RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 003575
(810 letters)
>gnl|CDD|178056 PLN02437, PLN02437, ribonucleoside--diphosphate reductase large
subunit.
Length = 813
Score = 1725 bits (4469), Expect = 0.0
Identities = 669/813 (82%), Positives = 747/813 (91%), Gaps = 3/813 (0%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQKVCAGVYKGVTTTQLDELA 60
MYV+KRDGR+E V FDKITARLKKLSYGLS++HCDPVLVAQKVCAGVYKGVTT+QLDELA
Sbjct: 1 MYVVKRDGRQETVHFDKITARLKKLSYGLSQDHCDPVLVAQKVCAGVYKGVTTSQLDELA 60
Query: 61 AETAAAMTVNHPDYALLAGRVAVSNLHKITKNSFSETIKDMYNYYNKRSGKKASLVADDV 120
AETAAAMT NHPDYA+LA R+AVSNLHK TK SFSET+KDMYN+ N+RSG KA L+ADDV
Sbjct: 61 AETAAAMTTNHPDYAILAARIAVSNLHKNTKKSFSETVKDMYNHVNERSGLKAPLIADDV 120
Query: 121 YEIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLKMDSRVVERPQHMLMRVSVGIHK 180
Y+IIMKNAA LD IIYDRDFD+DYFGFKTLERSYLLK++ +VVERPQHMLMRVSVGIHK
Sbjct: 121 YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVNGKVVERPQHMLMRVSVGIHK 180
Query: 181 DDTDSALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAI 240
DD +SA+KTYHLMSQ WFTHA+PTLFNAGTP+PQLSSCFL+CMKDDSIEGIYDTLK+CA+
Sbjct: 181 DDIESAIKTYHLMSQRWFTHASPTLFNAGTPRPQLSSCFLICMKDDSIEGIYDTLKECAV 240
Query: 241 ISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIY 300
ISKSAGGIGLS+HNIRA+GSYI GTNG+SNGIVPML+VFNDTARYVDQGGGKRKGAFAIY
Sbjct: 241 ISKSAGGIGLSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAIY 300
Query: 301 LEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLA 360
LEPWHADIFEFLDLRKN GKEE RARDLFYALW+PDLFMERV+ +G WSLFCP++A GLA
Sbjct: 301 LEPWHADIFEFLDLRKNHGKEEHRARDLFYALWIPDLFMERVQSNGDWSLFCPNEAPGLA 360
Query: 361 DSWGIEFEHLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNL 420
D WG EFE LY++YE EG+AK V+ A++LWF IL SQIETGTPYMLFKDSCNRKSNQQNL
Sbjct: 361 DCWGEEFERLYTKYEREGKAKKVVQAQQLWFAILESQIETGTPYMLFKDSCNRKSNQQNL 420
Query: 421 GTIKSSNLCTEIVEFSSPEETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLF 480
GTIKSSNLCTEI+E++SP ETAVCNLASIALPR+VREKGVP++S+ SKLVGS SKNR F
Sbjct: 421 GTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKGVPLESHPSKLVGSLGSKNRYF 480
Query: 481 DFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFES 540
DFE+LAEVT ++T NLNKIIDVN+YP+ET RRSN+RHRPIGIG+QGLAD FILLG+PF+S
Sbjct: 481 DFEKLAEVTAVVTRNLNKIIDVNYYPVETARRSNMRHRPIGIGVQGLADAFILLGMPFDS 540
Query: 541 PEAQQLNKDIFETIYYHALKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDW 600
PEAQQLNKDIFETIYYHALKAS+ELA ++GPYETY GSP+SKGILQ DMW +TPS RWDW
Sbjct: 541 PEAQQLNKDIFETIYYHALKASSELAAREGPYETYAGSPVSKGILQPDMWGVTPSGRWDW 600
Query: 601 SSLREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHL 660
++LREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIY+RRVLSGEF+VVNKHL
Sbjct: 601 AALREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL 660
Query: 661 LKDLTELGLWSHALKTKIIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCY 720
L DLTE+GLW+ LK KII ENGSV KI EIP++LKAIYKTVWEIKQ+TLVDMAADRGCY
Sbjct: 661 LHDLTEMGLWTPTLKNKIIAENGSVQKIPEIPDDLKAIYKTVWEIKQRTLVDMAADRGCY 720
Query: 721 IDQSQSLNIHMEQPDHGKLTSLHFYAWSKGMKTGMYYLRTRAAADAIKFTVDTSVLN--- 777
IDQSQSLNIHM+QP+ GKLTSLHFYAWSKG+KTGMYYLR+RAAADAIKFTVDT+ L
Sbjct: 721 IDQSQSLNIHMDQPNFGKLTSLHFYAWSKGLKTGMYYLRSRAAADAIKFTVDTASLKPSA 780
Query: 778 NEKANRADNDVEANLAQVVCSLKNQEECMACGS 810
A + DVE +AQ+VCSL N+EEC+ACGS
Sbjct: 781 TGVAAPEEEDVETKMAQMVCSLDNREECLACGS 813
>gnl|CDD|217257 pfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel
domain.
Length = 516
Score = 788 bits (2038), Expect = 0.0
Identities = 285/545 (52%), Positives = 364/545 (66%), Gaps = 30/545 (5%)
Query: 215 LSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVP 274
LSSCFLL DDS++ IYDTLK+ A++SKS GGIG+++ IRA GS I GT G S+G+VP
Sbjct: 1 LSSCFLLPSVDDSLDSIYDTLKEAALLSKSGGGIGINLSKIRAKGSPIRGTGGVSSGVVP 60
Query: 275 MLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWV 334
L+VF+DTARYV+QGG KR+GA A+YLE WH DI EFLDL+KN G EE RAR+L +WV
Sbjct: 61 FLKVFDDTARYVNQGG-KRRGAVAVYLEVWHPDIEEFLDLKKNNGDEERRARNLNLGVWV 119
Query: 335 PDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRAKMVISARKLWFEIL 394
PDLFM+RV +D W+LF P +A GL D +G EFE Y + E G+ K + AR+LWF+I+
Sbjct: 120 PDLFMKRVENDEDWTLFSPREAPGLEDLYGEEFEEEYEKLEANGKVKKTVKARELWFKIV 179
Query: 395 NSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAVCNLASIALPRY 454
S ETG PY+LFKD+ NR + Q++LGTIKSSNLCTEIV+ +SP E AVCNLASI L ++
Sbjct: 180 ESAWETGEPYILFKDAVNRHNPQKHLGTIKSSNLCTEIVQPTSPGEDAVCNLASINLAKF 239
Query: 455 VREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSN 514
V FDFE L EV ++ L+ +ID+N YP+ R+SN
Sbjct: 240 VENDFT-------------------FDFEELREVVRLAVRALDNVIDLNDYPVPEARKSN 280
Query: 515 LRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYET 574
RHR IG+G+ GLAD LG+P++S EA++L +IFETIYY+ALKAS ELA + GP+
Sbjct: 281 KRHRSIGLGVMGLADALAKLGIPYDSEEARELADEIFETIYYYALKASNELAKEKGPFPG 340
Query: 575 YFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNNE 634
+ GS +KG R DW LRE I K+G+RNS L A PT S SQI G E
Sbjct: 341 FEGSKYAKG---EFHAIPL---REDWEELREDIKKHGLRNSQLTAIAPTGSISQIAGTTE 394
Query: 635 CFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEIPEE 694
EP SN+Y+RR SGEF+VVN +LL+DL E LWS +K + + NGSV I EIPEE
Sbjct: 395 GIEPIFSNVYSRRSKSGEFLVVNPYLLRDLRE--LWSEEMKNE-LAYNGSVQPIPEIPEE 451
Query: 695 LKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHM-EQPDHGKLTSLHFYAWSKGMKT 753
+KA+YKT ++I K +DMAA R ++DQS S + + E L SL+ YAW G+KT
Sbjct: 452 IKALYKTAFDIDPKGHIDMAAARQPFVDQSISKTLFLPEDATASDLKSLYLYAWKLGLKT 511
Query: 754 GMYYL 758
G YY
Sbjct: 512 GTYYR 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 = 728 bits (1881), Expect = 0.0
Identities = 288/600 (48%), Positives = 350/600 (58%), Gaps = 146/600 (24%)
Query: 167 PQHMLMRVSVGIHKDDTDSALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMKDD 226
PQ LMRV++G+ D + A + Y L+S+ FT ATPTLFNAGTP+ QLSSCFLL + DD
Sbjct: 1 PQDRLMRVALGLASGDLEWAKEFYDLLSKQRFTPATPTLFNAGTPRGQLSSCFLLTV-DD 59
Query: 227 SIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYV 286
S+E IYDT+K+CA +SK GGIGL++ NIRA+GS I GTNG+SNG++P L++ NDTARYV
Sbjct: 60 SLESIYDTIKECAQLSKIGGGIGLNLSNIRATGSPIRGTNGASNGVIPFLKLLNDTARYV 119
Query: 287 DQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDG 346
DQ GG+RKGA A+YLE WH DI EFLDL+KN G E RARDLFY +W+PDLFMERV
Sbjct: 120 DQ-GGQRKGAGAVYLEIWHPDIEEFLDLKKNNGDERRRARDLFYGVWIPDLFMERVE--- 175
Query: 347 KWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYML 406
R LW +IL SQ ETG PY+L
Sbjct: 176 ----------------------------------------RDLWRKILESQFETGYPYIL 195
Query: 407 FKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSP-----EETAVCNLASIALPRYVREKGVP 461
FKD+CNRK+ Q++LGTIKSSNLCTEI++ +SP E AVCNLASI L +V
Sbjct: 196 FKDTCNRKNPQKHLGTIKSSNLCTEILQPTSPSEDEPGEDAVCNLASINLGNFV------ 249
Query: 462 VQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIG 521
FE+L EV K+ L+ +ID+N+YP+ +RSN+RHR IG
Sbjct: 250 -------------------TFEKLEEVVKLAVRALDNVIDLNYYPVPEAKRSNMRHRAIG 290
Query: 522 IGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETYFGSPMS 581
+G+ GL D LL +P+ES EA LN IFETI Y+ALKAS ELA + G
Sbjct: 291 LGVMGLHDYLALLRIPYESEEALDLNDRIFETINYYALKASCELAKERG----------- 339
Query: 582 KGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTS 641
G+RNSLL+A PTAS SQILG EP TS
Sbjct: 340 -----------------------------GLRNSLLLAIAPTASISQILGATPSIEPITS 370
Query: 642 NIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEIPEELKAIYKT 701
NIY RRVLSGEF VVN HL KDL E GL YKT
Sbjct: 371 NIYVRRVLSGEFPVVNPHLEKDLWEYGL-----------------------------YKT 401
Query: 702 VWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQP-DHGKLTSLHFYAWSKGMKTGMYYLRT 760
+EI Q+ L+D+AADR +IDQ QSLN+ + P L SL+FYAW KG+KT YYLRT
Sbjct: 402 AYEIDQRWLIDLAADRQKHIDQGQSLNLFLTPPATTRDLNSLYFYAWKKGLKTL-YYLRT 460
>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 (1793), Expect = 0.0
Identities = 291/639 (45%), Positives = 386/639 (60%), Gaps = 44/639 (6%)
Query: 145 YFGFKTLERSYLLKM--DSRVVERPQHMLMRVSVGIH-----KDDTDSALKTYHLMSQHW 197
Y G K L YLL+ + E PQ MRV++G+ A++ Y L+S+
Sbjct: 1 YMGLKELYNRYLLRNAATGAIYESPQEAYMRVAMGLASLEPKDTRLADAIRFYDLLSRLK 60
Query: 198 FTHATPTLFNAGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRA 257
+ ATPTLFNAGTP+ QLSSCFLL + DD++E IY + A +SK GGIGL++ +RA
Sbjct: 61 ISPATPTLFNAGTPRGQLSSCFLLDVTDDTLESIYKAIDDVAQLSKHGGGIGLNLTKLRA 120
Query: 258 SGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKN 317
GS I GTN +S GI+P L++ + + V+QGG KR GA A+YLE WH DI EFLDL+KN
Sbjct: 121 IGSPIRGTNNASKGIIPFLKLLDSSVEAVNQGG-KRPGAAAVYLEVWHPDIEEFLDLKKN 179
Query: 318 QGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEEE 377
G E R +LFY LW+PDLFM+RV +D W LF P D GL +G EFE Y + E++
Sbjct: 180 NGDERRRCDNLFYGLWIPDLFMKRVEEDKDWYLFSPYDVPGLYGLYGEEFEEEYERLEKD 239
Query: 378 GRAK---MVISARKLWFEILNSQIETGTPYMLFKDSCNRK-SNQQNLGTIKSSNLCTEIV 433
A+ +SAR L +IL +++ETG PY+LFKD+ N+ + G IK SNLCTEI
Sbjct: 240 VEARKKIRKVSARDLMKDILRTRVETGRPYILFKDAVNKHNPFKTGGGAIKMSNLCTEIT 299
Query: 434 EFSSPE---ETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTK 490
+ + ETAVCNLAS+ L +V E FDF L + +
Sbjct: 300 QPTDDSHKGETAVCNLASVNLANFVMED--------------------KFDFSELEDAVR 339
Query: 491 IITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDI 550
I L+ +ID+ +YP +SN R R IGIG+ GL D LGLP++S EA+ LN I
Sbjct: 340 IAVRFLDNVIDLQNYPTAPAAKSNQRRRSIGIGVMGLHDVLAKLGLPYDSEEARDLNDRI 399
Query: 551 FETIYYHALKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRW-------DWSSL 603
FE IYY+A+KASAELA + GP+ + GS +KG L D W T + DW +L
Sbjct: 400 FEAIYYYAIKASAELAKEKGPFPGFSGSKYAKGWLHPDTWEKTIDPKTSMAPTEEDWEAL 459
Query: 604 REMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHLLKD 663
RE I + G+RNS L A MPTAS+SQ+ G E EP SNI+T++ LSGEF++ NK+L+K+
Sbjct: 460 RERIKEYGLRNSQLTALMPTASSSQLTGVTESIEPVFSNIFTKKTLSGEFLIPNKYLMKE 519
Query: 664 LTELGLWSHALKTKIIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQ 723
L ELGLW + I+ GS I+ IPE LK YKT +E+ Q+ L+DMAADR ++DQ
Sbjct: 520 LEELGLWDADRRGDIVENVGSPQPIAAIPETLKYKYKTAYELDQEALIDMAADRQKFVDQ 579
Query: 724 SQSLNIHM-EQPDHGKLTSLHFYAWSKGMKTGMYYLRTR 761
S SLN+ + E+ L L AW KG+KT MYY R+R
Sbjct: 580 SISLNLFLTEEVTAKDLLKLLLLAWKKGLKT-MYYCRSR 617
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 637 bits (1645), Expect = 0.0
Identities = 313/847 (36%), Positives = 456/847 (53%), Gaps = 70/847 (8%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQKVCAGVYKGVTTTQLDELA 60
+ V DG + P+ ++ A +++ GL E D + + +Y GV ++ +
Sbjct: 149 LNVTLDDGVRRPLDMARLRALIEEACEGL--EAVDAEPILAETLKNLYDGVPMDEVYKAL 206
Query: 61 AETAAAMTVNHPDYALLAGRVAVSNLHKITKNSFSE-------TIKDMYNYYNK------ 107
A + P+Y+ + R+ L + + + T +M Y +
Sbjct: 207 ILAARTLIEKEPNYSYVTARLL---LDTLRREALGFLGVPEEVTQAEMATRYAEYFPAFI 263
Query: 108 RSGKKASLVADDVYEIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLKMDSRVVERP 167
+ G +A L+ + + + L A+ +RD F Y G +TL Y L +D +E P
Sbjct: 264 KKGIEAELLDPKLAQF---DLERLGAALDPERDLQFTYLGLQTLYDRYFLHVDGTRIELP 320
Query: 168 QHMLMRVSVGI---HKDDTDSALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMK 224
Q MRV++G+ D A++ Y+L+S F +TPTLFN+GT +PQLSSC+L +
Sbjct: 321 QAFFMRVAMGLALNEIDREARAIEFYNLLSSFDFMSSTPTLFNSGTLRPQLSSCYLTTVP 380
Query: 225 DDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTAR 284
DD ++GIY+ +K A++SK AGG+G +RA GS+I GTNG S G+VP L+V NDTA
Sbjct: 381 DD-LDGIYEAIKDNALLSKFAGGLGNDWTPVRALGSHIKGTNGKSQGVVPFLKVVNDTAV 439
Query: 285 YVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRD 344
V+QGG KRKGA YLE WH DI EFL+LRKN G + R D+ A W+PDLFM+RV +
Sbjct: 440 AVNQGG-KRKGAVCAYLETWHLDIEEFLELRKNTGDDRRRTHDMNTANWIPDLFMKRVME 498
Query: 345 DGKWSLFCPSDASGLADSWGIEFEHLYSQYEE---EGRAKMV--ISARKLWFEILNSQIE 399
DG+W+LF PS+ L D +G FE Y+ YE G K+ I A LW ++L+ E
Sbjct: 499 DGEWTLFSPSEVPDLHDLFGKAFEEAYTAYEAKAARGEIKLFKKIPAVDLWRKMLSMLFE 558
Query: 400 TGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAVCNLASIALPRYVREKG 459
TG P++ FKD CN +S QQ++G + SSNLCTEI +S +E AVCNL S+ L ++++
Sbjct: 559 TGHPWITFKDPCNLRSPQQHVGVVHSSNLCTEITLNTSDDEIAVCNLGSVNLVAHIKDGA 618
Query: 460 VPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRP 519
D E+L L+ +ID+N+Y + R SNLRHRP
Sbjct: 619 K-------------------LDHEKLKRTVSTAMRMLDNVIDINYYAVPKARNSNLRHRP 659
Query: 520 IGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETYFGSP 579
+G+GI G D LL +P+ S EA + E + Y+A+ AS ELA + G Y +Y GS
Sbjct: 660 VGLGIMGFQDALYLLRIPYASDEAVEFADRSMEAVSYYAIWASTELAEERGRYSSYEGSL 719
Query: 580 MSKGILQVD-----------MWNITPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQ 628
S+GIL +D + S DW +LR I K+G+RNS +A PTA+ S
Sbjct: 720 WSRGILPIDSLKLLAEARGGYLEVDRSSTLDWDALRARIKKHGMRNSNCMAIAPTATISN 779
Query: 629 ILGNNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKI 688
I+G ++ EP N+Y + LSGEF VVN +L++DL GLW + + Y +GS+ +I
Sbjct: 780 IIGVSQSIEPTYQNLYVKSNLSGEFTVVNPYLVRDLKARGLWDEVMVNDLKYFDGSLQRI 839
Query: 689 SEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQPDHGKLTSLHFYAWS 748
IP +LKA+Y T +E+ + LV+ A+ R +IDQ+QSLN++M KL + AW
Sbjct: 840 DRIPADLKALYATAFEVDPRWLVEAASRRQKWIDQAQSLNLYMAGASGKKLDETYKLAWL 899
Query: 749 KGMKTGMYYLRTRAAADAIKFTVDTSVLNNEKANRADNDVEANLAQV-------VCSLKN 801
+G+KT YYLRT A K TV+T LN + A A CS+ +
Sbjct: 900 RGLKT-TYYLRTLGATHVEKSTVNTGALNAVSSGGGGAGGAAAAAAAPPAADPKACSIDD 958
Query: 802 QEECMAC 808
+C AC
Sbjct: 959 -PDCEAC 964
>gnl|CDD|223287 COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide
transport and metabolism].
