEHRARDLFYALWIPDLFMERVQSNGDWSLFCPNEAPGLA 360
Query: 297 NKFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRS 356
+ +G+EFE Y YE + GK K K + A LW IL ETG P++ FKD+CN +S
Sbjct: 361 DCWGEEFERLYTKYERE---GKAK--KVVQAQQLWFAILESQIETGTPYMLFKDSCNRKS 415
Query: 357 PQQHVGIIHSSNLCTEITLNTSKNEIGVCNLGSINL--------------------TLHM 396
QQ++G I SSNLCTEI TS E VCNL SI L +L
Sbjct: 416 NQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKGVPLESHPSKLVGSLGS 475
Query: 397 KNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMK 456
KN D KL + + R L+ +ID+NYY V+ A+ SN+RHRP+G+G+ G D ++
Sbjct: 476 KNRYFDFEKLAEVTAVVTRNLNKIIDVNYYPVETARRSNMRHRPIGIGVQGLADAFILLG 535
Query: 457 IPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEK 516
+P+ S EA + E I Y+A AS+ELA +G Y +Y GS +GIL D +
Sbjct: 536 MPFDSPEAQQLNKDIFETIYYHALKASSELAAREGPYETYAGSPVSKGILQPDMWGVTPS 595
Query: 517 ERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNL 576
R +W LR I K G+RNS VA PTA+ S I+G + EP N+
Sbjct: 596 GR------------WDWAALREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNI 643
Query: 577 HIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAF 636
+ + LSGEF +N++L+ +L + GLW ++ + +G++ +I IPDDL+ IY T +
Sbjct: 644 YSRRVLSGEFVVVNKHLLHDLTEMGLWTPTLKNKIIAENGSVQKIPEIPDDLKAIYKTVW 703
Query: 637 EISPNWIIEAGSVRQKWIDQSQSLNIYISNKSGKKLDETYKLAWLRGLKT-TYYLRSISA 695
EI +++ + R +IDQSQSLNI++ + KL + AW +GLKT YYLRS +A
Sbjct: 704 EIKQRTLVDMAADRGCYIDQSQSLNIHMDQPNFGKLTSLHFYAWSKGLKTGMYYLRSRAA 763
Query: 696 NYAKK 700
A K
Sbjct: 764 ADAIK 768
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 463 bits (1194), Expect = e-153
Identities = 266/739 (35%), Positives = 387/739 (52%), Gaps = 113/739 (15%)
Query: 2 EKDPVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEY--FSKFINKGIDNKLLNPKLA 59
+ +P + V ARL ++ + KE +I+ Y + + + K ++ KL L
Sbjct: 82 KTNPNWQYVAARLYVFDLYKEA------RINRHYNSFGYGDYYELVKKLVEEKLYGEYLL 135
Query: 60 E----FNLSLLSNALLPERDLQFNYLGLKILYDRYFLH-IEGIRIEMPQFFFMRIAMGLS 114
+ + L + PERD FNY GLK+L DRY + +E+PQ FM IAM L+
Sbjct: 136 QNYSKEEIKELEKYIKPERDFLFNYEGLKLLADRYLVKGFNREILELPQERFMGIAMHLA 195
Query: 115 LNE--SNREKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESI 172
+ E R A KFY+LLS +TPTL N+GT QLSSC++S V D+L+ I++
Sbjct: 196 IPEGKEKRVYYAKKFYDLLSELKATVATPTLSNAGTPFYQLSSCFISVVDDNLWSIYDVN 255
Query: 173 KENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGA 232
++ A +SK+ G LG ++R+L S I+G S GVIP++K+ ND A+AV+Q GKRKG
Sbjct: 256 QKFAQVSKHGGALGIYTGKIRALNSEIRGFKNASGGVIPWIKLYNDTAIAVDQLGKRKGG 315
Query: 233 ICAYLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDV 292
L+ WH DI EF++L+ N GDDRR+ HD+ + PDLFMKR+ K+ W+LF P+++
Sbjct: 316 AAITLDIWHKDIPEFLDLKTNNGDDRRKAHDIFPGVSYPDLFMKRLEKRENWSLFDPHEI 375
Query: 293 PD-----LHNKFG----KEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGH 343
L + + KEF + Y+ E T + + + L + +KI+ ETG
Sbjct: 376 KKVKGYSLEDYYDEEDRKEFTKKYLECEEDTNIPRRT----VPVLDIMKKIMKSAVETGT 431
Query: 344 PWITFKDACNIRSPQQHVGIIHSSNLCTEITLNTSKNEIG-------------------- 383
P+I F+D N +P +H G+I+SSNLC EI N S++E+
Sbjct: 432 PFIFFRDTVNKANPNKHKGMIYSSNLCHEIAQNMSESELLEEEIIDENGYYEVVQKIKAG 491
Query: 384 ---VCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRP 440
CNL SI L G +D +L++ I +RMLDNVI +NYY V +A+ ++ ++R
Sbjct: 492 DMVTCNLNSIVL------GNVDDEELEEVIPTQIRMLDNVISLNYYPVPEAEITSDKYRA 545
Query: 441 VGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSL 500
+GLG G+ L KI + S E IKFAD+ E I YYA AS ELA+EKG Y ++ GS
Sbjct: 546 IGLGTSGYHHMLANNKIRWESDEHIKFADKIYEEIAYYAIKASMELAKEKGSYPAFKGSE 605
Query: 501 WDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATIS 560
W+ G KY + S WKKL+ IKK+GMRN A+APT + S
Sbjct: 606 WETG----------------KYFERRGYNSERWKKLKEEIKKYGMRNGYITAVAPTGSTS 649
Query: 561 NIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQ 620
NI +A I+P + R+ ++E KKG S
Sbjct: 650 NIANTTAGIDPVF----------------KRFFMEE--KKG-----------------SF 674
Query: 621 ISRIPDDLRK----IYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYISNK-SGKKLDET 675
+ DL + Y A I W I+A VRQ+ IDQ+QS N+YI+ + K++
Sbjct: 675 TPKTAPDLNEENFWYYKEAHTIDQQWSIKACGVRQRHIDQAQSFNLYITPEYKAKQILNL 734
Query: 676 YKLAWLRGLKTTYYLRSIS 694
Y AW +G+KT YY+R+ S
Sbjct: 735 YIEAWKQGVKTIYYVRNKS 753
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 441 bits (1135), Expect = e-143
Identities = 249/730 (34%), Positives = 382/730 (52%), Gaps = 103/730 (14%)
Query: 5 PVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFSKFINKGIDNKLLNPKLAEFNLS 64
P + + ARLLM K++ GK ++++ I + + +G+ + + +
Sbjct: 165 PDWEFIAARLLMLQFSKKL-GKSLEKLGIH-SFYDKIKYLTEEGLYGSYILEHYSREEIE 222
Query: 65 LLSNALLPERDLQFNYLGLKILYDRYFLHI-EGIRIEMPQFFFMRIAMGLSLNE-SNREK 122
+ + PERD F Y GL +L RY + +E PQ F+ IA+ L++ E +R
Sbjct: 223 EAAGFIDPERDKLFTYSGLDLLLKRYVIRTHSHEPLESPQEMFLGIALHLAMPEKQDRMG 282
Query: 123 CAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLSKYA 182
+FY++LS +TPTL N+ QLSSC++ TVPD L GI+ SI A +SK+
Sbjct: 283 WVKRFYDMLSKLKVTMATPTLSNARKPFHQLSSCFIDTVPDSLDGIYRSIDNFAQVSKFG 342
Query: 183 GGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHM 242
GG+G + +VR++GS I+G G + GVI ++K+ ND AVAV+Q G R+GA+ YL+ WH
Sbjct: 343 GGMGLYFGKVRAVGSNIRGFQGVAGGVIRWIKLANDTAVAVDQLGMRQGAVAVYLDVWHK 402
Query: 243 DIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIK--KSTWTLFSPYDVPD-----L 295
DI EF++LR N GDDR + HD+ A+ PDLF K V +W LF P+++ L
Sbjct: 403 DIPEFLQLRTNNGDDRMKAHDVFPAVCYPDLFWKMVRDDINQSWYLFCPHEILTVKGYAL 462
Query: 296 HNKFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIR 355
+ +G+E+E+ Y+ N ++ K + I L R IL ETG P+ +D N
Sbjct: 463 EDYYGEEWEKRYLDCVNDARISK----RSIPIKDLVRLILKSAVETGTPFTFNRDTVNRA 518
Query: 356 SPQQHVGIIHSSNLCTEITLNTS---------KNEIG--------------VCNLGSINL 392
+P +H G+I+ SNLCTEI N S + E G VCNL S++L
Sbjct: 519 NPNKHKGMIYCSNLCTEIAQNMSAIETVSTEIETEDGDTVVVTTTRPGDFVVCNLASLSL 578
Query: 393 TLHMKNGKLD---PIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQ 449
G +D +L++ +R +R LDNVID+N+Y V A+ +N R+R +GLG+ G+
Sbjct: 579 ------GNIDLEDEEELEEVVRTVVRALDNVIDLNFYPVPYAQITNKRYRSIGLGVSGYH 632
Query: 450 DCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQD 509
L I + S+E ++FAD+ E I Y A AS E+A+EKG Y ++GS W G
Sbjct: 633 HALAKNGIRWESEEHLEFADRVFERINYAAIKASMEIAKEKGAYGYFEGSDWQTG----- 687
Query: 510 SLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASI 569
Y + S W++L + + GMRN+ +A+APT++ S I G +A +
Sbjct: 688 -----------AYFRKRGYTSEEWQRLAREVAENGMRNAYLLAVAPTSSTSIIAGTTAGV 736
Query: 570 EPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLR 629
+P + RY ++E KKG + + R+ +L
Sbjct: 737 DPV----------------MKRYFLEE--KKG-----------------ALMPRVAPELS 761
Query: 630 K----IYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYISNK-SGKKLDETYKLAWLRGL 684
+Y A I W I A VRQ+ IDQ+QS+N+YI+N+ + +++ + Y LAW G+
Sbjct: 762 DKTFWLYKNAHLIDQKWSIRAAGVRQRHIDQAQSVNLYITNEFTMRQVLDLYLLAWEEGV 821
Query: 685 KTTYYLRSIS 694
KT YY+RS S
Sbjct: 822 KTIYYVRSKS 831
>gnl|CDD|181700 PRK09209, PRK09209, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 761
Score = 436 bits (1124), Expect = e-142
Identities = 237/731 (32%), Positives = 364/731 (49%), Gaps = 97/731 (13%)
Query: 2 EKDPVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFS---KFINKGIDNKLLNPKL 58
++P ++ ARL + + K + D KY + +GI + L +
Sbjct: 79 LEEPEWTFFAARLYLNRLYKRA--SRNRFYDASEKYGSFVGLQESLAERGIYSNDLLKRY 136
Query: 59 AEFNLSLLSNALLPERDLQFNYLGLKILYDRYFLHIEGIRI-EMPQFFFMRIAMGLSLNE 117
++ L + PERD F Y+GL +L DRY + E+PQ ++ IA+ L NE
Sbjct: 137 SKEELIEAGKMIDPERDKLFTYIGLYLLADRYLATDSDRNVYELPQERWLTIALYLMQNE 196
Query: 118 SNREKCAI--KFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKEN 175
+ + + Y LS+ +TPTL N+G + QLSSC++ TV D L GI++S +
Sbjct: 197 PRERRMQLVKEAYWALSNLYMTVATPTLANAGKVGGQLSSCFIDTVDDSLQGIYDSNTDV 256
Query: 176 ALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICA 235
A +SK+ GG+G +VRS GS I+G G S GVIP++K +N+ AV+V+Q G+RKGAI
