RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 003561
(811 letters)
>gnl|CDD|178056 PLN02437, PLN02437, ribonucleoside--diphosphate reductase large
subunit.
Length = 813
Score = 1834 bits (4752), Expect = 0.0
Identities = 724/813 (89%), Positives = 764/813 (93%), Gaps = 2/813 (0%)
Query: 1 MYVVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQKVCAGVYKGVTTSQLDELA 60
MYVVKRDGRQE VHFDKITARLKKLSYGLS +HCDPVLV+QKVCAGVYKGVTTSQLDELA
Sbjct: 1 MYVVKRDGRQETVHFDKITARLKKLSYGLSQDHCDPVLVAQKVCAGVYKGVTTSQLDELA 60
Query: 61 AETAAAMTTNHPDYASLAARIAVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDI 120
AETAAAMTTNHPDYA LAARIAVSNLHKNTKKSFSET+KDMYNH NERSGLKAPLIADD+
Sbjct: 61 AETAAAMTTNHPDYAILAARIAVSNLHKNTKKSFSETVKDMYNHVNERSGLKAPLIADDV 120
Query: 121 YEIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVSIGIHK 180
Y+IIMKNAA LDSEIIYDRDFDYDYFGFKTLERSYLLKV GKVVERPQHMLMRVS+GIHK
Sbjct: 121 YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVNGKVVERPQHMLMRVSVGIHK 180
Query: 181 DDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMKDDSIEGIYETLKECAV 240
DDI+SAIKTYH+MSQRWFTHASPTLFNAGTPRPQLSSCFL+CMKDDSIEGIY+TLKECAV
Sbjct: 181 DDIESAIKTYHLMSQRWFTHASPTLFNAGTPRPQLSSCFLICMKDDSIEGIYDTLKECAV 240
Query: 241 ISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVY 300
ISKSAGGIG+SVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFA+Y
Sbjct: 241 ISKSAGGIGLSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAIY 300
Query: 301 LEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLA 360
LEPWHADIFEFL+L+KNHGKEEHRARDLFYALW+PDLFMERVQ+NG WSLFCPNEA GLA
Sbjct: 301 LEPWHADIFEFLDLRKNHGKEEHRARDLFYALWIPDLFMERVQSNGDWSLFCPNEAPGLA 360
Query: 361 DCWGAEFEKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNL 420
DCWG EFE+LYT YEREGKAKKVVQAQ LWF IL SQIETGTPYMLFKD+CNRKSNQQNL
Sbjct: 361 DCWGEEFERLYTKYEREGKAKKVVQAQQLWFAILESQIETGTPYMLFKDSCNRKSNQQNL 420
Query: 421 GTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFF 480
GTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREK VP+ESHPS++VGS GSKNR+F
Sbjct: 421 GTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKGVPLESHPSKLVGSLGSKNRYF 480
Query: 481 DFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFES 540
DFEKLAEVTA+VT NLNKIIDVNYYPVETARRSN+RHRPIGIGVQGLAD FILLGM F+S
Sbjct: 481 DFEKLAEVTAVVTRNLNKIIDVNYYPVETARRSNMRHRPIGIGVQGLADAFILLGMPFDS 540
Query: 541 PEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDW 600
PEAQQLNKDIFETIYYHALK SSE+AA+EGPYETY SPVSKGILQPDMW V PS RWDW
Sbjct: 541 PEAQQLNKDIFETIYYHALKASSELAAREGPYETYAGSPVSKGILQPDMWGVTPSGRWDW 600
Query: 601 GVLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL 660
LR+MISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL
Sbjct: 601 AALREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL 660
Query: 661 LHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCY 720
LHDLTEMG+W+PT+KNKII ++GSVQKIPEIP++LK IYKTVWEIKQ TLVDMA DRGCY
Sbjct: 661 LHDLTEMGLWTPTLKNKIIAENGSVQKIPEIPDDLKAIYKTVWEIKQRTLVDMAADRGCY 720
Query: 721 IDQSQSLNIHMDQPNFKKVTSLHFRTWSRGLKTGMYYLRSRAAADAIKFTVDTSVFKEKP 780
IDQSQSLNIHMDQPNF K+TSLHF WS+GLKTGMYYLRSRAAADAIKFTVDT+ K
Sbjct: 721 IDQSQSLNIHMDQPNFGKLTSLHFYAWSKGLKTGMYYLRSRAAADAIKFTVDTASLKPSA 780
Query: 781 EKPELV--VDDETKMAQVVCSLTNREECMACGS 811
D ETKMAQ+VCSL NREEC+ACGS
Sbjct: 781 TGVAAPEEEDVETKMAQMVCSLDNREECLACGS 813
>gnl|CDD|217257 pfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel
domain.