Length = 651
Score = 569 bits (1469), Expect = 0.0
Identities = 245/756 (32%), Positives = 355/756 (46%), Gaps = 132/756 (17%)
Query: 39 VAQKVCAGVYKGVTTTQLDELAAETAAAMTVNHPDYALLAGRVAVSNLHKITKNSFSETI 98
+ G Y G+T + LAA T + + PD LA R+A S+L K F
Sbjct: 1 RELRTVIGFYDGITIAENLILAALTV--IEEDDPDVQRLAARLAGSDLRKEAVRQF---- 54
Query: 99 KDMYNYYNKRSGKKASLVADDVYEIIM------KNAACLDGAIIYDRDFDFDYFGFKTLE 152
++ K +LVA+ Y+ + ++ L+ I+ +RD F Y K L
Sbjct: 55 ----GRFDVLDEKVFALVANGYYDQRLLRLYSREDLDDLNKKILLERDRQFSYAAAKVLY 110
Query: 153 RSYLLK--MDSRVVERPQHMLMRVSVGIHKDDTD-----SALKTYHLMSQHWFTHATPTL 205
YLLK S ++E PQ + MRV++ + +++ A + Y LMS F ATPTL
Sbjct: 111 SRYLLKDEDGSEILELPQDLFMRVALLLAQNEAPERRLEWAKEFYDLMSSLRFMPATPTL 170
Query: 206 FNAGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGT 265
N GTP+ QLSSCF+L ++DDS
Sbjct: 171 LNGGTPRGQLSSCFVLPVEDDS-------------------------------------- 192
Query: 266 NGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRA 325
+G+VP +++ +D ++QGG R+GA A+YL+ WH DI EFLD ++N G E RA
Sbjct: 193 ----SGVVPFMKLLDDAFDAINQGG-VRRGAQAVYLDIWHPDIEEFLDAKRNNGDEILRA 247
Query: 326 RDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRAKMVIS 385
D+ +W+PDLFM+R ++ W+LF P D D +G EFE + G K I
Sbjct: 248 FDISVGVWIPDLFMKRAKEGEDWTLFSPRDGYEAPDVYGAEFEEYAEYEADPGIRKKRIK 307
Query: 386 ARKLWFEILNSQIETGTPYMLFKDSCNRKSNQ-QNLGTIKSSNLCTEIVEFSSP------ 438
AR+L+ ++ + ETG PY++F D+ NR++ + G I++SNLC+EI++ + P
Sbjct: 308 ARELFDKLAEAAFETGDPYLIFVDTLNRRNPNAEGGGAIRASNLCSEILQRTKPLSLEQP 367
Query: 439 -EETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLN 497
E A CNL SI L ++V+ + LAE+ + L+
Sbjct: 368 LGEDASCNLGSINLAKFVKY------------------------GDGLAELVAVAVRALD 403
Query: 498 KIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYH 557
+ID+N YP+ R+N R IG+G+ GLAD LG+P+ S EA + N +FE I Y+
Sbjct: 404 NVIDLNPYPVPEAERANAESRAIGLGVMGLADLLAQLGIPYGSEEALKFNDRLFEYIAYY 463
Query: 558 ALKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLL 617
ALKASAELA + GPY + GS ++GIL +D + DW LRE I K+G+RNS L
Sbjct: 464 ALKASAELAKERGPYPYFEGSRWARGILPIDYPRLFGIT-EDWEKLREDIKKHGLRNSYL 522
Query: 618 VAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTK 677
A PT S S I G EP + +Y R G F V L +DL
Sbjct: 523 TAIAPTGSISYIAGTTSGIEPIFALVYFRETKGGRFYYVVPPLFEDLLAYYGL------- 575
Query: 678 IIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQPDHG 737
+EI +DM A +IDQ S +++
Sbjct: 576 ------------------------AYEIDPLWHIDMQAAAQRWIDQGISKTLNLPNTATT 611
Query: 738 K-LTSLHFYAWSKGMKTGMYYLRTRAAADAIKFTVD 772
K L + YAW G+KT YY RT AA + +D
Sbjct: 612 KDLNKAYLYAWKLGLKT-TYYRRTSQAAQVLTVVLD 646
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 511 bits (1316), Expect = e-167
Identities = 299/842 (35%), Positives = 455/842 (54%), Gaps = 70/842 (8%)
Query: 3 VIKRDGRKEPVRFDKITARLKKLSYGLSK--EHCDPVLVAQKVCAGVYKGVTTTQLDELA 60
V+ +DG + ++ A ++ S+ E D L+A A Y G+ +++
Sbjct: 238 VLSKDGSTYTMTKSQLLAHF---AWACSRFPETTDAALLADMAFANFYSGIKESEVVLAC 294
Query: 61 AETAAAMTVNHPDYALLAGRVAVSNLHK--ITKNSFSETIKDMYNYYNKRSGKKASLVAD 118
A A PDYA +A + + ++K + K+ + E +++ + + KR ++
Sbjct: 295 IMAARANIEKEPDYAFVAAELLLDVVYKEALGKSKYDEDLEEAHKDHFKRY-----ILEG 349
Query: 119 DVY----EIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLKMDSRVVERPQHMLMRV 174
D Y E+ + L A+ RD F Y G + L Y + R +E PQ MRV
Sbjct: 350 DTYRLNPELKHYDLDALAEALDLSRDLQFSYMGVQNLYDRYFNHHEGRRLETPQIFWMRV 409
Query: 175 SVGI----HKDDTDSALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMKDDSIEG 230
S+G+ +D T A+ Y+L+S +T ATPTLFN+G QLSSC+L ++DD +
Sbjct: 410 SMGLALNEGQDKTSWAITFYNLLSTFRYTPATPTLFNSGMRHSQLSSCYLSTVQDD-LVH 468
Query: 231 IYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGG 290
IY + A++SK AGGIG +RA+G+ I GTNG S G++P ++V NDTA V+QGG
Sbjct: 469 IYKVISDNAMLSKWAGGIGNDWTAVRATGALIKGTNGKSQGVIPFIKVANDTAVAVNQGG 528
Query: 291 GKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSL 350
KRKGA +YLE WH D +FL+LRKN G E R D+ A W+PDLF +R++ G W+L
Sbjct: 529 -KRKGAVCVYLEVWHLDYEDFLELRKNTGDERRRTHDINTASWIPDLFFKRLQQKGTWTL 587
Query: 351 FCPSDASGLADSWGIEFEHLYSQYE---EEGRAKMV--ISARKLWFEILNSQIETGTPYM 405
F P D GL +++G EFE LY +YE + G ++ + A LW ++L+ ETG P+M
Sbjct: 588 FSPDDVPGLHEAYGEEFEKLYEEYERKVDTGEIRLYKKVEAEDLWRKMLSMLYETGHPWM 647
Query: 406 LFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAVCNLASIALPRYVREKGVPVQSN 465
FKD N +S Q + G ++ SNLCTEI+ S ETAVCNL SI L ++ G+
Sbjct: 648 TFKDPSNIRSAQDHKGVVRCSNLCTEILLNCSETETAVCNLGSINLVEHIVNDGL----- 702
Query: 466 VSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQ 525
D E+L+E I L+ +ID+N YP + + +NL HR IG+G+
Sbjct: 703 ---------------DEEKLSETISIAIRILDNVIDINFYPTKEAKEANLAHRAIGLGVM 747
Query: 526 GLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETYFGSPMSKGIL 585
G D L + + S EA + E I Y+A+ AS+ LA + G Y +Y GS +G L
Sbjct: 748 GFQDALYKLNISYASQEAVEFADYSSELIAYYAILASSLLAKERGTYSSYKGSKWDRGYL 807
Query: 586 QVDMWNI------------TPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNN 633
+D + S R DW +R +I + G+RNS L+A PTA+ S I+G
Sbjct: 808 PIDTIELLKEYRGEANLLMDTSSRKDWEPVRSLIKEYGMRNSQLMAIAPTATISNIIGVT 867
Query: 634 ECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEIPE 693
+ EP +++ + LSGEF + N +L++ L +LG+W + + Y +GS+ +I IP+
Sbjct: 868 QSIEPTYKHLFVKSNLSGEFTIPNVYLIEKLKKLGIWDADMLDDLKYFDGSLLEIERIPD 927
Query: 694 ELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQPDHGKLTSLHFYAWSKGMKT 753
LK I+ T +EI+ + +++ A+ R +ID QSLN+++ +PD KL++++ AW KG+KT
Sbjct: 928 HLKKIFLTAFEIEPEWIIECASRRQKWIDMGQSLNLYLAEPDGKKLSNMYLTAWKKGLKT 987
Query: 754 GMYYLRTRAAADAIKFTVDTSV-------LNNEKANRADNDVEANLAQVVCSLKNQEECM 806
YYLR+ AA K VD + + N+ A+ VE VCSL +E C
Sbjct: 988 -TYYLRSSAATSVEKSFVDINKRGIQPRWMKNKSAS-TSIVVERAKKTPVCSL--EEGCE 1043
Query: 807 AC 808
+C
Sbjct: 1044 SC 1045
>gnl|CDD|180610 PRK06539, PRK06539, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 822
Score = 475 bits (1224), Expect = e-156
Identities = 269/794 (33%), Positives = 421/794 (53%), Gaps = 52/794 (6%)
Query: 3 VIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQKVCAGVYKGVTTTQLDELAAE 62
V+KRDG KEP +K+ A ++ + GL +A ++ ++ G+TT QLDE +
Sbjct: 5 VVKRDGSKEPYDANKVNAAIEDAARGLDDAITWVTQLASELEITLFDGITTQQLDEAVIQ 64
Query: 63 TAAAMTVNHPDYALLAGRVAVSNLHKITKNSFS--ETIKDMYNYYNKRSGKKASLVADDV 120
A + P + +A R+ + ++K + E ++D++ + +R+ +K VA+ +
Sbjct: 65 VALQNVKDDPAFDTVAARLLLKKIYKRVLGDYDSPEELQDLHANHFRRTIEK--GVAEGL 122
Query: 121 YEIIMKNAACLD---GAIIYDRDFDFDYFGFKTLERSYLLKM-DSRVVERPQHMLMRVSV 176
+ + L+ A+ RD Y G TL Y ++ + +E PQ+ MR+++
Sbjct: 123 LDSRLGGLFDLERLAAALDPTRDELLKYIGVVTLNNRYGIRARNGDALEVPQYFWMRIAM 182
Query: 177 GI---HKDDTDSALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMKDDSIEGIYD 233
G+ D T SAL Y MS+ + A TL NAGTP PQLS+CF++ M+DD IE I
Sbjct: 183 GLSLNEDDPTSSALAFYEKMSKLEYLAAGSTLVNAGTPYPQLSNCFVMEMQDD-IEHIAK 241
Query: 234 TLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKR 293
T + ++K GGIGLS+ +RA GS I N +S G +P + + R V +GG K+
Sbjct: 242 TTRDVMWLTKGTGGIGLSVSKLRAQGSPIRSNNTTSTGPIPFMHTIDSVLRAVSRGG-KK 300
Query: 294 KGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCP 353
GA Y+E WH D EFLDLR+N G R R A+W+ D FM+RV++D W LF P
Sbjct: 301 FGALCFYMENWHMDFPEFLDLRQNSGDPYRRTRTANTAVWISDEFMKRVQNDEDWYLFDP 360
Query: 354 SDASGLADSWGIEFEHLYSQY---EEEGRAKMV--ISARKLWFEILNSQIETGTPYMLFK 408
+ L + +G F Y+QY E GR +M I+AR+ + IL S T P++ +K
Sbjct: 361 LETPDLNELYGKAFSKRYAQYVEQAEAGRIRMFKRITAREQFRAILMSLQTTSHPWLTWK 420
Query: 409 DSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAVCNLASIALPRYVREKGVPVQSNVSK 468
D+ N ++ N GTI SNLCTEI + +VCNLASI L R+
Sbjct: 421 DTINNRALNNNTGTIHLSNLCTEICLPQDRDNVSVCNLASINLSRH-------------- 466
Query: 469 LVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLA 528
L D+ +L E T++ L+ +ID+ ++ SN ++R IG+G+ G
Sbjct: 467 LADGE------LDWAQLEESTRLAVRQLDNLIDITASSVKEADFSNQQNRAIGLGVMGFT 520
Query: 529 DTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETYFGSPMSKGILQVD 588
D LG +ES EA L I E I Y A+ SA+LA + G Y + GS S+G++ VD
Sbjct: 521 DMVERLGYSYESEEAYDLIDRIMEHISYAAIDESADLAAERGAYPNFEGSRWSRGMVPVD 580
Query: 589 MWNITPSD-----------RWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNNECFE 637
+ +D R DW +LR + + G+RN+ L+A PTAS + G +
Sbjct: 581 SIALLEADRGVPVDVNRTTRLDWDALRAKV-RGGMRNATLMAIAPTASIGLVAGTTPGLD 639
Query: 638 PYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEIPEELKA 697
P S I++R SG+F+ VN++L+ DL ELGLW ++ +I+ G + +I+ IP+E+KA
Sbjct: 640 PQFSQIFSRSTSSGKFLEVNRNLVADLKELGLW-ETVREEILRSQGDIQEIAAIPDEIKA 698
Query: 698 IYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQPDHGKLTSLHFYAWSKGMKTGMYY 757
+Y+T +++ +++AA ++DQ+ S N+++E D G + ++ AW G+KT YY
Sbjct: 699 LYRTSFQLSPYAFLEVAARAQKWVDQAISRNMYLESRDIGDMMDIYTAAWEMGVKT-TYY 757
Query: 758 LRTRAAADAIKFTV 771
L + A + TV
Sbjct: 758 LHMKPRHTAEQSTV 771
>gnl|CDD|236266 PRK08447, PRK08447, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 789
Score = 451 bits (1162), Expect = e-147
Identities = 281/836 (33%), Positives = 432/836 (51%), Gaps = 115/836 (13%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQ---KVCAGVY--KGVTTTQ 55
+ V+KR+GR EP+ KI GL V+Q +V A + G+TT +
Sbjct: 2 ITVVKRNGRIEPLDISKIQKYTSDAVEGLEG-------VSQSELEVDAKIQFRDGITTEE 54
Query: 56 LDELAAETAA-AMTVNHPDYALLAGRVAVSNL-HKITKNSFSETIKDMYNYYNKRSGKKA 113
+ + +TA + ++ P++ +A R+ + +L HK++ + +K+ Y+ K G+K
Sbjct: 55 IQQTLIKTAVDKIDIDRPNWTFVAARLFLYDLYHKVSGFTGYNHLKE---YFEK--GEKE 109
Query: 114 SLVADDVYEIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLK-MDSRVVERPQHMLM 172
+ + E + L+ I +RD F+Y G KTL YL+K ++ +E PQHM M
Sbjct: 110 GRILLGLKE--KYDLDDLNAYIKPERDLQFNYLGIKTLYDRYLIKDRNNNPIELPQHMFM 167
Query: 173 RVSVGIHKDDTDS---ALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMKDDSIE 229
+++ + +++ D A K Y ++S+ ATPTL NA T + QLSSC++ D+ IE
Sbjct: 168 AIAMFLAQNELDPQKWAKKFYDVISKFEVMLATPTLSNARTTRHQLSSCYIGSTPDN-IE 226
Query: 230 GIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQG 289
GI+D+ K+ A++SK GGIG +RA GSYI G ++ GI+P L++ ND A VDQ