Sbjct: 257 ARVSKHGGGVGAYLGKVRSRGSDIRGFKGVSSGVIPWIKQLNNTAVSVDQLGQRKGAIAV 316
Query: 236 YLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDL 295
YL+ WH DIE F++LR N GD+R R HD+ + +PDLFM+ V ++ W LF P++V +
Sbjct: 317 YLDVWHKDIESFLDLRLNNGDERLRAHDVFTGVCIPDLFMEAVERRGDWYLFDPHEVKKV 376
Query: 296 ----------HNKFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPW 345
K F E Y +L + K + A+ + ++I+ ETG+P+
Sbjct: 377 MGWYLEDFYDEKKGDGSFREKYEECVADERLSR----KTVKAIDIMKRIMVSQLETGNPF 432
Query: 346 ITFKDACNIRSPQQHVGIIHSSNLCTEITLN----------TSKNEI------G---VCN 386
+ ++D N +P +H G+I+SSNLCTEI N S +I G VCN
Sbjct: 433 MFYRDEVNRMNPNKHEGMIYSSNLCTEIMQNMSPTVMIQEIISGGQIVITKQPGDFVVCN 492
Query: 387 LGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIM 446
L SINL + L++ I I +RMLDNVID+N V +A +N ++R +GLG
Sbjct: 493 LSSINLGRAVTAD-----VLERLIPIQVRMLDNVIDLNQLPVPQATITNQKYRAIGLGTF 547
Query: 447 GFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGIL 506
G+ L + I + S+EA+++AD+ E I Y AS ELA+EKG Y + GS W G
Sbjct: 548 GWHHLLALKGIAWESEEAVQYADELYERINYLTIQASMELAKEKGAYPVFKGSDWQTG-- 605
Query: 507 PQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVS 566
+Y + S W +L ++ + G+RN+ +A+AP + + I G +
Sbjct: 606 --------------EYFERRGYNSPQWDELAAQVAENGVRNAYLMAVAPNMSTAQIAGST 651
Query: 567 ASIEPTYRNLHI--KSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRI 624
ASI+P Y + K + T +L Y++
Sbjct: 652 ASIDPIYSAFYYEEKKDYRRPVT------APDLSLDTWP---------YYE--------- 687
Query: 625 PDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYISNK-SGKKLDETYKLAWLRG 683
A+++ W I + RQ+ +DQS S N Y+ + +L + + AW G
Sbjct: 688 --------KGAYKVDQFWSIRQNAARQRHVDQSISFNFYVPSTIRASELLDLHMTAWKEG 739
Query: 684 LKTTYYLRSIS 694
LKTTYY+RS
Sbjct: 740 LKTTYYVRSTD 750
>gnl|CDD|236378 PRK09102, PRK09102, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 601
Score = 390 bits (1003), Expect = e-126
Identities = 227/696 (32%), Positives = 329/696 (47%), Gaps = 129/696 (18%)
Query: 73 ERDLQFNYLGLKILYDRYFLHIEGIRIEMPQFFFMRIAMGLSLNESNREKCAIKFYNLLS 132
RD G L DRY L EG E Q F RIA + A +FY+ +S
Sbjct: 16 SRDAWLTEFGKATLRDRYLL--EG---ESYQDLFARIA---EAYADIDPEHAQRFYDYMS 67
Query: 133 SFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLSKYAGGLGNDWTQV 192
FM +TP L N GT R SC+L+ V D L GI + EN L+K GG+G+ W V
Sbjct: 68 RGWFMPATPVLSNGGTDRGLPISCFLNYVEDSLEGIVNTWNENVWLAKRGGGIGSYWGNV 127
Query: 193 RSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRK 252
RS+G PI+ NG+S G+IPF+KV++ + +A++QG R+G+ YL+ H +IEEF+++RK
Sbjct: 128 RSIGEPIRN-NGKSSGIIPFIKVMDSLTLAISQGSLRRGSFAVYLDIEHPEIEEFLDIRK 186
Query: 253 NTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEESYILYEN 312
TGD R+ +++ + V D FM+ V W L SP D
Sbjct: 187 PTGDPNRKALNLHHGVCVTDEFMEAVEDGDEWDLISPKDK-------------------- 226
Query: 313 QTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQH--VGI-IHSSNL 369
+ + + A LW KIL ETG P++ F D N P+ + +G+ + +SNL
Sbjct: 227 -------SVIRTVKARDLWAKILETRIETGEPYLLFIDNVNRALPEVYKDLGLKVKASNL 279
Query: 370 CTEITLNT-----SKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNV---- 420
C+EITL T ++ VC L S+NL + K I MR LDNV
Sbjct: 280 CSEITLPTGIDHLGEDRTAVCCLSSLNL-EYYDEWKDTD----AFIEDLMRFLDNVLQDF 334
Query: 421 IDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAY 480
ID +++AKYS +R R VGLG+MGF L IP+ S A ++ + + I A
Sbjct: 335 IDKAPDEMERAKYSAMRERSVGLGVMGFHSYLQSKMIPFESVMAKQWNKKIFKHIREQAD 394
Query: 481 YASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRI 540
AS ELA+EKG D+ G
Sbjct: 395 KASKELAKEKGE--------------CPDA-----AGYGVM------------------- 416
Query: 541 KKFGMRNSNCVAIAPTATISNIIG-VSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKK 599
R S +AIAPTA+IS I+G S IEP N + L G FT N+YL K L++
Sbjct: 417 ----RRFSTKMAIAPTASISIILGNTSPGIEPIAANYYTHKTLKGSFTVKNKYLEKLLEE 472
Query: 600 KGL-----WDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWI 654
KG W S++ N +G++ + + ++ + ++ TAFEI WIIE + RQK+I
Sbjct: 473 KGKDTDEVW-SSILTN----EGSVQHLDFLSEEEKDVFKTAFEIDQRWIIELAADRQKYI 527
Query: 655 DQSQSLNIYI-SNKSGKKLDETYKLAWLRGLKTTYYLRSISANYAKKSNFEMGIDSVNLD 713
DQ+QSLN+++ +N + L++ + AW +G+K+ YY RS S A K + ++ +
Sbjct: 528 DQAQSLNLFLPANVPKRDLNKLHFEAWKKGVKSLYYQRSKSVQRADKVSHDVLKKRLVEK 587
Query: 714 EISIKGYNKNLQEIKNNKKCLINSEINDVNECESCQ 749
D +EC +CQ
Sbjct: 588 SA----------------------FNRDYDECLACQ 601
>gnl|CDD|233900 TIGR02504, NrdJ_Z, ribonucleoside-diphosphate reductase,
adenosylcobalamin-dependent. This model represents a
group of adenosylcobalamin(B12)-dependent ribonucleotide
reductases (Class II RNRs) related to the characterized
species from Pyrococcus , Thermoplasma , Corynebacterium
and Deinococcus. RNR's are responsible for the
conversion of the ribose sugar of RNA into the
deoxyribose sugar of DNA. This is the rate-limiting step
of DNA biosynthesis. This model identifies genes in a
wide range of deeply branching bacteria. All are
structurally related to the class I (non-heme iron
dependent) RNRs. In most species this gene is known as
NrdJ, while in mycobacteria it is called NrdZ [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 589
Score = 385 bits (990), Expect = e-125
Identities = 205/620 (33%), Positives = 314/620 (50%), Gaps = 57/620 (9%)
Query: 85 ILYDRYFLHIE-GIRIEMPQFFFMRIAMGLSLNE--SNREKC---AIKFYNLLSSFNFMC 138
+L RY E G +E P+ F R+A L+ E N +FY+L+ + FM
Sbjct: 1 VLAARYLRKDEDGNILESPEDLFRRVARALAAAEDKYNSPVWKQLYERFYDLMVNLGFMP 60
Query: 139 STPTLFN-SGTIRSQLSSCYLSTVPDDLYGIFESIKENALLSKYAGGLGNDWTQVRSLGS 197
++PTL N GT QLS+C++ V DD+ IFE+ KE AL+ K GG+G +++ +R G
Sbjct: 61 NSPTLMNAGGTRLGQLSACFVLPVEDDMESIFEAAKEAALIFKRGGGVGYNFSTLRPKGD 120
Query: 198 PIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRKNTGDD 257
+ GT G + G + F++V + A + QGG R+GA L+ WH DIEEFIE +K G
Sbjct: 121 KVSGTGGVASGPVSFMRVFDAAAGVIKQGGTRRGAQMGILDVWHPDIEEFIEAKKKEGKL 180
Query: 258 RRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEESYILYENQTKLG 317
+ NI++ V D FM+ V + L +P G+E EE E
Sbjct: 181 T----NFNISVGVTDAFMEAVEADEEYKLRNPRT--------GEEIEELAEKREP----- 223
Query: 318 KIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVGIIHSSNLCTEITLNT 377
K+ ++K++ A LW KI+ +++ P + F D N + ++G I+++N C E L
Sbjct: 224 KLVVYKEVPARELWDKIVEAAWKSAEPGLLFIDTINKWNNLPYLGRINATNPCGEQPLL- 282
Query: 378 SKNEIGVCNLGSINLTLHMKNGKLDPI----KLKKTIRIAMRMLDNVIDINYYAVKKAKY 433
CNLGSINL +KN +L++ +R+A R LDNVID+N + + +
Sbjct: 283 ---PYESCNLGSINLAKFVKNDFGGASFDFERLREVVRLATRFLDNVIDLNRFPLPEIAE 339
Query: 434 SNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRY 493
+ + R +GLGIMG D L + IPY S+EA FA++ M I AY AS ELA+E+G +
Sbjct: 340 ATKKTRRIGLGIMGLADLLIKLGIPYDSEEARAFAEELMRFIADAAYRASAELAKERGAF 399
Query: 494 SSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAI 553
++ S + G KV S +LR I K+G+RN+ I
Sbjct: 400 PLFEASKYLMG-------------------KVARIPSALPAELREAIAKYGIRNAQLTTI 440
Query: 554 APTATISNIIGVSASIEPTYRNLHIKSNLS--GEFTEINRYLVKELKKKGLWDESMIANL 611
APT TIS I G S+ IEP + L N++ GE E+N + L++ G + + ++
Sbjct: 441 APTGTISLIAGTSSGIEPVF-ALVYFRNVTVGGELLEVNPLVELALRELGYYSDEIVKIE 499
Query: 612 KYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYISNKSGKK 671
G + +P++L K++ TA +ISP + + Q W+D S S I + + + +
Sbjct: 500 VAEKGTVEGAPDLPEELPKVFVTANDISPEDHVLMQAAIQPWVDSSISKTINMPSDATVE 559
Query: 672 -LDETYKLAWLRGLK--TTY 688
+ Y AW GLK T Y
Sbjct: 560 DVKAVYLEAWKLGLKGITVY 579
>gnl|CDD|153089 cd02888, RNR_II_dimer, Class II ribonucleotide reductase, dimeric
form. Ribonucleotide reductase (RNR) catalyzes the
reductive synthesis of deoxyribonucleotides from their
corresponding ribonucleotides. It provides the
precursors necessary for DNA synthesis. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs, found in
eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class are found to be
homodimers. Adenosylcobalamin interacts directly with an
active site cysteine to form the reactive cysteine
radical.