Length = 516
Score = 806 bits (2083), Expect = 0.0
Identities = 282/545 (51%), Positives = 364/545 (66%), Gaps = 30/545 (5%)
Query: 215 LSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVP 274
LSSCFL+ DDS++ IY+TLKE A++SKS GGIG+++ IRA GS IRGT G S+G+VP
Sbjct: 1 LSSCFLLPSVDDSLDSIYDTLKEAALLSKSGGGIGINLSKIRAKGSPIRGTGGVSSGVVP 60
Query: 275 MLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWV 334
L+VF+DTARYV+QGG KR+GA AVYLE WH DI EFL+LKKN+G EE RAR+L +WV
Sbjct: 61 FLKVFDDTARYVNQGG-KRRGAVAVYLEVWHPDIEEFLDLKKNNGDEERRARNLNLGVWV 119
Query: 335 PDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGKAKKVVQAQNLWFEIL 394
PDLFM+RV+ + W+LF P EA GL D +G EFE+ Y E GK KK V+A+ LWF+I+
Sbjct: 120 PDLFMKRVENDEDWTLFSPREAPGLEDLYGEEFEEEYEKLEANGKVKKTVKARELWFKIV 179
Query: 395 TSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALPRF 454
S ETG PY+LFKD NR + Q++LGTIKSSNLCTEI++ TSP E AVCNLASI L +F
Sbjct: 180 ESAWETGEPYILFKDAVNRHNPQKHLGTIKSSNLCTEIVQPTSPGEDAVCNLASINLAKF 239
Query: 455 VREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSN 514
V FDFE+L EV + L+ +ID+N YPV AR+SN
Sbjct: 240 VENDF-------------------TFDFEELREVVRLAVRALDNVIDLNDYPVPEARKSN 280
Query: 515 LRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYET 574
RHR IG+GV GLAD LG+ ++S EA++L +IFETIYY+ALK S+E+A ++GP+
Sbjct: 281 KRHRSIGLGVMGLADALAKLGIPYDSEEARELADEIFETIYYYALKASNELAKEKGPFPG 340
Query: 575 YHNSPVSKGILQPDMWNVIPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQILGNNE 634
+ S +KG + W+ LR+ I K+G+RNS L A PT S SQI G E
Sbjct: 341 FEGSKYAKGEFHAI----PLREDWEE--LREDIKKHGLRNSQLTAIAPTGSISQIAGTTE 394
Query: 635 CFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEE 694
EP SN+YSRR SGEF+VVN +LL DL E+ WS +KN++ Y +GSVQ IPEIPEE
Sbjct: 395 GIEPIFSNVYSRRSKSGEFLVVNPYLLRDLREL--WSEEMKNELAY-NGSVQPIPEIPEE 451
Query: 695 LKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLNIHMDQ-PNFKKVTSLHFRTWSRGLKT 753
+K +YKT ++I +DMA R ++DQS S + + + + SL+ W GLKT
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 = 738 bits (1908), Expect = 0.0
Identities = 286/600 (47%), Positives = 350/600 (58%), Gaps = 146/600 (24%)
Query: 167 PQHMLMRVSIGIHKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMKDD 226
PQ LMRV++G+ D++ A + Y ++S++ FT A+PTLFNAGTPR QLSSCFL+ + DD
Sbjct: 1 PQDRLMRVALGLASGDLEWAKEFYDLLSKQRFTPATPTLFNAGTPRGQLSSCFLLTV-DD 59
Query: 227 SIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYV 286
S+E IY+T+KECA +SK GGIG+++ NIRATGS IRGTNG SNG++P L++ NDTARYV
Sbjct: 60 SLESIYDTIKECAQLSKIGGGIGLNLSNIRATGSPIRGTNGASNGVIPFLKLLNDTARYV 119
Query: 287 DQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNG 346
DQ GG+RKGA AVYLE WH DI EFL+LKKN+G E RARDLFY +W+PDLFMERV
Sbjct: 120 DQ-GGQRKGAGAVYLEIWHPDIEEFLDLKKNNGDERRRARDLFYGVWIPDLFMERV---- 174
Query: 347 QWSLFCPNEASGLADCWGAEFEKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYML 406
ER+ LW +IL SQ ETG PY+L