Sbjct: 227 GIFDSYKEMALLSKYGGGIGWDWSKVRAMGSYIDGHKNAAGGIIPFLKITNDIAIAVDQL 286
Query: 290 GGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWS 349
G RKGA A+YLEPWH DI +F+DLRKN G+E RA DLF ALW+ DLFM+RV +D W+
Sbjct: 287 G-TRKGAIAVYLEPWHMDISDFIDLRKNSGEERRRAHDLFPALWINDLFMKRVEEDAMWT 345
Query: 350 LFCPSDASGLADSWGIEFEHLYSQYE-EEGRAKMVISARKLWFEILNSQIETGTPYMLFK 408
LF P + L + +G EFE Y +YE +E K I+A++LW +IL + ETG P++ FK
Sbjct: 346 LFDPYECKDLTELYGEEFEKRYLEYEKDEKIIKEYINAKELWKKILTNYFETGLPFLCFK 405
Query: 409 DSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAV---CNLASIALPRYVREKGVPVQSN 465
D+ NR + + G I+SSNLCTEI + ++P + SI + E+ V V S
Sbjct: 406 DNANRANPNAHAGIIRSSNLCTEIFQNTAPNHYKIKIEFEDGSIEF--FEEEELVTVDSG 463
Query: 466 VSKL---VGSRDSKN--RLFDFER-----------LAEV--TKIITEN------------ 495
++K + S DS +++ E+ LA + +KI T+
Sbjct: 464 ITKKAKKITSLDSLKGKKIYIVEKEKKDGKTAVCNLASINLSKINTKEDIERVVPIAIRM 523
Query: 496 LNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIY 555
L+ +ID+N YP + +NL+ R IG+G+ G A + + S E + +I E I
Sbjct: 524 LDNVIDLNFYPNRKVKATNLKSRAIGLGVMGEAQMLAEHKIAWGSKEHLEKIDEIMEQIS 583
Query: 556 YHALKASAELAVKDGPYETYFGSPMSKGILQVDMWN-----ITP-----SDRWDWSSLRE 605
Y+A+ AS+ LA++ G Y + GS SKGI +D N + DW LRE
Sbjct: 584 YNAIDASSNLALEKGVYPDFEGSNWSKGIFPIDKANEEAKKLVERGGLFDSACDWEGLRE 643
Query: 606 MISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRV----LSGEFIVVNKHLL 661
+ K+G+RN L+A PT+S S ++G + EP +Y R+ LSG VV +L
Sbjct: 644 KVKKDGMRNGYLMAIAPTSSISILVGTTQTIEP----VYKRKWFEENLSGLIPVVVPNLS 699
Query: 662 KDLTELGLWSHALKTKIIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYI 721
+ W + Y +++ QK L+ AA R +I
Sbjct: 700 PE-----TWQY--------------------------YTPAYDLDQKDLIKAAAVRQKWI 728
Query: 722 DQSQSLNIHM--EQPDHGKLTSLHFYAWSKGMKTGMYYLRTRAAADAIKFTVDTSV 775
DQ QSLNI + ++ L ++ AW G+K+ YYLR+ + D S+
Sbjct: 729 DQGQSLNIFLSLDKASGKYLNEIYTLAWKLGLKS-TYYLRSESPESEEVSVADRSI 783
>gnl|CDD|236378 PRK09102, PRK09102, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 601
Score = 382 bits (984), Expect = e-123
Identities = 223/683 (32%), Positives = 321/683 (46%), Gaps = 108/683 (15%)
Query: 137 YDRDFDFDYFGFKTLERSYLLKMDSRVVERPQHMLMRVSVGIHKDDTDSALKTYHLMSQH 196
RD FG TL YLL+ E Q + R++ D + A + Y MS+
Sbjct: 15 RSRDAWLTEFGKATLRDRYLLEG-----ESYQDLFARIAEAYADIDPEHAQRFYDYMSRG 69
Query: 197 WFTHATPTLFNAGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIR 256
WF ATP L N GT + SCFL + +DS+EGI +T + ++K GGIG N+R
Sbjct: 70 WFMPATPVLSNGGTDRGLPISCFLNYV-EDSLEGIVNTWNENVWLAKRGGGIGSYWGNVR 128
Query: 257 ASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRK 316
+ G I NG S+GI+P ++V D+ G R+G+FA+YL+ H +I EFLD+RK
Sbjct: 129 SIGEPIRN-NGKSSGIIPFIKVM-DSLTLAISQGSLRRGSFAVYLDIEHPEIEEFLDIRK 186
Query: 317 NQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEE 376
G +A +L + + V D FME V D +W L P D
Sbjct: 187 PTGDPNRKALNLHHGVCVTDEFMEAVEDGDEWDLISPKD--------------------- 225
Query: 377 EGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRK--SNQQNLG-TIKSSNLCTEI- 432
+ AR LW +IL ++IETG PY+LF D+ NR ++LG +K+SNLC+EI
Sbjct: 226 -KSVIRTVKARDLWAKILETRIETGEPYLLFIDNVNRALPEVYKDLGLKVKASNLCSEIT 284
Query: 433 ----VEFSSPEETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFER-LAE 487
++ + TAVC L+S+ L Y K D+ + D R L
Sbjct: 285 LPTGIDHLGEDRTAVCCLSSLNLEYYDEWK---------------DTDAFIEDLMRFLDN 329
Query: 488 VTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLN 547
V L ID +E + S +R R +G+G+ G +PFES A+Q N
Sbjct: 330 V-------LQDFIDKAPDEMERAKYSAMRERSVGLGVMGFHSYLQSKMIPFESVMAKQWN 382
Query: 548 KDIFETIYYHALKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMI 607
K IF+ I A KAS ELA + G D + +R
Sbjct: 383 KKIFKHIREQADKASKELAKEKGE----------------------CPDAAGYGVMR--- 417
Query: 608 SKNGVRNSLLVAPMPTASTSQILGN-NECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTE 666
R S +A PTAS S ILGN + EP +N YT + L G F V NK+L K L E
Sbjct: 418 -----RFSTKMAIAPTASISIILGNTSPGIEPIAANYYTHKTLKGSFTVKNKYLEKLLEE 472
Query: 667 LGLWSHALKTKIIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQS 726
G + + + I+ GSV + + EE K ++KT +EI Q+ ++++AADR YIDQ+QS
Sbjct: 473 KGKDTDEVWSSILTNEGSVQHLDFLSEEEKDVFKTAFEIDQRWIIELAADRQKYIDQAQS 532
Query: 727 LNIHMEQPDHGK-LTSLHFYAWSKGMKTGMYYLRTRAAADAIKFTVDTSVLNNEKANRAD 785
LN+ + + L LHF AW KG+K+ +YY R+++ A +K +
Sbjct: 533 LNLFLPANVPKRDLNKLHFEAWKKGVKS-LYYQRSKSVQRA------------DKVSHDV 579
Query: 786 NDVEANLAQVVCSLKNQEECMAC 808
++ +EC+AC
Sbjct: 580 LKKRLVEKSA--FNRDYDECLAC 600
>gnl|CDD|181700 PRK09209, PRK09209, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 761
Score = 364 bits (935), Expect = e-114
Identities = 239/811 (29%), Positives = 365/811 (45%), Gaps = 123/811 (15%)
Query: 3 VIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQKVCAGVYKGVTTTQ---LDEL 59
V + RK P +++ + ++ D ++V V + + T +D L
Sbjct: 12 VKEAGNRKLPFDKERLDRYIDQIHAEFP--QLDVEDYKRRVFNFVERKESVTADDLVDYL 69
Query: 60 AAETAAAMTVNHPDYALLAGRVAVSNLHK-ITKNSFSETIKDMYNYYNKRSGKKASLVAD 118
E A + + P++ A R+ ++ L+K ++N F + + Y + G + SL
Sbjct: 70 IREAEARVDLEEPEWTFFAARLYLNRLYKRASRNRFYDA-SEKYGSF---VGLQESLAER 125
Query: 119 DVY----------EIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLK-MDSRVVERP 167
+Y E +++ +D +RD F Y G L YL D V E P
Sbjct: 126 GIYSNDLLKRYSKEELIEAGKMIDP----ERDKLFTYIGLYLLADRYLATDSDRNVYELP 181
Query: 168 QHMLMRVSVGI-HKDDTDSALK----TYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLC 222
Q + +++ + + + ++ Y +S + T ATPTL NAG QLSSCF+
Sbjct: 182 QERWLTIALYLMQNEPRERRMQLVKEAYWALSNLYMTVATPTLANAGKVGGQLSSCFIDT 241
Query: 223 MKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDT 282
+ DDS++GIYD+ A +SK GG+G + +R+ GS I G G S+G++P ++ N+T
Sbjct: 242 V-DDSLQGIYDSNTDVARVSKHGGGVGAYLGKVRSRGSDIRGFKGVSSGVIPWIKQLNNT 300
Query: 283 ARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERV 342
A VDQ G +RKGA A+YL+ WH DI FLDLR N G E RA D+F + +PDLFME V
Sbjct: 301 AVSVDQLG-QRKGAIAVYLDVWHKDIESFLDLRLNNGDERLRAHDVFTGVCIPDLFMEAV 359
Query: 343 RDDGKWSLFCPSDAS-----GLADSW-----GIEFEHLYSQYEEEGR-AKMVISARKLWF 391
G W LF P + L D + F Y + + R ++ + A +
Sbjct: 360 ERRGDWYLFDPHEVKKVMGWYLEDFYDEKKGDGSFREKYEECVADERLSRKTVKAIDIMK 419
Query: 392 EILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSP----EET------ 441
I+ SQ+ETG P+M ++D NR + ++ G I SSNLCTEI++ SP +E
Sbjct: 420 RIMVSQLETGNPFMFYRDEVNRMNPNKHEGMIYSSNLCTEIMQNMSPTVMIQEIISGGQI 479
Query: 442 ---------AVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKII 492
VCNL+SI L R V V ERL I
Sbjct: 480 VITKQPGDFVVCNLSSINLGRAVTA-DV---------------------LERL---IPIQ 514
Query: 493 TENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFE 552
L+ +ID+N P+ +N ++R IG+G G L G+ +ES EA Q +++E
Sbjct: 515 VRMLDNVIDLNQLPVPQATITNQKYRAIGLGTFGWHHLLALKGIAWESEEAVQYADELYE 574
Query: 553 TIYYHALKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKNGV 612
I Y ++AS ELA + G Y + GS G + + + W L +++NGV
Sbjct: 575 RINYLTIQASMELAKEKGAYPVFKGSDWQTG----EYFERRGYNSPQWDELAAQVAENGV 630
Query: 613 RNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSH 672
RN+ L+A P ST+QI G+ +P S Y V DL+
Sbjct: 631 RNAYLMAVAPNMSTAQIAGSTASIDPIYSAFYYEEKKDYRRPVT----APDLSL------ 680
Query: 673 ALKTKIIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHME 732
T YE K +++ Q + A R ++DQS S N ++
Sbjct: 681 --DTWPYYE------------------KGAYKVDQFWSIRQNAARQRHVDQSISFNFYVP 720
Query: 733 QPDHGK-LTSLHFYAWSKGMKTGMYYLRTRA 762
L LH AW +G+KT YY+R+
Sbjct: 721 STIRASELLDLHMTAWKEGLKT-TYYVRSTD 750
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 355 bits (912), Expect = e-111
Identities = 246/802 (30%), Positives = 376/802 (46%), Gaps = 99/802 (12%)
Query: 5 KRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQKVCAGVYKGVTTTQLDELAAETA 64
KRDG+ EP++ +K +K GL CDP+ + G+TT ++ + +TA
Sbjct: 7 KRDGQYEPLQVEKTKKMVKLACEGL--YGCDPLELELDSRIQFRDGMTTKEIQKSLIQTA 64
Query: 65 -------------AAMTVNHPDYALLAGRVAVSNLHK---ITKNSFSETIKDMYNYYNKR 108
+P++ +A R+ V +L+K I ++ S D Y K
Sbjct: 65 IEKVIQNSKDNNGNNTKKTNPNWQYVAARLYVFDLYKEARINRHYNSFGYGDYYELVKK- 123
Query: 109 SGKKASLVADDVY-EIIMKNAACLD-----GAIIYDRDFDFDYFGFKTLERSYLLKMDSR 162
LV + +Y E +++N + + I +RDF F+Y G K L YL+K +R
Sbjct: 124 ------LVEEKLYGEYLLQNYSKEEIKELEKYIKPERDFLFNYEGLKLLADRYLVKGFNR 177
Query: 163 -VVERPQHMLMRVSVGIHKDDTDS-----ALKTYHLMSQHWFTHATPTLFNAGTPQPQLS 216
++E PQ M +++ + + A K Y L+S+ T ATPTL NAGTP QLS
Sbjct: 178 EILELPQERFMGIAMHLAIPEGKEKRVYYAKKFYDLLSELKATVATPTLSNAGTPFYQLS 237
Query: 217 SCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPML 276
SCF+ + DD++ IYD +K A +SK G +G+ IRA S I G +S G++P +
Sbjct: 238 SCFISVV-DDNLWSIYDVNQKFAQVSKHGGALGIYTGKIRALNSEIRGFKNASGGVIPWI 296
Query: 277 QVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPD 336
+++NDTA VDQ G KRKG AI L+ WH DI EFLDL+ N G + +A D+F + PD
Sbjct: 297 KLYNDTAIAVDQLG-KRKGGAAITLDIWHKDIPEFLDLKTNNGDDRRKAHDIFPGVSYPD 355
Query: 337 LFMERVRDDGKWSLFCPSDAS-----GLADSWG----IEFEHLYSQYEEEGR-AKMVISA 386
LFM+R+ WSLF P + L D + EF Y + EE+ + +
Sbjct: 356 LFMKRLEKRENWSLFDPHEIKKVKGYSLEDYYDEEDRKEFTKKYLECEEDTNIPRRTVPV 415
Query: 387 RKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAVCNL 446
+ +I+ S +ETGTP++ F+D+ N+ + ++ G I SSNLC EI + S E +
Sbjct: 416 LDIMKKIMKSAVETGTPFIFFRDTVNKANPNKHKGMIYSSNLCHEIAQNMSESELLEEEI 475
Query: 447 ASIALPRYVREKGVP---VQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVN 503
V +K V N++ +V E L EV L+ +I +N
Sbjct: 476 IDENGYYEVVQKIKAGDMVTCNLNSIVLGNVDD------EELEEVIPTQIRMLDNVISLN 529
Query: 504 HYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASA 563
+YP+ ++ ++R IG+G G + +ES E + I+E I Y+A+KAS
Sbjct: 530 YYPVPEAEITSDKYRAIGLGTSGYHHMLANNKIRWESDEHIKFADKIYEEIAYYAIKASM 589
Query: 564 ELAVKDGPYETYFGSPMSKG-ILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMP 622
ELA + G Y + GS G + +N S+R W L+E I K G+RN + A P
Sbjct: 590 ELAKEKGSYPAFKGSEWETGKYFERRGYN---SER--WKKLKEEIKKYGMRNGYITAVAP 644
Query: 623 TASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYEN 682
T STS I +P + G F DL E W