Length = 464
Score = 333 bits (855), Expect = e-106
Identities = 146/454 (32%), Positives = 231/454 (50%), Gaps = 54/454 (11%)
Query: 126 KFYNLLSSFNFMCSTPTLFNSGTI-RSQLSSCY-LSTVPDDLYGIFESIKENALLSKYAG 183
+F+ LL S F+ ++PTL N+GT QLS+C+ L D + GIF+++KE AL+ K G
Sbjct: 3 EFFYLLLSQGFIPNSPTLMNAGTGELGQLSACFVLPVEDDSIEGIFDALKEAALIFKRGG 62
Query: 184 GLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMD 243
G+G +++++R G +K T G + G + F++V + + QGG R+GA L+ H D
Sbjct: 63 GVGYNFSRLRPKGDIVKSTGGVASGPVSFMRVFDAATGVIKQGGTRRGANMGVLDVDHPD 122
Query: 244 IEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEF 303
IEEFI+ + + NI++ V D FM+ V W L +P +
Sbjct: 123 IEEFIDAKMKEEKTVVLQN-FNISVAVTDAFMEAVENDEPWELRNPREPDTG-------- 173
Query: 304 EESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVGI 363
K+++ + A LW KI+ +++ P + F D N +P +G
Sbjct: 174 ----------------KVYRTVPARELWDKIVEAAWDSADPGVLFIDTINRWNPLPGLGR 217
Query: 364 IHSSNLCTEITLNTSKNEIGVCNLGSINLTLHMKNGKLDPI----KLKKTIRIAMRMLDN 419
I+++N C E L CNLGSINL+ +KN +L++ +R+A+R LDN
Sbjct: 218 INATNPCGEQPLL----PYESCNLGSINLSKFVKNPFGGASFDFERLREAVRLAVRFLDN 273
Query: 420 VIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYA 479
VID+N Y + + R +GLG+MG D L + IPY S+EA + A++ M I A
Sbjct: 274 VIDVNRYPLPEIAEETKATRRIGLGVMGLADMLIKLGIPYDSEEARELAERIMSFIRDAA 333
Query: 480 YYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNR 539
Y AS ELA+E+G + +D S + + ++ +L +
Sbjct: 334 YRASAELAKERGPFPLFDASRYLMLKVIVNAKEL-------------------PDDVLEE 374
Query: 540 IKKFGMRNSNCVAIAPTATISNIIGVSASIEPTY 573
I+K+G+RN++ IAPT TIS I G S+ IEP +
Sbjct: 375 IEKYGIRNAHLTTIAPTGTISLIAGTSSGIEPIF 408
>gnl|CDD|236330 PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 752
Score = 324 bits (834), Expect = e-100
Identities = 195/629 (31%), Positives = 313/629 (49%), Gaps = 91/629 (14%)
Query: 75 DLQFNYLGLKILYDRYFLHIE-GIRIEMPQFFFMRIA-----MGLSLNESNR-EKCAIKF 127
D++ L +L RY E G IE P+ F R+A L + E A +F
Sbjct: 9 DMKLTDNALTVLEKRYLKKDEDGKPIETPEDMFRRVARTIAAAELIYDSKADVEALADRF 68
Query: 128 YNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLSKYAGGLGN 187
Y+L++S F+ ++PTL N+G QLS+C++ V D + IF+++K AL+ K GG G
Sbjct: 69 YDLMTSLEFLPNSPTLMNAGRELGQLSACFVLPVGDSIEEIFDAVKHAALIHKSGGGTGF 128
Query: 188 DWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEF 247
++++R + T G + G + F++V + A+ QGG R+GA L H DI EF
Sbjct: 129 SFSRLRPKNDRVGSTGGVASGPVSFMRVFDAATEAIKQGGTRRGANMGILRVDHPDIMEF 188
Query: 248 IELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEESY 307
I +++ G+ + NI++ + + FM+ V + L +P
Sbjct: 189 ITCKEDNGELT----NFNISVAITEAFMEAVEADEEYDLINPRT---------------- 228
Query: 308 ILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVGIIHSS 367
G++ +++A ++ I+ M +E G P I F D N +P H+G I S+
Sbjct: 229 ---------GEVV--GRLNAREVFDLIVEMAWENGEPGIVFIDRINRDNPTPHLGEIEST 277
Query: 368 NLCTEITLNTSKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYA 427
N C E L CNLGSINL+ +KNG +D KL++ + +A+R LDNVID N Y
Sbjct: 278 NPCGEQPLLP----YESCNLGSINLSKMVKNGDVDWEKLREVVHLAVRFLDNVIDANKYP 333
Query: 428 VKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELA 487
+ + + +R +GLG+MG+ D L + IPY S+EA++ A++ M+ I A+ AS ELA
Sbjct: 334 LPQIEEMTKGNRKIGLGVMGWADMLIQLGIPYDSEEAVELAEKVMKFIQDEAHAASRELA 393
Query: 488 EEKGRYSSYDGSLWD-QGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMR 546
EE+G + +Y+GS++D G+ P MR
Sbjct: 394 EERGPFPNYEGSIYDKDGLGP-------------------------------------MR 416
Query: 547 NSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGE-FTEINRYLVKELKKKGLW-D 604
N+ IAPT TIS I G S+ IEP + ++ + GE E+N K++G + +
Sbjct: 417 NATVTTIAPTGTISIIAGCSSGIEPLFALSFTRNVMDGERLVEVNPVFEAAAKEEGFYSE 476
Query: 605 ESM--IANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNI 662
E M IA G++ I +P+D+R+++ TA +ISP W + + QK D + S +
Sbjct: 477 ELMEKIAE----KGSIQDIDEVPEDVRRVFVTAHDISPEWHVRMQAAFQKHTDNAVSKTV 532
Query: 663 YISNKSGKK-LDETYKLAWLRGLK--TTY 688
N++ + + E Y+LA+ G K T Y
Sbjct: 533 NFPNEATIEDVREVYRLAYELGCKGVTIY 561
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 298 bits (766), Expect = 2e-90
Identities = 212/717 (29%), Positives = 332/717 (46%), Gaps = 91/717 (12%)
Query: 3 KDPVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFSKFINKGIDNKLLNPKLAEFN 62
++P Y V ARLLM+ ++K+V+G Q + P + ++ SK +N+G + + K +
Sbjct: 71 EEPDYQYVAARLLMFALRKQVYG----QFE-PPSFIDHISKCVNEGKYDPEILSKYSAEE 125
Query: 63 LSLLSNALLPERDLQFNYLGLKILYDRYFLH--IEGIRIEMPQFFFMRIAMGLSLNE--S 118
++ L + + +RD +F Y G L ++Y + G E PQF +M IAM L +E
Sbjct: 126 ITYLESFIDHDRDFEFTYAGAMQLKEKYLVQDRSTGEIYETPQFAYMLIAMALHQDEPKE 185
Query: 119 NREKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENAL- 177
+R + I+FYN +S+ TP + T Q SSC + D L I ++ A+
Sbjct: 186 DRLEHVIRFYNAVSTRKISLPTPIMAGVRTPTRQFSSCVVIESGDSLDSINKT--AMAIV 243
Query: 178 --LSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICA 235
+SK AG +G + +R+ GS I+G R GVIPF K + +QGG R GA A
Sbjct: 244 KYISKRAG-IGINAGMIRAEGSKIRGGEVRHTGVIPFWKHFQTAVKSCSQGGIRGGAATA 302
Query: 236 YLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPD- 294
Y WH+++E+ + L+ N G + R ++ + + DL +R IK TLFSP+DV
Sbjct: 303 YYPIWHLEVEDLLVLKNNKGVEENRIRHLDYGVQINDLMYERFIKNDYITLFSPHDVGGE 362
Query: 295 LHNKFGK---EFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDA 351
L++ + F E Y E + K K+I A L+ +L ETG +I F D
Sbjct: 363 LYDAYFADQDRFRELYEALEKDPSVRK----KRIKAQELFLLLLKERSETGRIYIMFIDH 418
Query: 352 CNIRSPQQHVGIIHSSNLCTEITLNTS-------KNEIGVCNLGSINLTLHMKNGKL-DP 403
CN SP I SNLC EI L T + EI +C L +I L G D
Sbjct: 419 CNNHSP--FKDPIRQSNLCCEIALPTKPLNHIDGEGEIALCTLSAIVL------GNFEDQ 470
Query: 404 IKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKE 463
++++ +A+R LDN++D Y V A + R +G+G+ + L Y
Sbjct: 471 DEIEELAEVAVRALDNLLDYQDYPVPAAL-KAKKRRSLGVGVTNYAHYLAKNFASYEDAN 529
Query: 464 AIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKL-LEKERGSKY 522
A + E + YY AS +LA+EKG + + + +G LP D K +++ KY
Sbjct: 530 A-DLVHELFERLQYYLIKASNKLAKEKGACEYFSDTKYSRGELPIDWYKKKVDELVAPKY 588
Query: 523 LKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNL 582
+ +W+ LR +KK+G+RNS A+ P + S + + IEP + IK +
Sbjct: 589 -------NCDWESLREDLKKYGIRNSTLSALMPCESSSQVSNSTNGIEPPRGPVSIKKSK 641
Query: 583 SGEFTEI--NRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISP 640
G F ++ N +K+L LWD + N Y L+Q+
Sbjct: 642 EGPFNQVVPNVETLKDLYDL-LWDLAKKGNKGY----LTQV------------------- 677
Query: 641 NWIIEAGSVRQKWIDQSQSLN------IYISNK--SGKKLDETYKLAWLRGLKTTYY 689
++ QK++DQ+ S N Y + K LD+ + G KT YY
Sbjct: 678 -------AIMQKFVDQAISANTSYDPENYPNGKVPMSVMLDDLLY-FYYYGGKTLYY 726
>gnl|CDD|235796 PRK06406, PRK06406, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 771
Score = 294 bits (753), Expect = 2e-88
Identities = 180/557 (32%), Positives = 292/557 (52%), Gaps = 75/557 (13%)
Query: 126 KFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLSKYAGGL 185
KF ++S+ F+ ++PTL N+GT QLS+C++ VPD + GIF ++K A++ K GG
Sbjct: 222 KFEEVMSNLKFVPNSPTLMNAGTKLGQLSACFVLPVPDSIEGIFNALKYTAMIHKSGGGT 281
Query: 186 GNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIE 245
G ++++R + T G + G + F+++ + + QGGKR+GA L H DI
Sbjct: 282 GFSFSRLRPKDDIVASTKGVASGPLSFMRIFDVTTDVIKQGGKRRGANMGILSYHHPDIM 341
Query: 246 EFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEE 305
EFI K++ + + + NI++ V D F ++ + L +P + GKE
Sbjct: 342 EFI-TSKDS--ENKVLSNFNISVAVTDEFFDKLDNDDYYPLRNPRN--------GKEV-- 388
Query: 306 SYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVGIIH 365
K+I A +W I++ ++TG P + F D N ++P +++G I
Sbjct: 389 -----------------KRIKARQVWDLIITQAWKTGDPGVIFLDEINRKNPVKNLGEIE 431
Query: 366 SSNLCTEITLNTSKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINY 425
S+N C E L ++ CNLGSINL+ ++NGK+D +L++T+ IA R LDNVID N
Sbjct: 432 STNPCGEQPLLPYES----CNLGSINLSKFVENGKIDWDRLRETVHIATRFLDNVIDANK 487
Query: 426 YAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTE 485
+ V + K R +GLG+MGF D L + IPY+S+EA++ A++ M+ I ++ AS +
Sbjct: 488 FPVPQIKEMTRMTRKIGLGVMGFADMLIKLGIPYNSEEALEIAEKVMKFINEESHRASQK 547
Query: 486 LAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGM 545
LAEE+G + ++ GS W KK IK M
Sbjct: 548 LAEERGVFPAWYGSEW-------------------------------EKK---GIK---M 570
Query: 546 RNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSG-EFTEINRYLVKELKKKGLWD 604
RNS IAPT TIS I G S+SIEP + ++ L+G E E+N + +K+GL+
Sbjct: 571 RNSTTTTIAPTGTISIIAGCSSSIEPLFAIAFVRHVLNGQELLEVNPLFEEITRKRGLYS 630