Sbjct: 645 TGSTSNIANTTAGIDPVFKRFFMEEK-KGSFT---PKTAPDLNEENFW------------ 688
Query: 683 GSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQPDHGKLTSL 742
YK I Q+ + R +IDQ+QS N+++ P++ L
Sbjct: 689 ---------------YYKEAHTIDQQWSIKACGVRQRHIDQAQSFNLYI-TPEYKAKQIL 732
Query: 743 HFY--AWSKGMKTGMYYLRTRA 762
+ Y AW +G+KT +YY+R ++
Sbjct: 733 NLYIEAWKQGVKT-IYYVRNKS 753
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 332 bits (853), Expect = e-101
Identities = 230/754 (30%), Positives = 363/754 (48%), Gaps = 109/754 (14%)
Query: 53 TTQLDELAAETAAAM---TVNHPDYALLAGRVAVSNL-HKITKNSFSETIKDMYN--YYN 106
++ + LAA AA+ T PD+ +A R+ + K+ K+ I Y+ Y
Sbjct: 143 MSEGESLAALIKAAVELTTQEAPDWEFIAARLLMLQFSKKLGKSLEKLGIHSFYDKIKYL 202
Query: 107 KRSGKKASLVADDVYEIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLKM-DSRVVE 165
G S + + ++ AA G I +RD F Y G L + Y+++ +E
Sbjct: 203 TEEGLYGSYILEHYSREEIEEAA---GFIDPERDKLFTYSGLDLLLKRYVIRTHSHEPLE 259
Query: 166 RPQHMLMRVSVGIHKDDTDSAL----KTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLL 221
PQ M + +++ + + + + Y ++S+ T ATPTL NA P QLSSCF+
Sbjct: 260 SPQEMFLGIALHLAMPEKQDRMGWVKRFYDMLSKLKVTMATPTLSNARKPFHQLSSCFID 319
Query: 222 CMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFND 281
+ D S++GIY ++ A +SK GG+GL +RA GS I G G + G++ +++ ND
Sbjct: 320 TVPD-SLDGIYRSIDNFAQVSKFGGGMGLYFGKVRAVGSNIRGFQGVAGGVIRWIKLAND 378
Query: 282 TARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMER 341
TA VDQ G R+GA A+YL+ WH DI EFL LR N G + +A D+F A+ PDLF +
Sbjct: 379 TAVAVDQLG-MRQGAVAVYLDVWHKDIPEFLQLRTNNGDDRMKAHDVFPAVCYPDLFWKM 437
Query: 342 VRDD--GKWSLFCPSDAS-----GLADSWGIEFEHLYSQYEEEGR-AKMVISARKLWFEI 393
VRDD W LFCP + L D +G E+E Y + R +K I + L I
Sbjct: 438 VRDDINQSWYLFCPHEILTVKGYALEDYYGEEWEKRYLDCVNDARISKRSIPIKDLVRLI 497
Query: 394 LNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEET------------ 441
L S +ETGTP+ +D+ NR + ++ G I SNLCTEI + S ET
Sbjct: 498 LKSAVETGTPFTFNRDTVNRANPNKHKGMIYCSNLCTEIAQNMSAIETVSTEIETEDGDT 557
Query: 442 -----------AVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTK 490
VCNLAS++L + ++ D E L EV +
Sbjct: 558 VVVTTTRPGDFVVCNLASLSLGN------IDLE-----------------DEEELEEVVR 594
Query: 491 IITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDI 550
+ L+ +ID+N YP+ + +N R+R IG+G+ G G+ +ES E + +
Sbjct: 595 TVVRALDNVIDLNFYPVPYAQITNKRYRSIGLGVSGYHHALAKNGIRWESEEHLEFADRV 654
Query: 551 FETIYYHALKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKN 610
FE I Y A+KAS E+A + G Y + GS G T +W L +++N
Sbjct: 655 FERINYAAIKASMEIAKEKGAYGYFEGSDWQTGAY-FRKRGYTSE---EWQRLAREVAEN 710
Query: 611 GVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLW 670
G+RN+ L+A PT+STS I G +P V+ ++ L++
Sbjct: 711 GMRNAYLLAVAPTSSTSIIAGTTAGVDP----------------VMKRYFLEE------- 747
Query: 671 SHALKTKIIYENGSVSKIS-EIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNI 729
+ + +++ E+ ++ +YK I QK + A R +IDQ+QS+N+
Sbjct: 748 ---------KKGALMPRVAPELSDKTFWLYKNAHLIDQKWSIRAAGVRQRHIDQAQSVNL 798
Query: 730 HMEQP-DHGKLTSLHFYAWSKGMKTGMYYLRTRA 762
++ ++ L+ AW +G+KT +YY+R+++
Sbjct: 799 YITNEFTMRQVLDLYLLAWEEGVKT-IYYVRSKS 831
>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 = 313 bits (803), Expect = 8e-97
Identities = 193/621 (31%), Positives = 301/621 (48%), Gaps = 67/621 (10%)
Query: 151 LERSYLLK-MDSRVVERPQHMLMRVSVGI-HKDDTDSALKT-------YHLMSQHWFTHA 201
L YL K D ++E P+ + RV+ + +D ++ Y LM F
Sbjct: 2 LAARYLRKDEDGNILESPEDLFRRVARALAAAEDKYNSPVWKQLYERFYDLMVNLGFMPN 61
Query: 202 TPTLFN-AGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGS 260
+PTL N GT QLS+CF+L ++DD +E I++ K+ A+I K GG+G + +R G
Sbjct: 62 SPTLMNAGGTRLGQLSACFVLPVEDD-MESIFEAAKEAALIFKRGGGVGYNFSTLRPKGD 120
Query: 261 YIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGK 320
+ GT G ++G V ++VF+ A + QGG R+GA L+ WH DI EF++ +K +GK
Sbjct: 121 KVSGTGGVASGPVSFMRVFDAAAGVIKQGG-TRRGAQMGILDVWHPDIEEFIEAKKKEGK 179
Query: 321 EECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRA 380
+ ++ V D FME V D ++ L P E E L + E +
Sbjct: 180 L----TNFNISVGVTDAFMEAVEADEEYKLRNPRTGE--------EIEELAEKREPKLVV 227
Query: 381 KMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEI--VEFSSP 438
+ AR+LW +I+ + ++ P +LF D+ N+ +N LG I ++N C E + + S
Sbjct: 228 YKEVPARELWDKIVEAAWKSAEPGLLFIDTINKWNNLPYLGRINATNPCGEQPLLPYES- 286
Query: 439 EETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNK 498
CNL SI L ++V+ D FDFERL EV ++ T L+
Sbjct: 287 -----CNLGSINLAKFVKN----------------DFGGASFDFERLREVVRLATRFLDN 325
Query: 499 IIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHA 558
+ID+N +P+ + + R IG+GI GLAD I LG+P++S EA+ +++ I A
Sbjct: 326 VIDLNRFPLPEIAEATKKTRRIGLGIMGLADLLIKLGIPYDSEEARAFAEELMRFIADAA 385
Query: 559 LKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLV 618
+ASAELA + G + + S G + LRE I+K G+RN+ L
Sbjct: 386 YRASAELAKERGAFPLFEASKYLMGKVARIP------SALPA-ELREAIAKYGIRNAQLT 438
Query: 619 APMPTASTSQILGNNECFEPYTSNIYTRRVL-SGEFIVVNKHLLKDLTELGLWSHALKTK 677
PT + S I G + EP + +Y R V GE + VN + L ELG +S +
Sbjct: 439 TIAPTGTISLIAGTSSGIEPVFALVYFRNVTVGGELLEVNPLVELALRELGYYSDEIVKI 498
Query: 678 IIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHM------ 731
+ E G+V ++PEEL ++ T +I + V M A ++D S S I+M
Sbjct: 499 EVAEKGTVEGAPDLPEELPKVFVTANDISPEDHVLMQAAIQPWVDSSISKTINMPSDATV 558
Query: 732 EQPDHGKLTSLHFYAWSKGMK 752
E +++ AW G+K
Sbjct: 559 EDVK-----AVYLEAWKLGLK 574
>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 = 281 bits (721), Expect = 2e-86
Identities = 147/455 (32%), Positives = 221/455 (48%), Gaps = 57/455 (12%)
Query: 190 YHLMSQHWFTHATPTLFNAGT-PQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGI 248
++L+ F +PTL NAGT QLS+CF+L ++DDSIEGI+D LK+ A+I K GG+
Sbjct: 5 FYLLLSQGFIPNSPTLMNAGTGELGQLSACFVLPVEDDSIEGIFDALKEAALIFKRGGGV 64
Query: 249 GLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADI 308
G + +R G + T G ++G V ++VF+ + QGG R+GA L+ H DI
Sbjct: 65 GYNFSRLRPKGDIVKSTGGVASGPVSFMRVFDAATGVIKQGG-TRRGANMGVLDVDHPDI 123
Query: 309 FEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFE 368
EF+D K + ++ ++ ++ V D FME V +D W L P +
Sbjct: 124 EEFIDA-KMKEEKTVVLQNFNISVAVTDAFMEAVENDEPWELRNPREPDTG--------- 173
Query: 369 HLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNL 428
+ + AR+LW +I+ + ++ P +LF D+ NR + LG I ++N
Sbjct: 174 ------KVYRT----VPARELWDKIVEAAWDSADPGVLFIDTINRWNPLPGLGRINATNP 223
Query: 429 CTEIV--EFSSPEETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLA 486
C E + S CNL SI L ++V+ FDFERL
Sbjct: 224 CGEQPLLPYES------CNLGSINLSKFVKNPF----------------GGASFDFERLR 261
Query: 487 EVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQL 546
E ++ L+ +IDVN YP+ R IG+G+ GLAD I LG+P++S EA++L
Sbjct: 262 EAVRLAVRFLDNVIDVNRYPLPEIAEETKATRRIGLGVMGLADMLIKLGIPYDSEEAREL 321
Query: 547 NKDIFETIYYHALKASAELAVKDGPYETYFGS--PMSKGILQVDMWNITPSDRWDWSSLR 604
+ I I A +ASAELA + GP+ + S M K I+ + +
Sbjct: 322 AERIMSFIRDAAYRASAELAKERGPFPLFDASRYLMLKVIVN---------AKELPDDVL 372
Query: 605 EMISKNGVRNSLLVAPMPTASTSQILGNNECFEPY 639
E I K G+RN+ L PT + S I G + EP
Sbjct: 373 EEIEKYGIRNAHLTTIAPTGTISLIAGTSSGIEPI 407
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 275 bits (705), Expect = 5e-81
Identities = 235/822 (28%), Positives = 359/822 (43%), Gaps = 130/822 (15%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQKVCAGVYKGVTTTQLDELA 60
+ VIK G +P +KI K L + DP + + + G+TT + E+
Sbjct: 4 INVIKSSGVSQPFDLEKI---HKVLEWACEGTGVDPSELEENSKIQLRDGMTTKDIQEIL 60
Query: 61 AETAA-AMTVNHPDYALLAGRVAVSNLHKITKNSFSETIKDMYNYYNKRSGKK--ASLVA 117
++AA ++V PDY +A R+ + L K +Y + S + V
Sbjct: 61 IKSAADLISVEEPDYQYVAARLLMFALRK-----------QVYGQFEPPSFIDHISKCVN 109
Query: 118 DDVY--EIIMKNAA----CLDGAIIYDRDFDFDYFGFKTLERSYLLKMDS--RVVERPQH 169
+ Y EI+ K +A L+ I +DRDF+F Y G L+ YL++ S + E PQ
Sbjct: 110 EGKYDPEILSKYSAEEITYLESFIDHDRDFEFTYAGAMQLKEKYLVQDRSTGEIYETPQF 169
Query: 170 MLMRVSVGIHKDDT-----DSALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMK 224
M +++ +H+D+ + ++ Y+ +S + TP + TP Q SSC ++
Sbjct: 170 AYMLIAMALHQDEPKEDRLEHVIRFYNAVSTRKISLPTPIMAGVRTPTRQFSSCVVI-ES 228
Query: 225 DDSIEGIYDTLKKCAI---ISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFND 281
DS++ I T AI ISK AG IG++ IRA GS I G G++P + F
Sbjct: 229 GDSLDSINKTAM--AIVKYISKRAG-IGINAGMIRAEGSKIRGGEVRHTGVIPFWKHFQT 285
Query: 282 TARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMER 341
+ QGG R GA Y WH ++ + L L+ N+G EE R R L Y + + DL ER
Sbjct: 286 AVKSCSQGG-IRGGAATAYYPIWHLEVEDLLVLKNNKGVEENRIRHLDYGVQINDLMYER 344
Query: 342 VRDDGKWSLFCPSDASG-LADSWGI---EFEHLYSQYEEEGRA-KMVISARKLWFEILNS 396
+ +LF P D G L D++ F LY E++ K I A++L+ +L
Sbjct: 345 FIKNDYITLFSPHDVGGELYDAYFADQDRFRELYEALEKDPSVRKKRIKAQELFLLLLKE 404
Query: 397 QIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSP-------EETAVCNLASI 449
+ ETG Y++F D CN S I+ SNLC EI + P E A+C L++I
Sbjct: 405 RSETGRIYIMFIDHCNNHSP--FKDPIRQSNLCCEIALPTKPLNHIDGEGEIALCTLSAI 462
Query: 450 ALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIET 509
L + + E LAEV L+ ++D YP+
Sbjct: 463 VL----------------------GNFEDQDEIEELAEV---AVRALDNLLDYQDYPVPA 497
Query: 510 TRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKD 569
++ R R +G+G+ A +E A L ++FE + Y+ +KAS +LA +
Sbjct: 498 ALKAKKR-RSLGVGVTNYAHYLAKNFASYEDANA-DLVHELFERLQYYLIKASNKLAKEK 555
Query: 570 GPYETYFGSPMSKGILQVDMWN------ITPSDRWDWSSLREMISKNGVRNSLLVAPMPT 623
G E + + S+G L +D + + P DW SLRE + K G+RNS L A MP
Sbjct: 556 GACEYFSDTKYSRGELPIDWYKKKVDELVAPKYNCDWESLREDLKKYGIRNSTLSALMPC 615
Query: 624 ASTSQILGNNECFEPYTSNIYTRRVLSGEF--IVVNKHLLKDLTELGLWSHALKTKIIYE 681
S+SQ+ + EP + ++ G F +V N LKDL +L LW A K
Sbjct: 616 ESSSQVSNSTNGIEPPRGPVSIKKSKEGPFNQVVPNVETLKDLYDL-LWDLAKK------ 668
Query: 682 NGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHM--EQPDHGKL 739
Y T I QK ++DQ+ S N E +GK+
Sbjct: 669 -------GNKG------YLTQVAIMQK-----------FVDQAISANTSYDPENYPNGKV 704
Query: 740 TS-------LHFYAWSKGMKTGMYYLRTRAAADAIKFTVDTS 774
L+FY + G KT +YY TR + ++T
Sbjct: 705 PMSVMLDDLLYFYYY--GGKT-LYYHNTRDGKGTEDYEIETP 743
>gnl|CDD|236330 PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 752
Score = 261 bits (668), Expect = 9e-76
Identities = 172/568 (30%), Positives = 258/568 (45%), Gaps = 92/568 (16%)
Query: 151 LERSYLLK-MDSRVVERPQHMLMRVSVGIHKDDTDSALKT---------YHLMSQHWFTH 200
LE+ YL K D + +E P+ M RV+ I + K Y LM+ F
Sbjct: 20 LEKRYLKKDEDGKPIETPEDMFRRVARTIAAAELIYDSKADVEALADRFYDLMTSLEFLP 79
Query: 201 ATPTLFNAGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGS 260
+PTL NAG QLS+CF+L + DSIE I+D +K A+I KS GG G S +R
Sbjct: 80 NSPTLMNAGRELGQLSACFVLPV-GDSIEEIFDAVKHAALIHKSGGGTGFSFSRLRPKND 138
Query: 261 YIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGK 320
+ T G ++G V ++VF+ + QGG +R I L H DI EF+ +++ G
Sbjct: 139 RVGSTGGVASGPVSFMRVFDAATEAIKQGGTRRGANMGI-LRVDHPDIMEFITCKEDNG- 196
Query: 321 EECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRA 380
E ++ A+ + FME V D ++ L P G
Sbjct: 197 -ELTNFNISVAI--TEAFMEAVEADEEYDLINPRT----------------------GEV 231
Query: 381 KMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTE--IVEFSSP 438
++AR+++ I+ E G P ++F D NR + +LG I+S+N C E ++ + S
Sbjct: 232 VGRLNAREVFDLIVEMAWENGEPGIVFIDRINRDNPTPHLGEIESTNPCGEQPLLPYES- 290
Query: 439 EETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNK 498
CNL SI L + V+ V D+E+L EV + L+
Sbjct: 291 -----CNLGSINLSKMVKNGDV--------------------DWEKLREVVHLAVRFLDN 325
Query: 499 IIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHA 558
+ID N YP+ +R IG+G+ G AD I LG+P++S EA +L + + + I A
Sbjct: 326 VIDANKYPLPQIEEMTKGNRKIGLGVMGWADMLIQLGIPYDSEEAVELAEKVMKFIQDEA 385
Query: 559 LKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLV 618
AS ELA + GP+ Y GS +D L M RN+ +
Sbjct: 386 HAASRELAEERGPFPNYEGS------------------IYDKDGLGPM------RNATVT 421
Query: 619 APMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIV-VNKHLLKDLTELGLWSHALKTK 677
PT + S I G + EP + +TR V+ GE +V VN E G +S L K
Sbjct: 422 TIAPTGTISIIAGCSSGIEPLFALSFTRNVMDGERLVEVNPVFEAAAKEEGFYSEELMEK 481
Query: 678 IIYENGSVSKISEIPEELKAIYKTVWEI 705
I E GS+ I E+PE+++ ++ T +I
Sbjct: 482 IA-EKGSIQDIDEVPEDVRRVFVTAHDI 508
>gnl|CDD|235796 PRK06406, PRK06406, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 771
Score = 243 bits (622), Expect = 3e-69
Identities = 167/547 (30%), Positives = 260/547 (47%), Gaps = 83/547 (15%)
Query: 188 KTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGG 247
K +MS F +PTL NAGT QLS+CF+L + DSIEGI++ LK A+I KS GG
Sbjct: 222 KFEEVMSNLKFVPNSPTLMNAGTKLGQLSACFVLPV-PDSIEGIFNALKYTAMIHKSGGG 280
Query: 248 IGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHAD 307
G S +R + T G ++G + +++F+ T + QGG KR+GA L H D
Sbjct: 281 TGFSFSRLRPKDDIVASTKGVASGPLSFMRIFDVTTDVIKQGG-KRRGANMGILSYHHPD 339
Query: 308 IFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEF 367
I EF+ + ++ K + ++ V D F +++ +D + L P +
Sbjct: 340 IMEFITSKDSENKV---LSNFNISVAVTDEFFDKLDNDDYYPLRNPRNG----------- 385
Query: 368 EHLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSN 427
+E R I AR++W I+ +TG P ++F D NRK+ +NLG I+S+N
Sbjct: 386 -------KEVKR----IKARQVWDLIITQAWKTGDPGVIFLDEINRKNPVKNLGEIESTN 434
Query: 428 LCTEIVEFSSPEETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAE 487
C E + P E+ CNL SI L ++V +N D++RL E
Sbjct: 435 PCGE--QPLLPYES--CNLGSINLSKFV--------------------ENGKIDWDRLRE 470
Query: 488 VTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLN 547
I T L+ +ID N +P+ + R IG+G+ G AD I LG+P+ S EA ++
Sbjct: 471 TVHIATRFLDNVIDANKFPVPQIKEMTRMTRKIGLGVMGFADMLIKLGIPYNSEEALEIA 530
Query: 548 KDIFETIYYHALKASAELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMI 607
+ + + I + +AS +LA + G + ++GS +W
Sbjct: 531 EKVMKFINEESHRASQKLAEERGVFPAWYGS--------------------EW------- 563
Query: 608 SKNGV--RNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRVLSG-EFIVVNKHLLKDL 664
K G+ RNS PT + S I G + EP + + R VL+G E + VN +
Sbjct: 564 EKKGIKMRNSTTTTIAPTGTISIIAGCSSSIEPLFAIAFVRHVLNGQELLEVNPLFEEIT 623
Query: 665 TELGLWSHALKTKIIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQS 724
+ GL+S L K+ E G++ I ++PE++K I+ T EI + V M A Y D
Sbjct: 624 RKRGLYSEELMRKVA-ETGNLQNI-DVPEDIKRIFVTAHEIDPQWHVLMQATFQRYCDSG 681
Query: 725 QSLNIHM 731
S I++
Sbjct: 682 VSKTINL 688
Score = 32.5 bits (74), Expect = 1.0
Identities = 47/187 (25%), Positives = 65/187 (34%), Gaps = 51/187 (27%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKK--LSYGLSKEHCDPVLVAQKVCAGV--YKGVTTTQL 56
VIKRDG P KI + K LS D + KV + Y+ T Q+
Sbjct: 5 KEVIKRDGTVVPFDKKKIAMAIYKAMLSVKNGSME-DAEELTDKVVERLKKYERPTVEQI 63
Query: 57 DELAAETAAAMTVNHPDYALLAGRVAVSNLHKITKNSFSETIKDMYNYYNKR----SGKK 112
++ + MT KI F++ K Y KR K+
Sbjct: 64 QDIVEKVL--MT------------------KKINGKDFTDVAKSYILYREKRRKIREEKE 103
Query: 113 ASLVADDVYEIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLK-MDSRVVERPQHML 171
V DD+ + NA K LE YLLK D +++E P+ M
Sbjct: 104 LIGVKDDLK--LTLNA-------------------IKVLEARYLLKDEDGKIIETPRQMF 142
Query: 172 MRVSVGI 178
RV+ I
Sbjct: 143 RRVARHI 149
>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 = 230 bits (587), Expect = 2e-66
Identities = 164/626 (26%), Positives = 264/626 (42%), Gaps = 114/626 (18%)
Query: 151 LERSYLLK---MDSRVVERPQHMLMRVSVGIHKDDTDSALKTYHLMSQHWFTHATPTLFN 207
R YLLK ++ RV E + + +++ ++ ATP N
Sbjct: 14 FRRGYLLKGETVEGRVREIASTA------EKLDIRPGFEERFFEYLARGKYSLATPVWAN 67
Query: 208 AGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYIHGTNG 267
G + SC + DS+ I + + +++K+ GG + +IR G+ I TNG
Sbjct: 68 TGLDRGLPISCAGSYV-GDSVLDILEGQAEVGMMAKNGGGTSSYLGDIRPRGADIS-TNG 125
Query: 268 SSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARD 327
+SNG +F++ QG +R G +A Y++ H D E+L ++ E ++
Sbjct: 126 TSNGADGFAPLFDNFINVKTQGATRR-GEWAGYVDFEHPDFEEWLGIQL----ENPASQH 180
Query: 328 LFYALWVPDLFMERVRD-DGKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRAKMVISA 386
+ + + V D + E++ D +
Sbjct: 181 VGWGVEVGDDWYEKMIAGDPEK-------------------------------------- 202
Query: 387 RKLWFEILNSQIETGTPYMLFKDSCNRKSNQ--QNLG-TIKSSNLCTEIVEFSSPEETAV 443
R W +++ S+ TG PYM F+ + N + Q +N G I++SNLCTEI S E+ V
Sbjct: 203 RARWAKLMYSRARTGIPYMWFRWNANELAPQVIKNSGIPIRASNLCTEIALPSDDMESFV 262
Query: 444 CNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVN 503
C L+S+ + Y K V LV DS + +E + K ++
Sbjct: 263 CCLSSLNVLHYDEWKDT---DAVETLVRFLDS---------------VCSEFIAKAKGLS 304
Query: 504 HYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASA 563
+ + R R R IG+G G +PFES EA LN +I++TI A +AS
Sbjct: 305 Y--MHRAVRFAERARAIGLGTLGWHSYLQSNRIPFESGEAHILNAEIYKTIKERAEEASR 362
Query: 564 ELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMPT 623
ELA + +G P + RN+ L+A PT
Sbjct: 363 ELAER-------YGEP-------------------EVCEGTGR------RNATLIAIAPT 390
Query: 624 ASTSQILGN-NECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYEN 682
S++ ILG + EP SN + + G+ + N L K L E G + I Y N
Sbjct: 391 KSSAFILGQVSPSIEPLVSNYFIQDSNKGDVVRKNPVLAKVLKEKGTDQELVWDIITYHN 450
Query: 683 GSVSKISEIPEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLN--IHMEQPDHGKLT 740
GSV + + +E K+++KT +EI Q ++ +AA R +IDQ+QSLN I ++
Sbjct: 451 GSVQHLDFLTDEEKSVFKTFYEISQMAIIRLAAARQKHIDQAQSLNLFISPDEKPSVDAN 510
Query: 741 SLHFYAWSKGMKTGMYYLRTRAAADA 766
L +AW G+K+ +YY R+ A A
Sbjct: 511 VLRAFAWDPGLKS-LYYQRSERGAQA 535
>gnl|CDD|181649 PRK09103, PRK09103, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 758
Score = 229 bits (587), Expect = 2e-64
Identities = 200/668 (29%), Positives = 307/668 (45%), Gaps = 83/668 (12%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQ---KVCAGVYKGVTTTQLD 57
+ V KRDGR E + DKI + + GL V V+Q + Y G+ T+ +
Sbjct: 2 LLVTKRDGRTERINLDKIHRVITWAAEGL-----HNVSVSQVELRSHIQFYDGIKTSDIH 56
Query: 58 ELAAETAAAM-TVNHPDYALLAGRVAVSNLHKITKNSFSETIKDMYNYYNK--RSGK-KA 113
E + AA + + + PDY LA R+A+ +L K F +Y++ K GK
Sbjct: 57 ETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQF--EPPALYDHVVKMVEMGKYDK 114
Query: 114 SLVADDVYEIIMKNAACLDGAIIYDRDFDFDYFGFKTLERSYLLKMDSRVV----ERPQH 169
L+ D E + +D I + RD +F Y K LE YL++ +RV E Q
Sbjct: 115 HLLEDYTEEEFDQ----MDTFIDHWRDMNFSYAAVKQLEGKYLVQ--NRVTGEIYESAQF 168
Query: 170 MLMRVSV---GIHKDDT--DSALKTYHLMSQHWFTHATPTLFNAGTPQPQLSSCFLL-CM 223
+ + V+ + +T D + Y +S + TP + TP Q SSC L+ C
Sbjct: 169 LYILVAACLFSNYPKETRLDYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIEC- 227
Query: 224 KDDSIEGIYDTLKKCAII---SKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFN 280
DS++ I T AI+ S+ AG IG++ IRA GS I G G +P + F
Sbjct: 228 -GDSLDSINAT--SSAIVKYVSQRAG-IGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQ 283
Query: 281 DTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFME 340
+ QGG R GA ++ WH ++ L L+ N+G EE R R + Y + + L +
Sbjct: 284 TAVKSCSQGG-VRGGAATLFYPIWHLEVESLLVLKNNRGVEENRVRHMDYGVQINKLMYQ 342
Query: 341 RVRDDGKWSLFCPSDASGLADSWGI---EFEHLYSQYEEEGRA-KMVISARKLWFEILNS 396
R+ G +LF PSD GL D++ EFE LY++YE++ K + A +L+ ++
Sbjct: 343 RLIKGGDITLFSPSDVPGLYDAFFADQDEFERLYTKYEQDDSIRKKRVKAVELFSLMMQE 402
Query: 397 QIETGTPYMLFKDSCNRKSN-QQNLGTIKSSNLCTEIVEFSSP--------EETAVCNLA 447
+ TG Y+ D CN S + ++ SNLC EI + P E A+C L+
Sbjct: 403 RASTGRIYIQNVDHCNTHSPFDPKVAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLS 462
Query: 448 SIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPI 507
+ L G+ +S L + E LA+ + L+ ++D YPI
Sbjct: 463 AFNL-------------------GAINS---LDELEELAD---LAVRALDALLDYQDYPI 497
Query: 508 ETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAV 567
+R + R +GIG+ A G+ + A L FE I Y+ LKAS ELA
Sbjct: 498 PAAKRGAMGRRTLGIGVINFAYYLAKNGVRYSDGSANNLTHKTFEAIQYYLLKASNELAK 557
Query: 568 KDGPYETYFGSPMSKGILQVDMW-----NITPSD-RWDWSSLREMISKNGVRNSLLVAPM 621
+ G + + ++GIL +D + I +DW +LRE I +G+RNS L A M
Sbjct: 558 EQGACPWFNETTYAQGILPIDTYKKDLDAICNEPLHYDWETLREEIKTHGLRNSTLSALM 617
Query: 622 PTASTSQI 629
P+ ++SQI
Sbjct: 618 PSETSSQI 625
>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 = 208 bits (531), Expect = 2e-57
Identities = 177/674 (26%), Positives = 288/674 (42%), Gaps = 112/674 (16%)