Query: 605 ESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYI 664
E ++ + GNL I +P+D+++I+ TA EI P W + + Q++ D S I +
Sbjct: 631 EELMRKVAE-TGNLQNID-VPEDIKRIFVTAHEIDPQWHVLMQATFQRYCDSGVSKTINL 688
Query: 665 -SNKSGKKLDETYKLAW 680
+ + + + + Y+LA
Sbjct: 689 RYDATPEDIAKAYRLAK 705
>gnl|CDD|181649 PRK09103, PRK09103, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 758
Score = 261 bits (669), Expect = 2e-76
Identities = 216/732 (29%), Positives = 324/732 (44%), Gaps = 116/732 (15%)
Query: 2 EKDPVYSQVTARLLMYCIQKEVFGKEIKQIDIPIKYKEYFSKFINKGI-DNKLLNPKLAE 60
P Y + ARL ++ ++K+ +G Q + P Y ++ K + G D LL E
Sbjct: 69 RDAPDYQYLAARLAIFHLRKKAYG----QFEPPALY-DHVVKMVEMGKYDKHLLEDYTEE 123
Query: 61 FNLSLLSNALLPERDLQFNYLGLKILYDRYFLH--IEGIRIEMPQFFFMRIAMGLSLN-- 116
+ + RD+ F+Y +K L +Y + + G E QF ++ +A L N
Sbjct: 124 -EFDQMDTFIDHWRDMNFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYP 182
Query: 117 ESNREKCAIKFYNLLSSFNFMCSTPTLFNSG--TIRSQLSSCYLSTVPDDLYGIFESIKE 174
+ R +FY+ +S+F S PT SG T Q SSC L D L I
Sbjct: 183 KETRLDYVKRFYDAVSTFKI--SLPTPIMSGVRTPTRQFSSCVLIECGDSLDSI------ 234
Query: 175 NALLS---KYA---GGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGK 228
NA S KY G+G + ++R+LGSPI+G G IPF K + +QGG
Sbjct: 235 NATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGV 294
Query: 229 RKGAICAYLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFS 288
R GA + WH+++E + L+ N G + R M+ + + L +R+IK TLFS
Sbjct: 295 RGGAATLFYPIWHLEVESLLVLKNNRGVEENRVRHMDYGVQINKLMYQRLIKGGDITLFS 354
Query: 289 PYDVPDLHNKF---GKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPW 345
P DVP L++ F EFE Y YE + K K++ A+ L+ ++ TG +
Sbjct: 355 PSDVPGLYDAFFADQDEFERLYTKYEQDDSIRK----KRVKAVELFSLMMQERASTGRIY 410
Query: 346 ITFKDACNIRSP-QQHVGIIHSSNLCTEITL--------NTSKNEIGVCNLGSINLTLHM 396
I D CN SP V + SNLC EI L N EI +C L + NL
Sbjct: 411 IQNVDHCNTHSPFDPKVAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNL---- 466
Query: 397 KNGKLDPI-KLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIM 455
G ++ + +L++ +A+R LD ++D Y + AK + R +G+G++ F L
Sbjct: 467 --GAINSLDELEELADLAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKN 524
Query: 456 KIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLE 515
+ YS A ++ E I YY AS ELA+E+G ++ + + QGILP D+ K
Sbjct: 525 GVRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAQGILPIDTYK--- 581
Query: 516 KERGSKYLKVNMSESL--NWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTY 573
K L +E L +W+ LR IK G+RNS A+ P+ T S I + IEP
Sbjct: 582 -----KDLDAICNEPLHYDWETLREEIKTHGLRNSTLSALMPSETSSQISNATNGIEPPR 636
Query: 574 RNLHIKSNLSGEFTEINRYLVKELKKKG-----LWDESMIANLKYFDGNLSQISRIPDDL 628
+ IK++ G I + +V + ++ LW+ M N DG L +
Sbjct: 637 GYVSIKASKDG----ILKQVVPDYERLKDAYELLWE--MPNN----DGYLQLV------- 679
Query: 629 RKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNI------YISNKSG-----KKLDETYK 677
+ QK++DQS S N + S K K L YK
Sbjct: 680 -------------------GIMQKFVDQSISANTNYDPSRFPSGKVPMKQLLKDLLTAYK 720
Query: 678 LAWLRGLKTTYY 689
G+KT YY
Sbjct: 721 F----GVKTLYY 728
>gnl|CDD|211905 TIGR04170, RNR_1b_NrdE, ribonucleoside-diphosphate reductase, class
1b, alpha subunit. Members of this family are NrdE, the
alpha subunit of class 1b ribonucleotide reductase. This
form uses a dimanganese moiety associated with a
tyrosine radical to reduce the cellular requirement for
iron.
Length = 698
Score = 248 bits (636), Expect = 3e-72
Identities = 170/608 (27%), Positives = 291/608 (47%), Gaps = 67/608 (11%)
Query: 108 RIAM-GLSLNESNREKCAIKFYNLLSSFNFMCSTPTLFNSGTI-RSQLSSCYLSTVPDDL 165
R+ M L+L + E A + + + S + +TPT N+G R +L SC+L V D++
Sbjct: 115 RVCMVALTLANGDEEL-AKQLVDEMISQRYQPATPTFLNAGRARRGELVSCFLLRVEDNM 173
Query: 166 YGIFESIKENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQ 225
I +I LSK GG+ + + +R G+PIKG +S GVIP +K++ D NQ
Sbjct: 174 NSIGRAINSALQLSKRGGGVALNLSNLREAGAPIKGIENQSSGVIPVMKLLEDAFSYANQ 233
Query: 226 GGKRKGAICAYLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWT 285
G+R+GA YL +H DI F++ +K D++ R +++ + +PD F + +
Sbjct: 234 LGQRQGAGAVYLNAFHPDILRFLDTKKENADEKIRIKTLSLGVVIPDKFFELAKENKDMY 293
Query: 286 LFSPYDVPDLHNKFGKEFEESYI--LYENQTKLGKIKLFKKISALYLWRKILSMLFETGH 343
LFSPYDV ++G F++ I Y+ +I+ KKI+A ++ + + FE+G+
Sbjct: 294 LFSPYDV---EREYGVPFDDIDITEKYDEMVANPRIRK-KKINARDFFQTLAEIQFESGY 349
Query: 344 PWITFKDACNIRSPQQHVGIIHSSNLCTEI---------TLNTSKNEIGV---CNLGSIN 391
P+I F+D N +P +G I SNLC+EI +EIG CNLGS+N
Sbjct: 350 PYIMFEDTVNRANP--IIGRIKMSNLCSEILQVSEASLYNDYLEYDEIGHDISCNLGSLN 407
Query: 392 LTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDI-NYYAVKKAKYSNLRHRPVGLGIMGFQD 450
+ M + +T+ A+R L V D+ + V + N +GLG M
Sbjct: 408 IANVMDSP-----DFGRTVETAIRALTAVSDMSHIRNVPSIRKGNAASHAIGLGQMNLHG 462
Query: 451 CLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKG-RYSSYDGSLWDQG----- 504
L I Y S EA+ F + + YY+ S E+A E+G ++ ++ S + G
Sbjct: 463 YLAREGIAYGSPEALDFTNIYFMTVNYYSLRRSMEIARERGETFAGFEQSDYASGEYFDK 522
Query: 505 ILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIG 564
+ Q+ EK R + +++ +W +L++ + ++G+ + N +A+APT +IS I
Sbjct: 523 YVSQEFAPKTEKVR-ELFEGIHIPTREDWAELKDDVMEYGLYHQNRLAVAPTGSISYINH 581
Query: 565 VSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRI 624
++SI P + I+ E I + Y L+
Sbjct: 582 STSSIHPIVSKIEIRK------------------------EGKIGRVYYPAPFLT----- 612
Query: 625 PDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYISNK-SGKKLDETYKLAWLRG 683
++L + Y A++I II+ + + +DQ SL ++ + + + L+ AW +G
Sbjct: 613 NENL-EYYQDAYDIDMEKIIDTYATATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWHKG 671
Query: 684 LKTTYYLR 691
+KT YY+R
Sbjct: 672 IKTLYYIR 679
>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 721
Score = 233 bits (596), Expect = 2e-66
Identities = 178/593 (30%), Positives = 287/593 (48%), Gaps = 85/593 (14%)
Query: 136 FMCSTPTLFNSGTI-RSQLSSCYLSTVPDDLYGIFESIKENALLSKYAGGLGNDWTQVRS 194
F +TPT N+G R + SCYL V D++ I +I + LSK GG+ T +R
Sbjct: 149 FQPATPTFLNAGKKRRGEYISCYLLRVEDNMESISRAISTSLQLSKRGGGVALCLTNLRE 208
Query: 195 LGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRKNT 254
+G+PIKG ++ G+IP +K++ D NQ G+R+GA YL H D+ F++ ++
Sbjct: 209 IGAPIKGIENQATGIIPVMKLLEDSFSYANQLGQRQGAGAVYLHAHHPDVLTFLDTKREN 268
Query: 255 GDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEF------EESYI 308
D++ R +++ + +PD+ + + LFSPYD+ ++GK EE Y
Sbjct: 269 ADEKIRIKSLSLGLVIPDITFELAKENKDMALFSPYDI---KREYGKPMSDISITEEYYN 325
Query: 309 LYENQTKLGKIKLFKK-ISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVGIIHSS 367
L N IK K ISA L++ I + FE+G+P++ F D N R+P G I S
Sbjct: 326 LLANP----AIK--KTYISARKLFQTIAELHFESGYPYLLFDDTVNKRNPHAKKGRIVMS 379
Query: 368 NLCTEI-------TLNT--SKNEIG---VCNLGSINLTLHMKNGKLDPIKLKKTIRIAMR 415
NLC+EI T N S +IG CNLGS+N+ M++G + ++ I ++R
Sbjct: 380 NLCSEIAQVSTPSTFNEDLSFKKIGEDICCNLGSLNIAKAMESGP----EFEQLIYTSIR 435
Query: 416 MLDNVIDI-NYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEM 474
LD V + + + N + VGLG M L I Y SKEA+ F D
Sbjct: 436 ALDRVSRVSDLSCAPSIEKGNAANHAVGLGAMNLHGFLATNHIYYDSKEAVDFTDLFFYT 495
Query: 475 ICYYAYYASTELAEEKGRYSSY------DGSLWDQGILPQDSLKLLE----KERGSKYLK 524
+ YYA+ AS +LA+EKG ++ + DGS +D+ + KE KY
Sbjct: 496 MAYYAFKASNQLAKEKGAFAGFELSKYADGSYFDKYTKEDAKKWTPKTAKVKELLQKY-G 554
Query: 525 VNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSG 584
V + +W++L IKK G+ NS+ +A+APT +IS + + S++P + ++
Sbjct: 555 VTIPTQADWQELVEDIKKTGLANSHLLAVAPTGSISYLSSCTPSLQPVVAPVEVR----- 609
Query: 585 EFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQI----SRIPDDLRKIYAT-AFEIS 639
KE G L +I +I D Y A+E+
Sbjct: 610 ----------KE-------------------GKLGRIYVPAYKIDQDNYAYYERGAYEVG 640
Query: 640 PNWIIEAGSVRQKWIDQSQSLNIYISNK-SGKKLDETYKLAWLRGLKTTYYLR 691
P II+ + QK +DQ+ SL ++++++ + + L++ Y A+ + + YY+R
Sbjct: 641 PKPIIDIVAAAQKHVDQAISLTLFMTDQATTRDLNKAYIQAFKQKCASIYYVR 693
>gnl|CDD|188230 TIGR02510, NrdE-prime, ribonucleoside-diphosphate reductase, alpha
chain. This model represents a small clade of
ribonucleoside-diphosphate reductase, alpha chains which
are sufficiently divergent from the usual Class I RNR
alpha chains (NrdE or NrdA, TIGR02506) as to warrant
their own model. The genes from Thermus thermophilus,
Dichelobacter and Salinibacter are adjacent to the usual
RNR beta chain [Purines, pyrimidines, nucleosides, and
nucleotides, 2'-Deoxyribonucleotide metabolism].