Query: 136 IYDRDFDFDYF--GFKTLERSYLLKMD--SRVVERPQHMLMRVSVGIHKDDTDSALKTYH 191
Y F F F FK SY LK + R +ER + + V++ + D + A +
Sbjct: 78 AYASKFRFPSFMGAFK-FYTSYALKTNDGKRYLERYEDRVCMVALTLANGDEELAKQLVD 136
Query: 192 LMSQHWFTHATPTLFNAGTPQP-QLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGL 250
M + ATPT NAG + +L SCFLL + +D++ I + +SK GG+ L
Sbjct: 137 EMISQRYQPATPTFLNAGRARRGELVSCFLLRV-EDNMNSIGRAINSALQLSKRGGGVAL 195
Query: 251 SIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFE 310
++ N+R +G+ I G S+G++P++++ D Y +Q G +R+GA A+YL +H DI
Sbjct: 196 NLSNLREAGAPIKGIENQSSGVIPVMKLLEDAFSYANQLG-QRQGAGAVYLNAFHPDILR 254
Query: 311 FLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSD-----ASGLADSWGI 365
FLD +K E+ R + L + +PD F E +++ LF P D D I
Sbjct: 255 FLDTKKENADEKIRIKTLSLGVVIPDKFFELAKENKDMYLFSPYDVEREYGVPFDD---I 311
Query: 366 EFEHLYSQYEEEGR-AKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIK 424
+ Y + R K I+AR + + Q E+G PY++F+D+ NR +G IK
Sbjct: 312 DITEKYDEMVANPRIRKKKINARDFFQTLAEIQFESGYPYIMFEDTVNRA--NPIIGRIK 369
Query: 425 SSNLCTEIVEFSSP-------EETAV-----CNLASIALPRYVREKGVPVQSNVSKLVGS 472
SNLC+EI++ S E + CNL S+ +
Sbjct: 370 MSNLCSEILQVSEASLYNDYLEYDEIGHDISCNLGSL------------------NIANV 411
Query: 473 RDSKNRLFDFERLAEVTKIITENLNKIIDVNH-YPIETTRRSNLRHRPIGIGIQGLADTF 531
DS DF R E L + D++H + + R+ N IG+G L
Sbjct: 412 MDSP----DFGRTVETA---IRALTAVSDMSHIRNVPSIRKGNAASHAIGLGQMNLHGYL 464
Query: 532 ILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETYFG-------------- 577
G+ + SPEA F T+ Y++L+ S E+A + G ET+ G
Sbjct: 465 AREGIAYGSPEALDFTNIYFMTVNYYSLRRSMEIARERG--ETFAGFEQSDYASGEYFDK 522
Query: 578 ------SPMSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILG 631
+P ++ + ++ I R DW+ L++ + + G+ + +A PT S S I
Sbjct: 523 YVSQEFAPKTEKVREL-FEGIHIPTREDWAELKDDVMEYGLYHQNRLAVAPTGSISYINH 581
Query: 632 NNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEI 691
+ P S I R+ ++ Y ++
Sbjct: 582 STSSIHPIVSKIEIRK------------------------EGKIGRVYYPAPFLT----- 612
Query: 692 PEELKAIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQPDHGK-LTSLHFYAWSKG 750
E L Y+ ++I + ++D A ++DQ SL + + + L YAW KG
Sbjct: 613 NENL-EYYQDAYDIDMEKIIDTYATATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWHKG 671
Query: 751 MKTGMYYLRTRAAA 764
+KT +YY+R R A
Sbjct: 672 IKT-LYYIRLRQLA 684
>gnl|CDD|236069 PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 699
Score = 188 bits (479), Expect = 2e-50
Identities = 172/709 (24%), Positives = 307/709 (43%), Gaps = 97/709 (13%)
Query: 93 SFSETIKDMYNYYNKRSGKKASLVADDVYEIIMKNAACLD----GAIIYDRDFDF-DYFG 147
+ E IKD +++ + LV +D Y + + D Y F+F Y
Sbjct: 36 VYLEEIKDNTIFFDTEIERLRYLVDNDFYFNVFDIYSEEDLIEVTDYAYSIKFNFASYMS 95
Query: 148 FKTLERSYLLKMD--SRVVERPQHMLMRVSVGIHKDDTDSALKTYHLMSQHWFTHATPTL 205
+ Y LK + + +E + + V++ + D A + M + + ATPT
Sbjct: 96 ASKFYKDYALKTNDKKQYLEDYEDHVAIVALYLANGDKAKAKQFISAMVEQRYQPATPTF 155
Query: 206 FNAGTPQP-QLSSCFLLCMKD--DSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASGSYI 262
NAG + +L SCFLL + D +SI I T K+ +SK GG+ +++ +RA G I
Sbjct: 156 LNAGRARRGELVSCFLLEVDDSLNSINFIDSTAKQ---LSKIGGGVAINLSKLRARGEAI 212
Query: 263 HGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQGKEE 322
G G++ G++P+ ++ Y DQ G +R GA A+YL +H D+ EFLD +K E+
Sbjct: 213 KGIKGAAKGVLPVAKLLEGGFSYADQLG-QRPGAGAVYLNIFHYDVEEFLDTKKVNADED 271
Query: 323 CRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWG-----IEFEHLYSQYEEE 377
R + L VP F E ++ + +F P + +G I+ E +Y
Sbjct: 272 LRLSTISTGLIVPSKFFELAKEGKDFYMFAPHT---VYKEYGVTLDDIDLEEMYDDLVAN 328
Query: 378 GRA-KMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFS 436
K +AR++ +I +Q+++G PY++FKD+ N+ N+G IK SNLCTEI +
Sbjct: 329 PNVKKKKKNAREMLNKIAQTQLQSGYPYLMFKDNANKVHPNSNIGQIKMSNLCTEIFQLQ 388
Query: 437 SPEETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENL 496
ET++ N Y E ++ ++S +GS + N + + ++ + + L
Sbjct: 389 ---ETSIIN-------DYGIED--EIKRDISCNLGSLNIVN-VMESKKFRDSVHSGMDAL 435
Query: 497 NKIIDVNHYP-IETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIY 555
+ DV + R++N +G+G+ L + +ES EA+ F +
Sbjct: 436 TVVSDVANIQNAPGVRKANSELHSVGLGVMNLHGYLAKNKIGYESEEAKDFANTFFMMMN 495
Query: 556 YHALKASAELAVKDGP----YE-------TYFG-------SPMSKGILQV-DMWNITPSD 596
+++++ S E+A + G +E YF P + + ++ + +I +
Sbjct: 496 FYSIERSMEIAKERGETYQDFEKSDYANGKYFEKYTTQDFEPKFEKVRELFEGMHIPTKE 555
Query: 597 RWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVV 656
DW L++ + + G+ ++ +A PT S S + P I R + E
Sbjct: 556 --DWKKLQQDVEQYGLYHAYRLAIAPTQSISYVQNATSSVMPIVDQIERRTYGNAE---- 609
Query: 657 NKHLLKDLTELGLWSHALKTKIIYENGSVSKISEIPEELKAIYKTVWEIKQKTLVDMAAD 716
+ + L+ +W YK+ + Q L+D+ A
Sbjct: 610 TFYPMPFLSPQTMW---------------------------YYKSAFNTDQMKLIDLIAT 642
Query: 717 RGCYIDQSQS----LNIHMEQPDHGKLTSLHFYAWSKGMKTGMYYLRTR 761
+IDQ S +N + + L L+ YA KG+K+ +YY R +
Sbjct: 643 IQTHIDQGISTILYVNSEISTRE---LARLYVYAHHKGLKS-LYYTRNK 687
>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 721
Score = 181 bits (460), Expect = 9e-48
Identities = 160/630 (25%), Positives = 274/630 (43%), Gaps = 117/630 (18%)
Query: 182 DTDSALKTYHLMSQHWFTHATPTLFNAGTPQP-QLSSCFLLCMKDDSIEGIYDTLKKCAI 240
D A + F ATPT NAG + + SC+LL + +D++E I +
Sbjct: 133 DFTKAFDLLDQILLGRFQPATPTFLNAGKKRRGEYISCYLLRV-EDNMESISRAISTSLQ 191
Query: 241 ISKSAGGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIY 300
+SK GG+ L + N+R G+ I G + GI+P++++ D+ Y +Q G +R+GA A+Y
Sbjct: 192 LSKRGGGVALCLTNLREIGAPIKGIENQATGIIPVMKLLEDSFSYANQLG-QRQGAGAVY 250
Query: 301 LEPWHADIFEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLA 360
L H D+ FLD ++ E+ R + L L +PD+ E +++ +LF P D +
Sbjct: 251 LHAHHPDVLTFLDTKRENADEKIRIKSLSLGLVIPDITFELAKENKDMALFSPYD---IK 307
Query: 361 DSWGIEF------EHLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRK 414
+G E Y+ K ISARKL+ I E+G PY+LF D+ N++
Sbjct: 308 REYGKPMSDISITEEYYNLLANPAIKKTYISARKLFQTIAELHFESGYPYLLFDDTVNKR 367
Query: 415 SNQQNLGTIKSSNLCTEIVEFSSPE------------ETAVCNLASIALPRYVREKGVPV 462
+ G I SNLC+EI + S+P E CNL S+
Sbjct: 368 NPHAKKGRIVMSNLCSEIAQVSTPSTFNEDLSFKKIGEDICCNLGSL------------- 414
Query: 463 QSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGI 522
N++K + S +FE+L + + ++++ D++ P + + N + +G+
Sbjct: 415 --NIAKAMESGP------EFEQLIYTSIRALDRVSRVSDLSCAP--SIEKGNAANHAVGL 464
Query: 523 G---IQG-LADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYE----- 573
G + G LA I ++S EA F T+ Y+A KAS +LA + G +
Sbjct: 465 GAMNLHGFLATNHIY----YDSKEAVDFTDLFFYTMAYYAFKASNQLAKEKGAFAGFELS 520
Query: 574 -----TYF----------GSPMSKGILQV-DMWNITPSDRWDWSSLREMISKNGVRNSLL 617
+YF +P + + ++ + +T + DW L E I K G+ NS L
Sbjct: 521 KYADGSYFDKYTKEDAKKWTPKTAKVKELLQKYGVTIPTQADWQELVEDIKKTGLANSHL 580
Query: 618 VAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTK 677
+A PT S S + +P + + R+
Sbjct: 581 LAVAPTGSISYLSSCTPSLQPVVAPVEVRK------------------------------ 610
Query: 678 IIYENGSVSKI----SEIPEELKAIYKT-VWEIKQKTLVDMAADRGCYIDQSQSLNIHM- 731
G + +I +I ++ A Y+ +E+ K ++D+ A ++DQ+ SL + M
Sbjct: 611 ----EGKLGRIYVPAYKIDQDNYAYYERGAYEVGPKPIIDIVAAAQKHVDQAISLTLFMT 666
Query: 732 EQPDHGKLTSLHFYAWSKGMKTGMYYLRTR 761
+Q L + A+ + + +YY+R R
Sbjct: 667 DQATTRDLNKAYIQAFKQKCAS-IYYVRVR 695
>gnl|CDD|236179 PRK08188, PRK08188, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 714
Score = 176 bits (449), Expect = 2e-46
Identities = 187/692 (27%), Positives = 286/692 (41%), Gaps = 148/692 (21%)
Query: 137 YDRDFDFDYF--GFKTLERSYLLKM--DSRVVERPQHMLMRVSVGIHKDDTDSALKTYHL 192
Y + F F F FK SY LK R +ER + + V++ + + D A +
Sbjct: 93 YAKKFRFQTFLGAFK-YYTSYTLKTFDGKRYLERFEDRVCMVALTLAQGDETLARQLVDE 151
Query: 193 MSQHWFTHATPTLFNAGTPQP-QLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLS 251
+ F ATPT N G Q +L SCFLL + +D++E I ++ +SK GG+ L
Sbjct: 152 IISGRFQPATPTFLNCGKKQRGELVSCFLLRI-EDNMESIGRSINSALQLSKRGGGVALL 210
Query: 252 IHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEF 311
+ N+R +G+ I S+G++P++++ D Y +Q G R+GA A+YL H DI F
Sbjct: 211 LSNLREAGAPIKRIENQSSGVIPVMKLLEDAFSYANQLGA-RQGAGAVYLHAHHPDILRF 269
Query: 312 LDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEF---- 367
LD ++ E+ R + L + +PD+ E +++ LF P D + +G F
Sbjct: 270 LDTKRENADEKIRIKTLSLGVVIPDITFELAKENEDMYLFSPYDVERV---YGKPFADIS 326
Query: 368 --EHLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKS 425
E +E K I+AR+ + + Q E+G PY++F+D+ NR + G I
Sbjct: 327 VTEKYDEMVADERIRKKKINAREFFQTLAEIQFESGYPYIMFEDTVNRANPIA--GRINM 384
Query: 426 SNLCTEIVEFSSPEETA------------VCNLASIALPRYVREKGVPVQSNVSKLVGSR 473
SNLC+EI++ +S E CNL S+ N++ + S
Sbjct: 385 SNLCSEILQVNSASEYNEDLSYAHIGKDISCNLGSL---------------NIAHTMDSP 429
Query: 474 DSKNRLFDFERLAEVTKIITENLNKIIDVNH-YPIETTRRSNLRHRPIGIGIQGLADTFI 532
DF R E L + D++H + + + N IG+G L
Sbjct: 430 -------DFGRTVETA---IRALTAVSDMSHIRSVPSIEKGNAASHAIGLGQMNLHGYLA 479
Query: 533 LLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETYF-------GSPMSKGIL 585
G+ + S EA F T+ YHAL+AS LA + G F G K
Sbjct: 480 REGIFYGSEEALDFTNIYFYTVTYHALRASNLLARERGETFAGFEQSKYASGEYFDKYTQ 539
Query: 586 QVDMW--------------NITPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILG 631
Q W IT + DW+ LR+ + ++G+ N L A PT S S I
Sbjct: 540 QD--WQPKTAKVRELFARAGITIPTQEDWAQLRDDVMRHGIYNQNLQAVPPTGSISYI-- 595
Query: 632 NNECFEPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEI 691
N+ TS+I H + VSKI EI
Sbjct: 596 NHS-----TSSI----------------------------HPI----------VSKI-EI 611
Query: 692 PEELK----------------AIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHMEQPD 735
+E K Y+ +EI + ++D A ++DQ SL + PD
Sbjct: 612 RKEGKIGRVYYPAPYMTNDNLEYYQDAYEIGPEKIIDTYAAATQHVDQGLSLTLFF--PD 669
Query: 736 HGK---LTSLHFYAWSKGMKTGMYYLRTRAAA 764
+ YAW KG+KT +YY+R R A
Sbjct: 670 TATTRDINKAQIYAWRKGIKT-LYYIRLRQMA 700
>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 720
Score = 166 bits (421), Expect = 1e-42
Identities = 163/619 (26%), Positives = 273/619 (44%), Gaps = 129/619 (20%)
Query: 201 ATPTLFNAG-TPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGGIGLSIHNIRASG 259
ATP+ NAG + +L SCFL+ + DD + I ++ +S+ GG+G+++ N+R +G
Sbjct: 154 ATPSFLNAGRARRGELVSCFLIQVTDD-MNSIGRSINSALQLSRIGGGVGINLSNLREAG 212
Query: 260 SYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADIFEFLDLRKNQG 319
+ I G G+++G+VP++++F D+ Y +Q G +R+GA +YL +H DI FL +K
Sbjct: 213 APIKGYEGAASGVVPVMKLFEDSFSYSNQLG-QRQGAGVVYLNVFHPDIIAFLSTKKENA 271
Query: 320 KEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEH--LYSQYEE- 376
E+ R + L + VPD F E R + LF P + +G+ F + + +Y+E
Sbjct: 272 DEKVRVKTLSLGVTVPDKFYELARKNEDMYLFSPYS---VEKEYGVPFNYVDITKEYDEL 328
Query: 377 ---EGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIV 433
K I AR L EI Q E+G PY++ D+ NR +N + G I SNLC+EI+
Sbjct: 329 VANPNIRKTKIKARDLETEISKLQQESGYPYIINIDTANR-ANPID-GKIIMSNLCSEIL 386
Query: 434 EFSSPEE-----------TAV-CNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFD 481
+ +P T + CNL S N+ ++ S D
Sbjct: 387 QVQTPSLINDAQEYVKMGTDISCNLGST---------------NIVNMMTSP-------D 424
Query: 482 FERLAEVTKIITENLNKIIDVNHYP-IETTRRSNLRHRPIGIGIQGLADTFILLGLPFES 540
F R E + L + D ++ + + + N + IG+G GL + + S
Sbjct: 425 FGRSIET---MVRALTFVTDSSNIDAVPSIKHGNSQAHTIGLGAMGLHSYLAQNHIEYGS 481
Query: 541 PEAQQLNKDIFETIYYHALKASAELAVK--------------DGPY-----ETYFG--SP 579
PE+ + F + Y L AS +A + DG Y F S
Sbjct: 482 PESLEFTSIYFMLLNYWTLVASNNIARERGETFHNFEKSKYADGSYFDKYVTGDFVPKSD 541
Query: 580 MSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNNEC---F 636
K + + ++ T + DW++LR+ + K+G+ + +A P S S I N+
Sbjct: 542 KVKELFK-GIFIPTAA---DWAALRDAVMKDGLYHQNRLAVAPNGSISYI---NDTSASI 594
Query: 637 EPYTSNIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEIPEELK 696
P T I R+ ++G KI Y +S IP
Sbjct: 595 HPITQRIEERQE----------------KKIG--------KIYYPAPGLST-ETIP---- 625
Query: 697 AIYKTVWEIKQKTLVDMAADRGCYIDQSQSLNIHM--EQPDH--------GKLTS----- 741
Y + +++ + ++D+ A ++DQ SL + M P K+T+
Sbjct: 626 -YYTSAYDMDMRKVIDVYAAATEHVDQGLSLTLFMRSTLPKGLYEWKDRTNKMTTRDLSI 684
Query: 742 LHFYAWSKGMKTGMYYLRT 760
L YA++KG+K+ +YY+RT
Sbjct: 685 LRNYAFNKGIKS-IYYIRT 702
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 140 bits (354), Expect = 6e-34
Identities = 111/390 (28%), Positives = 178/390 (45%), Gaps = 60/390 (15%)
Query: 374 YEEEGRAKMVIS--ARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTE 431
Y EG ++VI+ +RKL+ E + + Y + K S + + + T++S + E
Sbjct: 1219 YRAEGYYELVIANYSRKLFAEKIGFE-----GYKMEKLSLQKTKIDEPIVTVESVEVLGE 1273
Query: 432 --IVEFSSPE--------------------ETAVCNLASIALPRYVR--EKGVPVQSNVS 467
+ +F+ PE E CNLASI L ++V+ E G P
Sbjct: 1274 EIVYDFTVPEHHSYISNGFMSHNCGEEPLYEYESCNLASINLAKFVKYDENGKP------ 1327
Query: 468 KLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGL 527
FD++ A V + + + L+ IDVN +P+ + R IG+G+ GL
Sbjct: 1328 -----------YFDWDEYAYVIQKVAKYLDNAIDVNKFPLPEIDYNTKLTRRIGVGMMGL 1376
Query: 528 ADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETYFGSPMSKGILQV 587
AD LG+P+ S E + + + E + ++A K S E A K G + Y + KG L V
Sbjct: 1377 ADALFKLGIPYNSEEGFKFMRKVTEYLTFYAYKYSVEAAKKRGTFPLYEKTEYPKGELPV 1436
Query: 588 ------DMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTS 641
++WN+ W L E I K GVRN+++ PT S S I + EP +
Sbjct: 1437 EGFYHPEIWNLP------WDKLVEEIKKYGVRNAMVTTCPPTGSVSMIADTSSGIEPIFA 1490
Query: 642 NIYTRRVLSGEFIVVNKHLLKDLTELGLWSHALKTKIIYENGSVSKISEIPEELKAIYKT 701
+Y + V GEF V+ +L + GL+S L KI GSV + EIPE+++ ++ T
Sbjct: 1491 LVYKKSVTVGEFYYVDPVFEAELKKRGLYSEELLKKISDNYGSVQGLEEIPEDMQRVFVT 1550
Query: 702 VWEIKQKTLVDMAADRGCYIDQSQSLNIHM 731
+I + A+ ++ S S I+M
Sbjct: 1551 ALDIHWLDHILAQANIQMWLTDSASKTINM 1580
Score = 45.1 bits (106), Expect = 2e-04
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 190 YHLMSQHWFTHATPTLFNAGTPQPQLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGG 247
+ LM+ F TP L N+G P LS+CF++ ++DD +E I A+I K+ GG
Sbjct: 245 FRLMTNQIFMPNTPALINSGRPLGMLSACFVVPIEDD-MESIMKAAHDVAMIQKAGGG 301
Score = 45.1 bits (106), Expect = 2e-04
Identities = 30/106 (28%), Positives = 53/106 (50%), Gaps = 4/106 (3%)
Query: 249 GLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHADI 308
GL+ +R G + T G+++G V + + + + + QGG R+GA LE WH DI
Sbjct: 757 GLNFSKLRPEGDIVGTTTGAASGPVSFMHLIDAVSDVIKQGG-VRRGANMGILEIWHPDI 815
Query: 309 FEFLDLR-KNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCP 353
+F+ + KN G ++ +W + F E +++ K+ L P
Sbjct: 816 EKFIHAKEKNIGTNVLSNFNISVGIW--EDFWEALKEGKKYPLINP 859
>gnl|CDD|180772 PRK06948, PRK06948, ribonucleotide reductase-like protein;
Provisional.
Length = 595
Score = 136 bits (345), Expect = 1e-33
Identities = 109/422 (25%), Positives = 179/422 (42%), Gaps = 69/422 (16%)
Query: 246 GGIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWH 305
GGIG I + + + S G+ L F+ + G+R A+ L H
Sbjct: 121 GGIGYDFSAIPPADARPDADHPDSPGVCAALDRFDRICAALPFRDGRRGAQMAV-LRCDH 179
Query: 306 ADIFEFLDLRKNQGKEECRAR--DLFYALWVPDLFMERVRDDGKWSLF---CPSDASGLA 360
D+ F+ ++ RAR ++ V D FM+ V D W+L P A+G A
Sbjct: 180 PDLLAFVAAKRG------RARWTTFNLSVAVTDAFMQAVAQDLPWALRHRAPPRRAAGGA 233
Query: 361 DSWGIEFEHLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNL 420
G + Y+ + AR LW EI+++ ++ P +LF D+ + + +
Sbjct: 234 LR-GADGAWTYA----------TVPARHLWREIVSAARDSAEPGLLFVDTIDAANPLREH 282
Query: 421 GTIKSSNLCTE--IVEFSSPEETAVCNLASIALPRYVREK-GVPVQSNVSKLVGSRDSKN 477
I ++N C E + + S C L I L R+VR GV +
Sbjct: 283 ERIDATNPCGEQPLPPYGS------CVLGPIDLSRFVRHPFGV-------------GGEP 323
Query: 478 RLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLP 537
R FDF LA +I L+ +D+ +P+ R + R IG+G+ GLAD ++ L
Sbjct: 324 R-FDFAALATAVRIQVRMLDNALDLTRWPLAAHAREARQKRRIGVGVTGLADALTMMRLR 382
Query: 538 FESPEAQQLNKDIFETIYYHALKASAELAVKDGPY-----ETYFGSPMSKGILQVDMWNI 592
++SP A+++ + I + +HA ASA LA + G Y + + + L
Sbjct: 383 YDSPAAREMARYIASDLRHHAYAASAALAAERGAYPLCDPAAHLDALRAGPPLPH----- 437
Query: 593 TPSDRWDWSSLREMISKNGVRNSLLVAPMPTASTSQILGNNEC---FEPYTSNIYTRRVL 649
++ I+++G+RNS L++ P S S G+N C EP + I R V
Sbjct: 438 ---------AVCHAIARHGLRNSHLLSFAPVGSVSLAFGDN-CSPGIEPARAWIEHRPVR 487
Query: 650 SG 651
+G
Sbjct: 488 AG 489
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 136 bits (344), Expect = 7e-33
Identities = 107/410 (26%), Positives = 179/410 (43%), Gaps = 74/410 (18%)
Query: 189 TYHLMSQHWFTHATPTLFNAGTPQP-QLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAGG 247
T+ L+ Q F+ +P FN GT P Q+S+CF+L + DDS+E I + K+ ++ K G
Sbjct: 123 TWLLLHQK-FSFNSPVWFNVGTESPQQVSACFILSV-DDSMESILNWYKEEGMLFKGGSG 180
Query: 248 IGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHAD 307
G ++ IR+S + G G+++G V ++ + +A + GG R+ A + L+ H D
Sbjct: 181 TGTNLSRIRSSKELLSG-GGTASGPVSFMRGADASAGTIKSGGATRRAAKMVILDVDHPD 239
Query: 308 IFEFLDLRKNQGKEECRARDL-----------------FY-----ALWVPDLFMERVRDD 345
I EF++ + KEE + R L Y ++ V D FM V +D
Sbjct: 240 IEEFIETK---AKEEDKIRALRDAGYDMDLGGEAYSSVQYQNANNSVRVSDEFMRAVEND 296
Query: 346 GKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYM 405
G++ L D IE + A++L+ +I + E P +
Sbjct: 297 GEFGL------RARTDGEVIE----------------TVDAKELFRKIAEAAWECADPGI 334
Query: 406 LFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAVCNLASIALPRYVREKGVPVQSN 465
+ D+ N G I +SN C+ E+ + ++ CNLAS+ L +++R+ G
Sbjct: 335 QYDDTINDWHTCPESGRINASNPCS---EYMFLDNSS-CNLASLNLMKFLRDDG------ 384
Query: 466 VSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQ 525
FD E +++ + I +P E R+ R +G+G
Sbjct: 385 -------------TFDVESFRHAVELVITAMEISICFADFPTEKIARNTRAFRQLGLGYA 431
Query: 526 GLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYETY 575
L + GLP++S + L I + A + SAELA GP+E Y
Sbjct: 432 NLGALLMATGLPYDSDGGRALAAAITSLMTGEAYRRSAELAGVVGPFEGY 481
>gnl|CDD|215855 pfam00317, Ribonuc_red_lgN, Ribonucleotide reductase, all-alpha
domain.
Length = 79
Score = 94.6 bits (236), Expect = 1e-23
Identities = 33/79 (41%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 141 FDFDYFGFKTLERSYLLKM-DSRVVERPQHMLMRVSVGIH-----KDDTDSALKTYHLMS 194
Y K LE YLLK D V+E PQ M MRV++ + +D + A + Y L+S
Sbjct: 1 RFLTYLAAKVLEDRYLLKDEDGEVLETPQDMFMRVALALAGAEPPEDRLELAEEFYDLLS 60
Query: 195 QHWFTHATPTLFNAGTPQP 213
F ATPTL NAGTP
Sbjct: 61 SLKFLPATPTLMNAGTPLG 79
>gnl|CDD|236152 PRK08115, PRK08115, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 858
Score = 106 bits (266), Expect = 1e-23
Identities = 83/303 (27%), Positives = 131/303 (43%), Gaps = 42/303 (13%)
Query: 373 QYEEEG---RAKMVISARKLWFEILNSQIETGTPYMLFKDSCNRKSNQQNLG-TIKSSNL 428
++E+ G R I A++LW I + P + F D+ N +N + G + ++N
Sbjct: 419 EWEKMGYPVRTYRKIKAKELWNLINICATYSAEPGIFFIDNANEMTNAKAYGQKVVATNP 478
Query: 429 CTE--IVEFSSPEETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLA 486
C E + +S VCNLA+I L D + + D+E+L
Sbjct: 479 CGEQPLAPYS------VCNLAAINLANMA------------------DKETKTVDYEKLK 514
Query: 487 EVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQL 546
++ + +ID Y +E ++ L R +G+G+ GL D I + S E QL
Sbjct: 515 RTVEVGVRMQDNVIDATPYFLEENKKQALGERRVGLGVMGLHDLLIYCETVYGSEEGNQL 574
Query: 547 NKDIFETIYYHALKASAELAVKDGPYETYFGSP------MSKGILQVDMWNITPSDRWDW 600
IFETI A + S ELA + G + G + + + P D
Sbjct: 575 VDQIFETIATTAYRTSIELAKEKGSFPFLVGQTEEETAKLREAFINTGYMKKMPED---- 630
Query: 601 SSLREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYTRRVLSGEFIVVNKHL 660
+RE I K G+RNS L+ PT ST ++G + EPY S Y R G+FI V +
Sbjct: 631 --IREDILKYGIRNSHLLTVAPTGSTGTMVGVSTGLEPYFSFSYYRSGRLGKFIEVKADI 688
Query: 661 LKD 663
+++
Sbjct: 689 VQE 691
Score = 59.5 bits (144), Expect = 5e-09
Identities = 41/126 (32%), Positives = 58/126 (46%), Gaps = 2/126 (1%)
Query: 188 KTYHLMSQHWFTHATPTLFNAGTPQP-QLSSCFLLCMKDDSIEGIYDTLKKCAIISKSAG 246
K Y + F A L+ AG+ +C+++ DS EGI + K+ I G
Sbjct: 158 KFYQELVNMNFVPAGRVLYGAGSKTDVTYFNCYVMPFVKDSREGISEHRKQVMEIMSRGG 217
Query: 247 GIGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIYLEPWHA 306
G+G + +R + G NG S+G V L V+Q GG R+GA I L WH
Sbjct: 218 GVGTNGSTLRPRNTLARGVNGKSSGSVSWLDDIAKLTHLVEQ-GGSRRGAQMIMLADWHP 276
Query: 307 DIFEFL 312
DI EF+
Sbjct: 277 DILEFI 282
>gnl|CDD|217585 pfam03477, ATP-cone, ATP cone domain.