Length = 548
Score = 215 bits (548), Expect = 3e-61
Identities = 158/593 (26%), Positives = 245/593 (41%), Gaps = 119/593 (20%)
Query: 120 REKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENALLS 179
R +F+ L+ + +TP N+G R SC S V D + I E E +++
Sbjct: 42 RPGFEERFFEYLARGKYSLATPVWANTGLDRGLPISCAGSYVGDSVLDILEGQAEVGMMA 101
Query: 180 KYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLET 239
K GG + +R G+ I TNG S G F + ++ QG R+G Y++
Sbjct: 102 KNGGGTSSYLGDIRPRGADIS-TNGTSNGADGFAPLFDNFINVKTQGATRRGEWAGYVDF 160
Query: 240 WHMDIEEFIEL-RKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNK 298
H D EE++ + +N + + + V D + +++I P+ +
Sbjct: 161 EHPDFEEWLGIQLENPA-----SQHVGWGVEVGDDWYEKMIAGD----------PEKRAR 205
Query: 299 FGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQ 358
+ K ++ TG P++ F+ N +PQ
Sbjct: 206 WAK--------------------------------LMYSRARTGIPYMWFRWNANELAPQ 233
Query: 359 --QHVGI-IHSSNLCTEITLNTSKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMR 415
++ GI I +SNLCTEI L + E VC L S+N+ + D K + +R
Sbjct: 234 VIKNSGIPIRASNLCTEIALPSDDMESFVCCLSSLNVLHY------DEWKDTDAVETLVR 287
Query: 416 MLDNVID--------INYY--AVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAI 465
LD+V ++Y AV+ A+ R R +GLG +G+ L +IP+ S EA
Sbjct: 288 FLDSVCSEFIAKAKGLSYMHRAVRFAE----RARAIGLGTLGWHSYLQSNRIPFESGEAH 343
Query: 466 KFADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKV 525
+ + I A AS ELAE G E E
Sbjct: 344 ILNAEIYKTIKERAEEASRELAERYG-----------------------EPEVCEGT--- 377
Query: 526 NMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIG-VSASIEPTYRNLHIKSNLSG 584
G RN+ +AIAPT + + I+G VS SIEP N I+ + G
Sbjct: 378 ------------------GRRNATLIAIAPTKSSAFILGQVSPSIEPLVSNYFIQDSNKG 419
Query: 585 EFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWII 644
+ N L K LK+KG E + + Y +G++ + + D+ + ++ T +EIS II
Sbjct: 420 DVVRKNPVLAKVLKEKGTDQELVWDIITYHNGSVQHLDFLTDEEKSVFKTFYEISQMAII 479
Query: 645 EAGSVRQKWIDQSQSLNIYIS--NKSGKKLDETYKLAWLRGLKTTYYLRSISA 695
+ RQK IDQ+QSLN++IS K + AW GLK+ YY RS
Sbjct: 480 RLAAARQKHIDQAQSLNLFISPDEKPSVDANVLRAFAWDPGLKSLYYQRSERG 532
>gnl|CDD|236069 PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 699
Score = 215 bits (550), Expect = 3e-60
Identities = 167/608 (27%), Positives = 286/608 (47%), Gaps = 75/608 (12%)
Query: 113 LSLNESNREKCAIKFYNLLSSFNFMCSTPTLFNSGTIR-SQLSSCYLSTVPDDLYGIFES 171
L L ++ K A +F + + + +TPT N+G R +L SC+L V D L I
Sbjct: 126 LYLANGDKAK-AKQFISAMVEQRYQPATPTFLNAGRARRGELVSCFLLEVDDSLNSINFI 184
Query: 172 IKENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKG 231
LSK GG+ + +++R+ G IKG G ++GV+P K++ +Q G+R G
Sbjct: 185 DSTAKQLSKIGGGVAINLSKLRARGEAIKGIKGAAKGVLPVAKLLEGGFSYADQLGQRPG 244
Query: 232 AICAYLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYD 291
A YL +H D+EEF++ +K D+ R ++ + VP F + + + +F+P+
Sbjct: 245 AGAVYLNIFHYDVEEFLDTKKVNADEDLRLSTISTGLIVPSKFFELAKEGKDFYMFAPHT 304
Query: 292 VPDLHNKFGKEFEESYI--LYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFK 349
V + ++G ++ + +Y++ +K KK +A + KI ++G+P++ FK
Sbjct: 305 V---YKEYGVTLDDIDLEEMYDDLVANPNVKK-KKKNAREMLNKIAQTQLQSGYPYLMFK 360
Query: 350 DACNIRSPQQHVGIIHSSNLCTEI--TLNTS-------KNEIGV---CNLGSINLTLHMK 397
D N P ++G I SNLCTEI TS ++EI CNLGS+N+ M+
Sbjct: 361 DNANKVHPNSNIGQIKMSNLCTEIFQLQETSIINDYGIEDEIKRDISCNLGSLNIVNVME 420
Query: 398 NGKLDPIKLKKTIRIAMRMLDNVIDI----NYYAVKKAKYSNLRHRPVGLGIMGFQDCLH 453
+ K + ++ M L V D+ N V+KA N VGLG+M L
Sbjct: 421 SK-----KFRDSVHSGMDALTVVSDVANIQNAPGVRKA---NSELHSVGLGVMNLHGYLA 472
Query: 454 IMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGR-YSSYDGSLWDQGILPQDSLK 512
KI Y S+EA FA+ M+ +Y+ S E+A+E+G Y ++ S + G + K
Sbjct: 473 KNKIGYESEEAKDFANTFFMMMNFYSIERSMEIAKERGETYQDFEKSDYANGKYFE---K 529
Query: 513 LLEKERGSKYLKV-------NMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGV 565
++ K+ KV ++ +WKKL+ ++++G+ ++ +AIAPT +IS +
Sbjct: 530 YTTQDFEPKFEKVRELFEGMHIPTKEDWKKLQQDVEQYGLYHAYRLAIAPTQSISYVQNA 589
Query: 566 SASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIP 625
++S+ P + ++ + E Y + L + +W
Sbjct: 590 TSSVMPIVDQIERRTYGNAE----TFYPMPFLSPQTMW---------------------- 623
Query: 626 DDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYI-SNKSGKKLDETYKLAWLRGL 684
Y +AF +I+ + Q IDQ S +Y+ S S ++L Y A +GL
Sbjct: 624 -----YYKSAFNTDQMKLIDLIATIQTHIDQGISTILYVNSEISTRELARLYVYAHHKGL 678
Query: 685 KTTYYLRS 692
K+ YY R+
Sbjct: 679 KSLYYTRN 686
>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 720
Score = 216 bits (551), Expect = 3e-60
Identities = 183/643 (28%), Positives = 284/643 (44%), Gaps = 111/643 (17%)
Query: 139 STPTLFNSG-TIRSQLSSCYLSTVPDDLYGIFESIKENALLSKYAGGLGNDWTQVRSLGS 197
+TP+ N+G R +L SC+L V DD+ I SI LS+ GG+G + + +R G+
Sbjct: 154 ATPSFLNAGRARRGELVSCFLIQVTDDMNSIGRSINSALQLSRIGGGVGINLSNLREAGA 213
Query: 198 PIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRKNTGDD 257
PIKG G + GV+P +K+ D NQ G+R+GA YL +H DI F+ +K D+
Sbjct: 214 PIKGYEGAASGVVPVMKLFEDSFSYSNQLGQRQGAGVVYLNVFHPDIIAFLSTKKENADE 273
Query: 258 RRRTHDMNIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEESYI----LYENQ 313
+ R +++ + VPD F + K LFSPY V ++G F +Y+ Y+
Sbjct: 274 KVRVKTLSLGVTVPDKFYELARKNEDMYLFSPYSV---EKEYGVPF--NYVDITKEYDEL 328
Query: 314 TKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVGIIHSSNLCTEI 373
I+ KI A L +I + E+G+P+I D N +P G I SNLC+EI
Sbjct: 329 VANPNIRK-TKIKARDLETEISKLQQESGYPYIINIDTANRANPID--GKIIMSNLCSEI 385
Query: 374 -------TLNTSKN--EIGV---CNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVI 421
+N ++ ++G CNLGS N+ M + ++I +R L V
Sbjct: 386 LQVQTPSLINDAQEYVKMGTDISCNLGSTNIVNMMTSPDFG-----RSIETMVRALTFVT 440
Query: 422 DI-NYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAY 480
D N AV K+ N + +GLG MG L I Y S E+++F ++ Y+
Sbjct: 441 DSSNIDAVPSIKHGNSQAHTIGLGAMGLHSYLAQNHIEYGSPESLEFTSIYFMLLNYWTL 500
Query: 481 YASTELAEEKG------RYSSY-DGSLWDQGILPQDSLKLLEKERGSKYLKV-------N 526
AS +A E+G S Y DGS +D K + + K KV
Sbjct: 501 VASNNIARERGETFHNFEKSKYADGSYFD---------KYVTGDFVPKSDKVKELFKGIF 551
Query: 527 MSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEF 586
+ + +W LR+ + K G+ + N +A+AP +IS I SASI P
Sbjct: 552 IPTAADWAALRDAVMKDGLYHQNRLAVAPNGSISYINDTSASIHPI-------------- 597
Query: 587 TEINRYLVKELKKKGLWDESMIANLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEA 646
R ++E ++K I + Y LS + Y +A+++ +I+
Sbjct: 598 --TQR--IEERQEK------KIGKIYYPAPGLS------TETIPYYTSAYDMDMRKVIDV 641
Query: 647 GSVRQKWIDQSQSLNIYISNKSGKKLDETYKLAW-LRGLKTTYYLRSISANYAKKSNFEM 705
+ + +DQ SL +++ + K L E W R K T SI NYA F
Sbjct: 642 YAAATEHVDQGLSLTLFMRSTLPKGLYE-----WKDRTNKMTTRDLSILRNYA----FNK 692
Query: 706 GIDSVNLDEISIKGYNKNLQEIKNNKKCLINSEINDVNECESC 748
GI S+ I+ + + +E+ N+CESC
Sbjct: 693 GIKSI----YYIRTFTDDGEEV-------------GANQCESC 718