Length = 88
Score = 72.3 bits (178), Expect = 1e-15
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 7/92 (7%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKKLSYGLSKE-HCDPVLVAQKVCAGVYKG--VTTTQLD 57
M VIKRDGR+EP +KI ++K + L +A++V + G ++T ++
Sbjct: 1 MKVIKRDGRREPFDREKIRRAIEKAARALRPVDPEQAEEIAEEVEEELRDGGEISTEEIQ 60
Query: 58 ELAAETAAAMTVNHPDYALLAGRVAVSNLHKI 89
+L +T HPDYA+ + NL K
Sbjct: 61 DLVEKTLME----HPDYAVARAYILYRNLRKE 88
>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 = 54.8 bits (132), Expect = 9e-08
Identities = 46/190 (24%), Positives = 70/190 (36%), Gaps = 21/190 (11%)
Query: 444 CNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVN 503
CNL S+ L R + EK + +V E L E+ + L+ +ID +
Sbjct: 200 CNLVSLNLARIM-EKAINGSMDVVL--------------EELEELAFLAVRALDCVIDSH 244
Query: 504 HYPIETTRRSNLRHRPIGIGIQGLADTFILLGLPF-ESPEAQQLNKDIFETIYYHALKAS 562
I T R +G+GI G+AD I LGL PEA L ++ + + H +KA+
Sbjct: 245 DERIPTIELGGDERRTVGLGIAGVADLLIKLGLEKVGDPEADDLAAELVDQLKKHLVKAT 304
Query: 563 AELAVKDGPYETYFGSPMSKGILQVDMWNITPSDRWDWSSLREMISKNGVRNSLLVAPMP 622
E + S S + +PS L I S VA +
Sbjct: 305 NERGFNFLLGLSPSESNSSGAPATNGV---SPSRGXIAIVLNGDIGPEESLAS--VAILQ 359
Query: 623 TASTSQILGN 632
+ + I
Sbjct: 360 FYADNGISDT 369
Score = 34.4 bits (79), Expect = 0.25
Identities = 29/140 (20%), Positives = 45/140 (32%), Gaps = 23/140 (16%)
Query: 205 LFNAGTPQPQLSSCF---LLCMKDDSIEGIYDTLKKC-----------AIISKSAGGIGL 250
+ G P + C D I+G+ +T K A+ + + G G+
Sbjct: 12 VITVGRPDLPFTGCVLVDYGDSLDPGIKGVNETAKSINEAIQKTYQIIALAASNQNGGGV 71
Query: 251 SIHN----IRASGSYIHG-TNGSSNGIVPMLQVFNDTARYVDQGGGKRKGAFAIY----L 301
S + GS + +G+ V FN + V QG G+ A
Sbjct: 72 SFARASSILSPYGSRDYAKGSGTETDAVEAADAFNLALKEVGQGNGRTGAATGFIGGVHK 131
Query: 302 EPWHADIFEFLDLRKNQGKE 321
EFL+L G E
Sbjct: 132 GKGDKISQEFLNLALANGGE 151
>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1220
Score = 51.1 bits (123), Expect = 2e-06
Identities = 55/242 (22%), Positives = 97/242 (40%), Gaps = 44/242 (18%)
Query: 334 VPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRAKMVISARKLWFEI 393
V D F+ V +DG W+L +D G+ + AR LW +I
Sbjct: 403 VTDEFLRAVENDGDWNLTARTD----------------------GKVAKTLKARDLWEKI 440
Query: 394 LNSQIETGTPYMLFKDSCNRKSNQQNLGTIKSSNLCTEIVEFSSPEETAVCNLASIALPR 453
+ + P + F + N G I++SN C+E + ++TA CNLAS+ L
Sbjct: 441 GYAAWASADPGLQFNTTINDWHTCPASGPIRASNPCSEYMFL---DDTA-CNLASLNLLT 496
Query: 454 YVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNHYPIETTRRS 513
+ RD + FD E ++ T L + + +P +
Sbjct: 497 F------------------RDEDTKRFDVEAYEHACRLWTVVLEISVLMAQFPSKEIAEL 538
Query: 514 NLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAELAVKDGPYE 573
+ R +G+G + + +G+P++S E + + + + A SAE+A + GP+
Sbjct: 539 SYEFRTLGLGYANIGGLLMTMGIPYDSDEGRAICGALSAIMTGVAYATSAEMAKELGPFP 598
Query: 574 TY 575
Y
Sbjct: 599 GY 600
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 39.9 bits (94), Expect = 0.005
Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 1/84 (1%)
Query: 482 FERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLGLP-FES 540
FE L + + ++I P L + + IGI GL + LG E
Sbjct: 301 FEELDRYDLAKRKLIEELIAAGLLPFYKQYLWRLDNHFLTIGINGLNEALANLGGTDIED 360
Query: 541 PEAQQLNKDIFETIYYHALKASAE 564
E ++ + + I A +A E
Sbjct: 361 EEGKKFGLRVLDFIREKAREAQEE 384
>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 = 32.1 bits (73), Expect = 1.2
Identities = 62/364 (17%), Positives = 117/364 (32%), Gaps = 87/364 (23%)
Query: 225 DDSIEGIYDTLKKCAIISKSAGG--IGLSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDT 282
DS EG +++ + + +IR +G + G G ++G P+ ++
Sbjct: 169 PDSREGWVKSVQLL-LDLYFNPAQTLIFDYSDIRPAGERLKGFGGIASGPEPLKKLHKAI 227
Query: 283 ARYVDQGGGKRKGAFAIYLEPWHADIFEFL-------DLRKN----QGKEECRA-RDLFY 330
A ++ GK + I D+ + ++R++ G+ E DL
Sbjct: 228 AAILNDRSGKPLTSVDI------VDLMNLIGVCVVSGNVRRSAEIAFGQPEDEDFADLKQ 281
Query: 331 ALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFEHLYSQYEEEGRAKMVISARKLW 390
W P R + W+ S+ S + +S + + L +
Sbjct: 282 YQWNPG------RREHGWA----SNNSVVFES---KPDRLEYSF---------------- 312
Query: 391 FEILNSQIETGTPYMLFKDSCNRKSNQQNL------GTIKSSNLCTEIVEFSSPEETAVC 444
G P + + D+ + L K N C EI S E +C
Sbjct: 313 --ACMLIRGNGEPGIAWLDNMKAYARMVLLTTPYHDLRAKGGNPCGEI----SLESYELC 366
Query: 445 NLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFDFERLAEVTKIITENLNKIIDVNH 504
NL + K + L D + + K + +
Sbjct: 367 NLVEV---------------FPLKH------EGDLEDLQETLYLAGR----YAKTVTLLP 401
Query: 505 YPIETTRRSNLRHRPIGIGIQGLADTFILLGLPFESPEAQQLNKDIFETIYYHALKASAE 564
E T LR+R IG+ + G+AD + G + ++ +E +Y + + S
Sbjct: 402 LHWEITNEIILRNRRIGVSMSGIADFIVRAGGDLTLHDLKRWRNIGYEAVYQYDERLSKW 461
Query: 565 LAVK 568
L +
Sbjct: 462 LGIP 465
>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 = 32.2 bits (73), Expect = 1.3
Identities = 50/294 (17%), Positives = 93/294 (31%), Gaps = 67/294 (22%)
Query: 250 LSIHNIRASGSYIHGTNGSSNGIVPMLQVFNDTARYV-DQGGGKRKGAFAIYLEPWHADI 308
L + +IR +G+ + G G+++G VP+ ++ D A + ++ GG+ A +
Sbjct: 212 LDLSDIRPAGAELKGFGGTASGPVPLAKMLTDVAEILSNKAGGRLTAVDAADICNLIGKA 271
Query: 309 FEFLDLRKNQGKEECRARDLFYALWVPDLFMERVRDDGKWSLFCPSDASGLADSWGIEFE 368
++R++ LF DD ++ +S+ E
Sbjct: 272 VVAGNVRRSAEMA------LFSN------------DDPEF------------ESFKQAKE 301
Query: 369 HLYSQYEEEGRAKMVISARKLWFEILNSQIETGTPYMLFKDSC-------NRKSNQQNLG 421
L + V SA +E G P + D N + G
Sbjct: 302 KLMHHRWASNNSVAVDSAFSGLARSAADILENGEPGQVNLDLSKSEGRIVNGRYQAGEDG 361
Query: 422 TIKSSNLCTEIVEFSSPEETAVCNLASIALPRYVREKGVPVQSNVSKLVGSRDSKNRLFD 481
++ +N C EI CNL + N+
Sbjct: 362 DVEGTNPCGEI----LLANGEPCNLFEV---------------NLLAFEEDGWG------ 396
Query: 482 FERLAEVTKIITENLNKIIDVNHYPIETTRRSNLRHRPIGIGIQGLADTFILLG 535
L + ++ Y E +R ++R IG+ + G+ D +L G
Sbjct: 397 ---LQRAFALAARYAKRVTFSP-YDDEISREIIQKNRRIGVSMSGIQDFLLLRG 446
>gnl|CDD|236436 PRK09263, PRK09263, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 711
Score = 32.2 bits (74), Expect = 1.3
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVL-VAQKVCAGV--YKGVTTTQL 56
VIKRDGRK P +KI ++K + + + D VA ++ + V V ++
Sbjct: 3 PKVIKRDGRKVPFDSEKIKNAIEKAAKAVEVDDEDYCATVAAEIASRVEGRDEVDIEEI 61
>gnl|CDD|222008 pfam13252, DUF4043, Protein of unknown function (DUF4043). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 369 and
424 amino acids in length. There is a single completely
conserved residue G that may be functionally important.
Length = 342
Score = 30.4 bits (69), Expect = 3.8
Identities = 12/65 (18%), Positives = 22/65 (33%)
Query: 56 LDELAAETAAAMTVNHPDYALLAGRVAVSNLHKITKNSFSETIKDMYNYYNKRSGKKASL 115
LD+L A ++ D+ + I N S D + + KA++
Sbjct: 94 LDQLFFVHLAGARGDNEDFDWVVPLAEDPKFDGIAVNDVSAPTADRHFRGGDATSDKANI 153
Query: 116 VADDV 120
+ D
Sbjct: 154 DSTDK 158
>gnl|CDD|235937 PRK07111, PRK07111, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 735
Score = 30.7 bits (70), Expect = 4.2
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 2 YVIKRDGRKEPVRFDKITARLKK 24
Y++KRDGR+ P +KIT + K
Sbjct: 4 YIVKRDGREVPFDEEKITNAIFK 26
>gnl|CDD|233006 TIGR00521, coaBC_dfp, phosphopantothenoylcysteine decarboxylase /
phosphopantothenate--cysteine ligase. This model
represents a bifunctional enzyme that catalyzes the
second and third steps (cysteine ligation, EC 6.3.2.5,
and decarboxylation, EC 4.1.1.36) in the biosynthesis of
coenzyme A (CoA) from pantothenate in bacteria. In early
descriptions of this flavoprotein, a ts mutation in one
region of the protein appeared to cause a defect in DNA
metaobolism rather than an increased need for the
pantothenate precursor beta-alanine. This protein was
then called dfp, for DNA/pantothenate metabolism
flavoprotein. The authors responsible for detecting
phosphopantothenate--cysteine ligase activity suggest
renaming this bifunctional protein coaBC for its role in
CoA biosynthesis. This enzyme contains the FMN cofactor,
but no FAD or pyruvoyl group. The amino-terminal region
contains the phosphopantothenoylcysteine decarboxylase
activity [Biosynthesis of cofactors, prosthetic groups,
and carriers, Pantothenate and coenzyme A].
Length = 390
Score = 30.0 bits (68), Expect = 4.7
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 6/58 (10%)
Query: 482 FERLAEVTKIITENLNKIID------VNHYPIETTRRSNLRHRPIGIGIQGLADTFIL 533
+ AEV I+TE K I ++ + + T + H + I + AD ++
Sbjct: 27 VRQGAEVKVIMTEAAKKFITPLTLEALSGHKVVTELWGPIEHNALHIDLAKWADLILI 84
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 30.0 bits (69), Expect = 5.8
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 494 ENLNKIIDVNHYPIETTRRSN 514
E+L+K+ID++ PI T RSN
Sbjct: 681 EHLDKVIDIDQSPIGRTPRSN 701
>gnl|CDD|236212 PRK08270, PRK08270, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 656
Score = 30.2 bits (69), Expect = 5.8
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 1 MYVIKRDGRKEPVRFDKITARLKK 24
+IKRDGR P +KIT + K
Sbjct: 3 TKIIKRDGRIVPFDAEKITEAIAK 26
>gnl|CDD|177979 PLN02345, PLN02345, endoglucanase.
Length = 469
Score = 30.1 bits (68), Expect = 6.1
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 9/64 (14%)
Query: 52 TTTQLDELAAETAAAMTV-------NHPDYA--LLAGRVAVSNLHKITKNSFSETIKDMY 102
T++ E+AAETAAAM + Y+ LL + N + S+SE+I ++
Sbjct: 136 TSSPGSEVAAETAAAMAAASLVFKSSDSTYSDTLLKHAKQLFNFADKYRGSYSESIPEVQ 195
Query: 103 NYYN 106
+YYN
Sbjct: 196 DYYN 199
>gnl|CDD|234774 PRK00464, nrdR, transcriptional regulator NrdR; Validated.
Length = 154
Score = 28.9 bits (66), Expect = 6.7
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 20/60 (33%)
Query: 3 VIKRDGRKEPVRFDKITARLKKLSYGLSKEHCDPVLVAQKVCAGVYKGVTTTQLDELAAE 62
VIK+DGR+EP FD+ +KL GL + +K + V++ Q++ +
Sbjct: 51 VIKKDGRREP--FDR-----EKLRRGLRR-------ACEK------RPVSSEQIEAAVSR 90
>gnl|CDD|223845 COG0774, LpxC, UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell
envelope biogenesis, outer membrane].
Length = 300
Score = 29.5 bits (67), Expect = 6.8
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 341 RVRDDGKWSLFCPSDASGLADSWGIEFEH 369
RV D KW+ F P D G S+ I+F+H
Sbjct: 137 RVEDGDKWAEFTPYD--GFRLSYTIDFDH 163
>gnl|CDD|143440 cd07122, ALDH_F20_ACDH, Coenzyme A acylating aldehyde dehydrogenase
(ACDH), ALDH family 20-like. Coenzyme A acylating
aldehyde dehydrogenase (ACDH, EC=1.2.1.10), an NAD+ and
CoA-dependent acetaldehyde dehydrogenase, functions as a
single enzyme (such as the Ethanolamine utilization
protein, EutE, in Salmonella typhimurium) or as part of
a multifunctional enzyme to convert acetaldehyde into
acetyl-CoA . The E. coli aldehyde-alcohol dehydrogenase
includes the functional domains, alcohol dehydrogenase
(ADH), ACDH, and pyruvate-formate-lyase deactivase; and
the Entamoeba histolytica aldehyde-alcohol dehydrogenase
2 (ALDH20A1) includes the functional domains ADH and
ACDH and may be critical enzymes in the fermentative
pathway.
Length = 436
Score = 29.8 bits (68), Expect = 7.0
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 18/74 (24%)
Query: 39 VAQKVCAGVYKGVTTTQLDELAAETAAAMTVNHPDYALLA------GRVAVSNLHKITKN 92
AQ+ + + Q+D++ A A + A +A G V K+ KN
Sbjct: 10 KAQRE----FATFSQEQVDKIVEAVAWAAADAAEELAKMAVEETGMGVVE----DKVIKN 61
Query: 93 SF-SETIKDMYNYY 105
F SE + YN
Sbjct: 62 HFASEYV---YNDI 72
>gnl|CDD|220654 pfam10254, Pacs-1, PACS-1 cytosolic sorting protein. PACS-1 is a
cytosolic sorting protein that directs the localisation
of membrane proteins in the trans-Golgi network
(TGN)/endosomal system. PACS-1 connects the clathrin
adaptor AP-1 to acidic cluster sorting motifs contained
in the cytoplasmic domain of cargo proteins such as
furin, the cation-independent mannose-6-phosphate
receptor and in viral proteins such as human
immunodeficiency virus type 1 Nef.
Length = 413
Score = 29.8 bits (67), Expect = 7.1
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 577 GSPMSKGILQVDMW-NITPSDRWDWSSLREMISKNGVR---NSLLVAPMPTAST 626
GSP+ LQVD W P +R S R+ KN ++ SL V+ +P++
Sbjct: 264 GSPVDAIGLQVDYWPAARPGERRKEGSKRDASGKNTLKSTFRSLQVSRLPSSGQ 317
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. 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 = 925
Score = 30.0 bits (68), Expect = 7.2
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 493 TENLNKIIDVNHYPIETTRRSN 514
E+L+K+I ++ PI T RSN
Sbjct: 679 LEHLDKVIHIDQSPIGRTPRSN 700
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.134 0.398
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,883,125
Number of extensions: 4029962
Number of successful extensions: 3584
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3368
Number of HSP's successfully gapped: 78
Length of query: 810
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 705
Effective length of database: 6,280,432
Effective search space: 4427704560
Effective search space used: 4427704560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (27.9 bits)