>gnl|CDD|236179 PRK08188, PRK08188, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 714
Score = 203 bits (519), Expect = 5e-56
Identities = 180/616 (29%), Positives = 290/616 (47%), Gaps = 81/616 (13%)
Query: 108 RIAM-GLSLNESNREKCAIKFYNLLSSFNFMCSTPTLFNSGTI-RSQLSSCYLSTVPDDL 165
R+ M L+L + + E A + + + S F +TPT N G R +L SC+L + D++
Sbjct: 129 RVCMVALTLAQGD-ETLARQLVDEIISGRFQPATPTFLNCGKKQRGELVSCFLLRIEDNM 187
Query: 166 YGIFESIKENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQ 225
I SI LSK GG+ + +R G+PIK +S GVIP +K++ D NQ
Sbjct: 188 ESIGRSINSALQLSKRGGGVALLLSNLREAGAPIKRIENQSSGVIPVMKLLEDAFSYANQ 247
Query: 226 GGKRKGAICAYLETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWT 285
G R+GA YL H DI F++ ++ D++ R +++ + +PD+ + +
Sbjct: 248 LGARQGAGAVYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFELAKENEDMY 307
Query: 286 LFSPYDVPDLHNKFGKEFEESYI--LYENQTKLGKIKLFKKISALYLWRKILSMLFETGH 343
LFSPYDV + +GK F + + Y+ +I+ KKI+A ++ + + FE+G+
Sbjct: 308 LFSPYDVERV---YGKPFADISVTEKYDEMVADERIRK-KKINAREFFQTLAEIQFESGY 363
Query: 344 PWITFKDACNIRSPQQHVGIIHSSNLCTEI-------TLNT--SKNEIG---VCNLGSIN 391
P+I F+D N +P G I+ SNLC+EI N S IG CNLGS+N
Sbjct: 364 PYIMFEDTVNRANPIA--GRINMSNLCSEILQVNSASEYNEDLSYAHIGKDISCNLGSLN 421
Query: 392 LTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINY-YAVKKAKYSNLRHRPVGLGIMGFQD 450
+ M D +T+ A+R L V D+++ +V + N +GLG M
Sbjct: 422 IAHTM-----DSPDFGRTVETAIRALTAVSDMSHIRSVPSIEKGNAASHAIGLGQMNLHG 476
Query: 451 CLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRY------SSY-DGSLWDQ 503
L I Y S+EA+ F + + Y+A AS LA E+G S Y G +D+
Sbjct: 477 YLAREGIFYGSEEALDFTNIYFYTVTYHALRASNLLARERGETFAGFEQSKYASGEYFDK 536
Query: 504 GILPQDSLKLLEKERGSKYLKVNMSESL----NWKKLRNRIKKFGMRNSNCVAIAPTATI 559
QD K R L ++ +W +LR+ + + G+ N N A+ PT +I
Sbjct: 537 -YTQQDWQPKTAKVRE---LFARAGITIPTQEDWAQLRDDVMRHGIYNQNLQAVPPTGSI 592
Query: 560 SNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKY---FDG 616
S I ++SI P I S + E++K+G I + Y +
Sbjct: 593 SYINHSTSSIHP------IVSKI-------------EIRKEG-----KIGRVYYPAPYMT 628
Query: 617 NLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQSLNIYISNK-SGKKLDET 675
N D+L + Y A+EI P II+ + + +DQ SL ++ + + + +++
Sbjct: 629 N--------DNL-EYYQDAYEIGPEKIIDTYAAATQHVDQGLSLTLFFPDTATTRDINKA 679
Query: 676 YKLAWLRGLKTTYYLR 691
AW +G+KT YY+R
Sbjct: 680 QIYAWRKGIKTLYYIR 695
>gnl|CDD|236152 PRK08115, PRK08115, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 858
Score = 157 bits (398), Expect = 9e-40
Identities = 117/410 (28%), Positives = 185/410 (45%), Gaps = 59/410 (14%)
Query: 265 NIAIWVPDLFMKRVIKKSTWTLFSPYDVPDLHNKFGKEFEESYILYENQT---------- 314
NI++ + FM+ V + L PD+ N + +E E Y N+
Sbjct: 370 NISVCLTKEFMEAVENDEEYEL----RFPDVEN-YTEEEMEIY----NEEWHEVGDVREW 420
Query: 315 -KLG-KIKLFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHVG-IIHSSNLCT 371
K+G ++ ++KI A LW I + P I F D N + + G + ++N C
Sbjct: 421 EKMGYPVRTYRKIKAKELWNLINICATYSAEPGIFFIDNANEMTNAKAYGQKVVATNPCG 480
Query: 372 EITLNTSKNEIGVCNLGSINLT--LHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVK 429
E L VCNL +INL + +D KLK+T+ + +RM DNVID Y ++
Sbjct: 481 EQPLAP----YSVCNLAAINLANMADKETKTVDYEKLKRTVEVGVRMQDNVIDATPYFLE 536
Query: 430 KAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEE 489
+ K L R VGLG+MG D L + Y S+E + DQ E I AY S ELA+E
Sbjct: 537 ENKKQALGERRVGLGVMGLHDLLIYCETVYGSEEGNQLVDQIFETIATTAYRTSIELAKE 596
Query: 490 KGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSN 549
KG + G +++ KL E + Y+K M E +R I K+G+RNS+
Sbjct: 597 KGSFPFLVGQ------TEEETAKLREAFINTGYMK-KMPED-----IREDILKYGIRNSH 644
Query: 550 CVAIAPTATISNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIA 609
+ +APT + ++GVS +EP + + +S G+F E+ +V+E K +
Sbjct: 645 LLTVAPTGSTGTMVGVSTGLEPYFSFSYYRSGRLGKFIEVKADIVQEYLDKHPEAD---- 700
Query: 610 NLKYFDGNLSQISRIPDDLRKIYATAFEISPNWIIEAGSVRQKWIDQSQS 659
+ L + + +A E+ P + + Q+W+D S S
Sbjct: 701 ---------------ENHLPEWFISAMELKPEAHADVQCIIQRWVDSSLS 735
Score = 65.2 bits (159), Expect = 7e-11
Identities = 47/146 (32%), Positives = 72/146 (49%), Gaps = 5/146 (3%)
Query: 108 RIAMGLSLNESN---REKCAIKFYNLLSSFNFMCSTPTLFNSGTIRS-QLSSCY-LSTVP 162
R A GL+ E R++ KFY L + NF+ + L+ +G+ +CY + V
Sbjct: 137 RNATGLAAVEKTEEKRKESFEKFYQELVNMNFVPAGRVLYGAGSKTDVTYFNCYVMPFVK 196
Query: 163 DDLYGIFESIKENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVA 222
D GI E K+ + GG+G + + +R + +G NG+S G + +L + +
Sbjct: 197 DSREGISEHRKQVMEIMSRGGGVGTNGSTLRPRNTLARGVNGKSSGSVSWLDDIAKLTHL 256
Query: 223 VNQGGKRKGAICAYLETWHMDIEEFI 248
V QGG R+GA L WH DI EFI
Sbjct: 257 VEQGGSRRGAQMIMLADWHPDILEFI 282
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 152 bits (386), Expect = 5e-38
Identities = 101/320 (31%), Positives = 166/320 (51%), Gaps = 24/320 (7%)
Query: 385 CNLGSINLTLHMK---NGK--LDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHR 439
CNL SINL +K NGK D + I+ + LDN ID+N + + + Y+ R
Sbjct: 1308 CNLASINLAKFVKYDENGKPYFDWDEYAYVIQKVAKYLDNAIDVNKFPLPEIDYNTKLTR 1367
Query: 440 PVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDGS 499
+G+G+MG D L + IPY+S+E KF + E + +YAY S E A+++G + Y+ +
Sbjct: 1368 RIGVGMMGLADALFKLGIPYNSEEGFKFMRKVTEYLTFYAYKYSVEAAKKRGTFPLYEKT 1427
Query: 500 LWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATI 559
+ +G LP + E +L W KL IKK+G+RN+ PT ++
Sbjct: 1428 EYPKGELPVEGFYHPE------------IWNLPWDKLVEEIKKYGVRNAMVTTCPPTGSV 1475
Query: 560 SNIIGVSASIEPTYRNLHIKSNLSGEFTEINRYLVKELKKKGLWDESMIANLKYFDGNLS 619
S I S+ IEP + ++ KS GEF ++ ELKK+GL+ E ++ + G++
Sbjct: 1476 SMIADTSSGIEPIFALVYKKSVTVGEFYYVDPVFEAELKKRGLYSEELLKKISDNYGSVQ 1535
Query: 620 QISRIPDDLRKIYATAFEISPNWI--IEAGSVRQKWIDQSQSLNIYISNKSG-KKLDETY 676
+ IP+D+++++ TA +I +W+ I A + Q W+ S S I + N++ + + Y
Sbjct: 1536 GLEEIPEDMQRVFVTALDI--HWLDHILAQANIQMWLTDSASKTINMINEATVEDVKAAY 1593
Query: 677 KLAWLRGLK--TTYYLRSIS 694
+A G K T Y S+S
Sbjct: 1594 LIAHFLGCKGVTVYRDGSLS 1613
Score = 59.4 bits (143), Expect = 7e-09
Identities = 31/97 (31%), Positives = 56/97 (57%), Gaps = 3/97 (3%)
Query: 174 ENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAI 233
EN ++ + GL +++++R G + T G + G + F+ +++ V+ + QGG R+GA
Sbjct: 747 ENGMIFVHNTGL--NFSKLRPEGDIVGTTTGAASGPVSFMHLIDAVSDVIKQGGVRRGAN 804
Query: 234 CAYLETWHMDIEEFIELR-KNTGDDRRRTHDMNIAIW 269
LE WH DIE+FI + KN G + ++++ IW
Sbjct: 805 MGILEIWHPDIEKFIHAKEKNIGTNVLSNFNISVGIW 841
Score = 44.0 bits (103), Expect = 3e-04
Identities = 21/67 (31%), Positives = 38/67 (56%)
Query: 118 SNREKCAIKFYNLLSSFNFMCSTPTLFNSGTIRSQLSSCYLSTVPDDLYGIFESIKENAL 177
EK +++ L+++ FM +TP L NSG LS+C++ + DD+ I ++ + A+
Sbjct: 235 DKYEKEIEEYFRLMTNQIFMPNTPALINSGRPLGMLSACFVVPIEDDMESIMKAAHDVAM 294
Query: 178 LSKYAGG 184
+ K GG
Sbjct: 295 IQKAGGG 301
>gnl|CDD|180772 PRK06948, PRK06948, ribonucleotide reductase-like protein;
Provisional.
Length = 595
Score = 141 bits (356), Expect = 4e-35
Identities = 135/606 (22%), Positives = 238/606 (39%), Gaps = 96/606 (15%)
Query: 67 SNALLPERDLQFNYLGLKILYDRYFLHIEGIRIEMPQFFFMRIAMGLSLNE--SNREKCA 124
+ + D+ + + DRY L E R ++ F R+A L+L E R A
Sbjct: 1 DSFVRMIGDMDEQPICDAVFADRYALPGETSRAQV----FARVARALALAEPPDTRAGAA 56
Query: 125 IKFY-NLLSSFNFMCSTPTLFNSGTIRSQ-LSSCYL------STVPDDLYGIFESIKENA 176
+FY NLL+ + + + N+G Q + +C++ + + + ++ +
Sbjct: 57 RRFYRNLLNGA--IGAGRIMANAGAAPDQTMVNCFVHPIRAPAALTAVHPNLDRALDDAR 114
Query: 177 LLSKYAGGLGNDWTQVRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAY 236
L GG+G D++ + + + S GV L + + A+ R+GA A
Sbjct: 115 LTLLMGGGIGYDFSAIPPADARPDADHPDSPGVCAALDRFDRICAALPFRDGRRGAQMAV 174
Query: 237 LETWHMDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLFMKRVIKKSTWTLF---SPYDVP 293
L H D+ F+ ++ R R N+++ V D FM+ V + W L P
Sbjct: 175 LRCDHPDLLAFVAAKRG----RARWTTFNLSVAVTDAFMQAVAQDLPWALRHRAPPRRAA 230
Query: 294 DLHNKFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKDACN 353
+ + G + + A +LWR+I+S ++ P + F D +
Sbjct: 231 G-----------GALRGAD----GAW-TYATVPARHLWREIVSAARDSAEPGLLFVDTID 274
Query: 354 IRSPQQHVGIIHSSNLCTEITLNTSKNEIGVCNLGSINLTLHMKN-----GK--LDPIKL 406
+P + I ++N C E L G C LG I+L+ +++ G+ D L
Sbjct: 275 AANPLREHERIDATNPCGEQPLPP----YGSCVLGPIDLSRFVRHPFGVGGEPRFDFAAL 330
Query: 407 KKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEAIK 466
+RI +RMLDN +D+ + + + R +G+G+ G D L +M++ Y S A +
Sbjct: 331 ATAVRIQVRMLDNALDLTRWPLAAHAREARQKRRIGVGVTGLADALTMMRLRYDSPAARE 390
Query: 467 FADQSMEMICYYAYYASTELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVN 526
A + ++AY AS LA E+G Y D P L +
Sbjct: 391 MARYIASDLRHHAYAASAALAAERGAYPLCD---------PAAHLD------ALRA---- 431
Query: 527 MSESLNWKKLRNRIKKFGMRNSNCVAIAPTATISNIIG--VSASIEPTY-----RNLHIK 579
+ + I + G+RNS+ ++ AP ++S G S IEP R +
Sbjct: 432 --GPPLPHAVCHAIARHGLRNSHLLSFAPVGSVSLAFGDNCSPGIEPARAWIEHRPVRAG 489
Query: 580 S-----------------NLSGEFTEINRYLVKELKKKGLWDESMIANLK-YFDGNLSQI 621
+ +L GE + Y V +M A L+ Y D +S+
Sbjct: 490 AGGARGMRAENHAYRLFRSLRGERAALPDYFVTAADVAPADHLAMRAALQPYVDAGISKT 549
Query: 622 SRIPDD 627
+P+
Sbjct: 550 VTLPNH 555
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 115 bits (290), Expect = 2e-26
Identities = 115/473 (24%), Positives = 179/473 (37%), Gaps = 102/473 (21%)
Query: 133 SFNFMCSTPTLFNSGTI-RSQLSSCYLSTVPDDLYGIFESIKENALLSKYAGGLGNDWTQ 191
SFN +P FN GT Q+S+C++ +V D + I KE +L K G G + ++
Sbjct: 132 SFN----SPVWFNVGTESPQQVSACFILSVDDSMESILNWYKEEGMLFKGGSGTGTNLSR 187
Query: 192 VRSLGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGK-RKGAICAYLETWHMDIEEFIEL 250
+RS + G G + G + F++ + A + GG R+ A L+ H DIEEFIE
Sbjct: 188 IRSSKELLSG-GGTASGPVSFMRGADASAGTIKSGGATRRAAKMVILDVDHPDIEEFIET 246
Query: 251 RKNTGDDRRRT-----HDMNI---------------AIWVPDLFMKRVIKKSTWTLFSPY 290
K +D+ R +DM++ ++ V D FM+ V + L +
Sbjct: 247 -KAKEEDKIRALRDAGYDMDLGGEAYSSVQYQNANNSVRVSDEFMRAVENDGEFGLRART 305
Query: 291 DVPDLHNKFGKEFEESYILYENQTKLGKIKLFKKISALYLWRKILSMLFETGHPWITFKD 350
D G+ E + A L+RKI +E P I + D
Sbjct: 306 D--------GEVIE-------------------TVDAKELFRKIAEAAWECADPGIQYDD 338
Query: 351 ACNIRSPQQHVGIIHSSNLCTEITL--NTSKNEIGVCNLGSINLTLHMK----NGKLDPI 404
N G I++SN C+E N+S CNL S+NL MK +G D
Sbjct: 339 TINDWHTCPESGRINASNPCSEYMFLDNSS------CNLASLNL---MKFLRDDGTFDVE 389
Query: 405 KLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHRPVGLGIMGFQDCLHIMKIPYSSKEA 464
+ + + + ++ I + +K + R +GLG L +PY S
Sbjct: 390 SFRHAVELVITAMEISICFADFPTEKIARNTRAFRQLGLGYANLGALLMATGLPYDSDGG 449
Query: 465 IKFADQSMEMICYYAYYASTELAEEKGRYSSYD-----------------GSLWDQGILP 507
A ++ AY S ELA G + Y ++ G +
Sbjct: 450 RALAAAITSLMTGEAYRRSAELAGVVGPFEGYARNAEPHLRVMRKHAAANDAIRPLGEVD 509
Query: 508 QDSLKLLEKERGSKYLKVNMSESLNWKKLRNRIKKFGMRNSNCVAIAPTATIS 560
LLE + + W +K G RN+ +APT TI
Sbjct: 510 AA---LLEAAKEA------------WDDALELGEKNGYRNAQASVLAPTGTIG 547
>gnl|CDD|215855 pfam00317, Ribonuc_red_lgN, Ribonucleotide reductase, all-alpha
domain.
Length = 79
Score = 95.0 bits (237), Expect = 9e-24
Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 3/74 (4%)
Query: 78 FNYLGLKILYDRYFLHIE-GIRIEMPQFFFMRIAMGLSLNE--SNREKCAIKFYNLLSSF 134
YL K+L DRY L E G +E PQ FMR+A+ L+ E +R + A +FY+LLSS
Sbjct: 3 LTYLAAKVLEDRYLLKDEDGEVLETPQDMFMRVALALAGAEPPEDRLELAEEFYDLLSSL 62
Query: 135 NFMCSTPTLFNSGT 148
F+ +TPTL N+GT
Sbjct: 63 KFLPATPTLMNAGT 76
>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1220
Score = 70.4 bits (173), Expect = 2e-12
Identities = 149/617 (24%), Positives = 239/617 (38%), Gaps = 161/617 (26%)
Query: 150 RSQLSSCYLSTVPDDLY---GIFESIKENALLSKYAGGLGNDWTQVRSLGSPIKGTNGRS 206
Q +C++ +V DDL GI + A L KY G G++++ +R G + G G+S
Sbjct: 193 HPQPHACFIQSVEDDLVNEGGIMDLWVREARLFKYGSGTGSNFSNLRGEGEKLSG-GGKS 251
Query: 207 QGVIPFLKVVNDVAVAVNQGG-KRKGAICAYLETWHMDIEEFIE---------------- 249
G++ FLK+ + A A+ GG R+ A ++ H DIEEFI+
Sbjct: 252 SGLMSFLKIGDRAAGAIKSGGTTRRAAKMVIVDIDHPDIEEFIDWKVKEEQKVAALVTGS 311
Query: 250 -------------LRKNTGD-----DRRRTHDMNIAI------WVPDLFMKRVIKKS--- 282
GD D + + I VP+ ++KRVI+ +
Sbjct: 312 KIVSKHLKAIMKACVNCEGDGDDCFDPAKNPALKREIKAAKKALVPENYIKRVIQFARQG 371
Query: 283 -TWTLFSPYDVPD-------------------LHNKFGKEFEES--YILYENQTKLGKIK 320
T F YD D + ++F + E + L K
Sbjct: 372 YTDIDFPTYDT-DWDSEAYLTVSGQNSNNSVRVTDEFLRAVENDGDWNLTARTDG----K 426
Query: 321 LFKKISALYLWRKILSMLFETGHPWITFKDACNIRSPQQHV----GIIHSSNLCTEITL- 375
+ K + A LW KI + + P + F N H G I +SN C+E
Sbjct: 427 VAKTLKARDLWEKIGYAAWASADPGLQFNTTIN----DWHTCPASGPIRASNPCSEYMFL 482
Query: 376 -NTSKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYS 434
+T+ CNL S+NL L ++ + + A R+ V++I +V A++
Sbjct: 483 DDTA------CNLASLNL-LTFRDEDTKRFDV-EAYEHACRLWTVVLEI---SVLMAQFP 531
Query: 435 -------NLRHRPVGLGIMGFQDCLHIMKIPYSSKE--AIKFADQS-MEMICYYAYYAST 484
+ R +GLG L M IPY S E AI A + M + AY S
Sbjct: 532 SKEIAELSYEFRTLGLGYANIGGLLMTMGIPYDSDEGRAICGALSAIMTGV---AYATSA 588
Query: 485 ELAEEKGRYSSYDGSLWDQGILPQDSLKLLEKERGSKYLKVNMSESLN------------ 532
E+A+E G + Y+ + L+++ R + + + E L+
Sbjct: 589 EMAKELGPFPGYEKN-------ADHMLRVIRNHRRAAHGESEGYEGLSVNPVPLDHANCP 641
Query: 533 -----------WKKLRNRIKKFGMRNSNCVAIAPTATISNIIGVSAS-IEPTYRNLHIKS 580
W K +K G RN+ IAPT TI ++ + IEP + + K
Sbjct: 642 DQDLVAHAKAAWDKALELGEKHGYRNAQVTVIAPTGTIGLVMDCDTTGIEPDFALVKFK- 700
Query: 581 NLS--GEFTEINRYLVKELKKKGLWDESMIANLKYF---DGNLSQISRI----------- 624
L+ G F INR + + L+ G + ES IA ++ + G L+Q I
Sbjct: 701 KLAGGGYFKIINRAVPEALRTLG-YSESQIAEIEAYAVGHGTLNQAPGINHSTLKAKGFT 759
Query: 625 PDDLRKIYA---TAFEI 638
+ + K+ A +AF+I
Sbjct: 760 DEKIEKVEAALKSAFDI 776
>gnl|CDD|153083 cd00576, RNR_PFL, Ribonucleotide reductase and Pyruvate formate
lyase. Ribonucleotide reductase (RNR) and pyruvate
formate lyase (PFL) are believed to have diverged from a
common ancestor. They have a structurally similar
ten-stranded alpha-beta barrel domain that hosts the
active site, and are radical enzymes. RNRs are found in
all organisms and provide the only mechanism by which
nucleotides are converted to deoxynucleotides. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs use a diiron-tyrosyl
radical while Class II RNRs use coenzyme B12
(adenosylcobalamin, AdoCbl). Class III RNRs use an FeS
cluster and S-adenosylmethionine to generate a glycyl
radical. PFL, an essential enzyme in anaerobic bacteria,
catalyzes the conversion of pyruvate and CoA to
acteylCoA and formate in a mechanism that uses a glycyl
radical.
Length = 401
Score = 42.9 bits (101), Expect = 5e-04
Identities = 29/108 (26%), Positives = 46/108 (42%), Gaps = 6/108 (5%)
Query: 385 CNLGSINLTLHMKNGKLDPIK-----LKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRHR 439
CNL S+NL M+ + L++ +A+R LD VID + + + R
Sbjct: 200 CNLVSLNLARIMEKAINGSMDVVLEELEELAFLAVRALDCVIDSHDERIPTIELGGDERR 259
Query: 440 PVGLGIMGFQDCL-HIMKIPYSSKEAIKFADQSMEMICYYAYYASTEL 486
VGLGI G D L + EA A + ++ + + A+ E
Sbjct: 260 TVGLGIAGVADLLIKLGLEKVGDPEADDLAAELVDQLKKHLVKATNER 307
Score = 41.7 bits (98), Expect = 0.001
Identities = 30/182 (16%), Positives = 51/182 (28%), Gaps = 34/182 (18%)
Query: 143 LFNSGTIRSQLSSCYLSTVPDDLYGIFESIKE---------NALLSKYA--------GGL 185
+ G + C L D L + + E A GG+
Sbjct: 12 VITVGRPDLPFTGCVLVDYGDSLDPGIKGVNETAKSINEAIQKTYQIIALAASNQNGGGV 71
Query: 186 GNDWTQ--VRSLGSPIKG-TNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWH- 241
+ GS +G + N V QG R GA ++ H
Sbjct: 72 SFARASSILSPYGSRDYAKGSGTETDAVEAADAFNLALKEVGQGNGRTGAATGFIGGVHK 131
Query: 242 ----MDIEEFIELRKNTGDDRRRTHDMNIAIWVPDLF---------MKRVIKKSTWTLFS 288
+EF+ L G + + N+++ V +K++I + S
Sbjct: 132 GKGDKISQEFLNLALANGGEGIPLNFPNLSVRVSSDKPGILVKAVELKQLIAEEARKTGS 191
Query: 289 PY 290
P
Sbjct: 192 PG 193
>gnl|CDD|233901 TIGR02505, RTPR, ribonucleoside-triphosphate reductase,
adenosylcobalamin-dependent. This model represents a
group of adenosylcobalamin(B12)-dependent ribonucleotide
reductases (RNR) related to the characterized species
from Lactococcus leichmannii. RNR's are responsible for
the conversion of the ribose sugar of RNA into the
deoxyribose sugar of DNA. This is the rate-limiting step
of DNA biosynthesis. Thus model identifies NrdJ enzymes
only in cyanobacteria, lactococcus and certain
bacteriophage. A separate model (TIGR02504) identifies a
larger group of divergent B12-dependent RNR's [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 713
Score = 37.6 bits (87), Expect = 0.026
Identities = 46/261 (17%), Positives = 86/261 (32%), Gaps = 67/261 (25%)
Query: 326 SALYLWRKILSMLFETGHPWITFKD-ACN---IRSPQQHVGI---IHSSNLCTEITLNTS 378
SA + + + E G P D + + I + + G + +N C EI L
Sbjct: 318 SAFSGLARSAADILENGEPGQVNLDLSKSEGRIVNGRYQAGEDGDVEGTNPCGEILLANG 377
Query: 379 KNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLRH 438
+ CNL +NL ++G L++ +A R V Y + ++ ++
Sbjct: 378 E----PCNLFEVNLLAFEEDG----WGLQRAFALAARYAKRVTFSPY-DDEISREIIQKN 428
Query: 439 RPVGLGIMGFQDCLHIMKIPYSSKEAIKFADQSMEMICYYAYYASTELAEEKGRYSSYDG 498
R +G+ + G QD L + + + + +
Sbjct: 429 RRIGVSMSGIQDFLLL------------------------RGGTGFKDDFDPETHEAIKV 464
Query: 499 SLWDQGILPQDSLKLLEKERGSKYLKVNMSESLNWKKLRNRI-----KKFGM-RNSNCVA 552
++D+ R +K+L K+ + K+ G
Sbjct: 465 RVYDK--------------RAAKFLD-------RMYKIVVKAAQDYSKELGCPEPIKHTT 503
Query: 553 IAPTATISNIIGVSASIEPTY 573
+ P+ TIS + G S I P Y
Sbjct: 504 VKPSGTISKLAGASEGIHPPY 524
>gnl|CDD|224875 COG1964, COG1964, Predicted Fe-S oxidoreductases [General function
prediction only].
Length = 475
Score = 31.2 bits (71), Expect = 2.5
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 404 IKLKKTIRIAMRMLD-NVIDINYYAVKKAKYSNLRH---RPVGLGIMGFQD 450
IKLKK I +V + Y A K Y L + +G+M F D
Sbjct: 362 IKLKKFIDEKKAPKGLDVKKLIYNAFVKGDYEALGEFHYNTLFIGMMHFMD 412
>gnl|CDD|239367 cd03069, PDI_b_ERp57, PDIb family, ERp57 subfamily, first redox
inactive TRX-like domain b; ERp57 (or ERp60) exhibits
both disulfide oxidase and reductase functions like PDI,
by catalyzing the formation of disulfide bonds of newly
synthesized polypeptides in the ER and acting as
isomerases to correct any non-native disulfide bonds. It
also displays chaperone activity to prevent protein
aggregation and facilitate the folding of newly
synthesized proteins. ERp57 contains two redox-active
TRX (a) domains and two redox inactive TRX-like (b)
domains. It shares the same domain arrangement of
abb'a' as PDI, but lacks the C-terminal acid-rich region
(c domain) that is present in PDI. ERp57 interacts with
the lectin chaperones, calnexin and calreticulin, and
specifically promotes the oxidative folding of
glycoproteins. Similar to PDI, the b domain of ERp57 is
likely involved in binding to substrates.
Length = 104
Score = 28.8 bits (65), Expect = 3.3
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 286 LFSPYDVPDLHNKFGKEFEESYILYENQTKLGKIKLF 322
LF P P L NKF E+S + ++ KIK F
Sbjct: 70 LFRP---PRLSNKF----EDSSVKFDGDLDSSKIKKF 99
>gnl|CDD|225313 COG2515, Acd, 1-aminocyclopropane-1-carboxylate deaminase [Amino
acid transport and metabolism].
Length = 323
Score = 30.0 bits (68), Expect = 4.4
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 678 LAWLRGLKTTYYLRSISANYAKKSNFE----MGIDSVNLDEISIKGYNKNLQEIK 728
+A GLK L +I ANY N MG + +D + G N + +E+
Sbjct: 84 VAAKLGLKCVLILENIEANYLLNGNLLLSKLMGAEVRAVDAGTDIGINASAEELA 138
>gnl|CDD|130737 TIGR01676, GLDHase, galactonolactone dehydrogenase. This model
represents L-Galactono-gamma-lactone dehydrogenase (EC
1.3.2.3). This enzyme catalyzes the final step in
ascorbic acid biosynthesis in higher plants. This
protein is homologous to ascorbic acid biosynthesis
enzymes of other species: L-gulono-gamma-lactone oxidase
in rat and L-galactono-gamma-lactone oxidase in yeast.
All three covalently bind the cofactor FAD.
Length = 541
Score = 30.0 bits (67), Expect = 5.8
Identities = 17/65 (26%), Positives = 33/65 (50%)
Query: 378 SKNEIGVCNLGSINLTLHMKNGKLDPIKLKKTIRIAMRMLDNVIDINYYAVKKAKYSNLR 437
S N IG+ G +NL L K ++D K + ++ +R+ V I Y + ++++R
Sbjct: 96 SPNGIGLSRAGMVNLALMDKVLEVDEEKKRVRVQAGIRVQQLVDAIKEYGITLQNFASIR 155
Query: 438 HRPVG 442
+ +G
Sbjct: 156 EQQIG 160
>gnl|CDD|143478 cd07562, Peptidase_S41_TRI, Tricorn protease; serine protease
family S41. The tricorn protease (TRI), a member of the
S41 peptidase family and named for its tricorn-like
shape, exists only in some archaea and eubacteria. It
has been shown to act as a carboxypeptidase, involved in
the degradation of proteasomal products to
preferentially yield di- and tripeptides, with
subsequent and final degradations to free amino acid
residues by tricorn interacting factors, F1, F2 and F3.
Tricorn is a hexameric D3-symmetric protease of 720kD,
and can self-associate further into a giant icosahedral
capsid structure containing twenty copies of the
complex. Each tricorn peptidase monomer consists of five
structural domains: a six-bladed beta-propeller and a
seven-bladed beta-propeller that limit access to the
active site, the two domains (C1 and C2) that carry the
active site residues, and a PDZ-like domain (proposed to
be important for substrate recognition) between the C1
and C2 domains. The active site tetrad residues are
distributed between the C1 and C2 domains, with serine
and histidine on C1 and serine and glutamate on C2.
Length = 266
Score = 29.5 bits (67), Expect = 6.0
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 576 LHIKSNLSGEFTEINRYLVKELKKKGL 602
+HI F E R L+ E+ K GL
Sbjct: 92 VHIPDMGDDGFAEFLRDLLAEVDKDGL 118
>gnl|CDD|184958 PRK14996, PRK14996, TetR family transcriptional regulator;
Provisional.
Length = 192
Score = 28.9 bits (65), Expect = 7.3
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 195 LGSPIKGTNGRSQGVIPFLKVVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRKNT 254
LGS +GR + P++++ + + ++ + K A ++ WH + IE K
Sbjct: 87 LGSE----DGRFE---PYIRLWREAQILADRDPEIKDAYLLTMQMWHQETVAIIEQGKAA 139
Query: 255 GDDRRRTHDMNIAIW 269
G+ R ++ +IA W
Sbjct: 140 GEFRSTSNATDIA-W 153
>gnl|CDD|201244 pfam00463, ICL, Isocitrate lyase family.
Length = 526
Score = 29.5 bits (66), Expect = 7.6
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 477 YYAYYASTELAEEKGR-YSSYDGSLWDQGILPQDSLKLLEKERG------SKYLKVNMSE 529
YY Y T+ A +G Y+ Y +W + LP D + E G ++L N+S
Sbjct: 358 YYRYQGGTQCAINRGLAYAPYADLIWMESKLP-DYEQAKEFAEGVHAKWPEQWLAYNLSP 416
Query: 530 SLNWKK 535
S NWKK
Sbjct: 417 SFNWKK 422
>gnl|CDD|198376 cd07810, FGGY_D-XK_2, D-xylulose kinases, subgroup 2; members of
the FGGY family of carbohydrate kinases. This subgroup
is predominantly composed of bacterial D-xylulose
kinases (XK, also known as xylulokinase; EC 2.7.1.17).
They share high sequence similarity with Escherichia
coli xylulokinase (EcXK), which catalyzes the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. EcXK exists as a dimer. Each monomer consists
of two large domains separated by an open cleft that
forms an active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 490
Score = 29.3 bits (66), Expect = 8.8
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 13/61 (21%)
Query: 527 MSESLNWKKLRNRIKK-----FGMRNSNCVAIAPT--------ATISNIIGVSASIEPTY 573
+SE + W +N + G+ S I P + I+ +G+S I TY
Sbjct: 178 LSEGMLWDFKKNEVAVELLEYLGLDRSLIPDIVPNFSEQGTVTSEIAAELGLSEGIPITY 237
Query: 574 R 574
R
Sbjct: 238 R 238
>gnl|CDD|153085 cd01676, RNR_II_monomer, Class II ribonucleotide reductase,
monomeric form. Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class, are found to be
homodimers. This particular subfamily is found to be
active as a monomer. Adenosylcobalamin interacts
directly with an active site cysteine to form the
reactive cysteine radical.
Length = 658
Score = 29.0 bits (65), Expect = 9.9
Identities = 30/129 (23%), Positives = 50/129 (38%), Gaps = 32/129 (24%)
Query: 161 VPDDLYGIFESIKENALLSKYAGGLGN---DWTQVRSLGSPIKGTNGRSQGVIPFLK--- 214
VPD G +S++ LL Y D++ +R G +KG G + G P K
Sbjct: 168 VPDSREGWVKSVQL--LLDLYFNPAQTLIFDYSDIRPAGERLKGFGGIASGPEPLKKLHK 225
Query: 215 ---------------------VVNDVAVAVNQGGKRKGAICAYLETWHMDIEEFIELRKN 253
++N + V V G R+ A A+ + + E+F +L++
Sbjct: 226 AIAAILNDRSGKPLTSVDIVDLMNLIGVCVVSGNVRRSAEIAFGQP---EDEDFADLKQY 282
Query: 254 TGDDRRRTH 262
+ RR H
Sbjct: 283 QWNPGRREH 291
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
0.319 0.136 0.402
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,126,559
Number of extensions: 3786565
Number of successful extensions: 3248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3066
Number of HSP's successfully gapped: 83
Length of query: 749
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 645
Effective length of database: 6,324,786
Effective search space: 4079486970
Effective search space used: 4079486970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (28.1 bits)