Sbjct: 175 ----------------------------ERD-----------LWRKILESQFETGYPYIL 195
Query: 407 FKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPT-----ETAVCNLASIALPRFVREKDVP 461
FKDTCNRK+ Q++LGTIKSSNLCTEI++ TSP+ E AVCNLASI L FV
Sbjct: 196 FKDTCNRKNPQKHLGTIKSSNLCTEILQPTSPSEDEPGEDAVCNLASINLGNFV------ 249
Query: 462 VESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIG 521
FEKL EV + L+ +ID+NYYPV A+RSN+RHR IG
Sbjct: 250 -------------------TFEKLEEVVKLAVRALDNVIDLNYYPVPEAKRSNMRHRAIG 290
Query: 522 IGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVS 581
+GV GL D LL + +ES EA LN IFETI Y+ALK S E+A + G
Sbjct: 291 LGVMGLHDYLALLRIPYESEEALDLNDRIFETINYYALKASCELAKERG----------- 339
Query: 582 KGILQPDMWNVIPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTS 641
G+RNSLL+A PTAS SQILG EP TS
Sbjct: 340 -----------------------------GLRNSLLLAIAPTASISQILGATPSIEPITS 370
Query: 642 NIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKT 701
NIY RRVLSGEF VVN HL DL E G +YKT
Sbjct: 371 NIYVRRVLSGEFPVVNPHLEKDLWEYG-----------------------------LYKT 401
Query: 702 VWEIKQMTLVDMAVDRGCYIDQSQSLNIHMDQP-NFKKVTSLHFRTWSRGLKTGMYYLRS 760
+EI Q L+D+A DR +IDQ QSLN+ + P + + SL+F W +GLKT YYLR+
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 = 701 bits (1810), Expect = 0.0
Identities = 282/639 (44%), Positives = 386/639 (60%), Gaps = 44/639 (6%)
Query: 145 YFGFKTLERSYLLKVQ--GKVVERPQHMLMRVSIGIH-----KDDIDSAIKTYHMMSQRW 197
Y G K L YLL+ G + E PQ MRV++G+ + AI+ Y ++S+
Sbjct: 1 YMGLKELYNRYLLRNAATGAIYESPQEAYMRVAMGLASLEPKDTRLADAIRFYDLLSRLK 60
Query: 198 FTHASPTLFNAGTPRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRA 257
+ A+PTLFNAGTPR QLSSCFL+ + DD++E IY+ + + A +SK GGIG+++ +RA
Sbjct: 61 ISPATPTLFNAGTPRGQLSSCFLLDVTDDTLESIYKAIDDVAQLSKHGGGIGLNLTKLRA 120
Query: 258 TGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKN 317
GS IRGTN S GI+P L++ + + V+QGG KR GA AVYLE WH DI EFL+LKKN
Sbjct: 121 IGSPIRGTNNASKGIIPFLKLLDSSVEAVNQGG-KRPGAAAVYLEVWHPDIEEFLDLKKN 179
Query: 318 HGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYERE 377
+G E R +LFY LW+PDLFM+RV+ + W LF P + GL +G EFE+ Y E++
Sbjct: 180 NGDERRRCDNLFYGLWIPDLFMKRVEEDKDWYLFSPYDVPGLYGLYGEEFEEEYERLEKD 239
Query: 378 GKAKK---VVQAQNLWFEILTSQIETGTPYMLFKDTCNRK-SNQQNLGTIKSSNLCTEII 433
+A+K V A++L +IL +++ETG PY+LFKD N+ + G IK SNLCTEI
Sbjct: 240 VEARKKIRKVSARDLMKDILRTRVETGRPYILFKDAVNKHNPFKTGGGAIKMSNLCTEIT 299
Query: 434 EYTSP---TETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTA 490
+ T ETAVCNLAS+ L FV E FDF +L +
Sbjct: 300 QPTDDSHKGETAVCNLASVNLANFVMEDK--------------------FDFSELEDAVR 339
Query: 491 IVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDI 550
I L+ +ID+ YP A +SN R R IGIGV GL D LG+ ++S EA+ LN I
Sbjct: 340 IAVRFLDNVIDLQNYPTAPAAKSNQRRRSIGIGVMGLHDVLAKLGLPYDSEEARDLNDRI 399
Query: 551 FETIYYHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRW-------DWGVL 603
FE IYY+A+K S+E+A ++GP+ + S +KG L PD W + DW L
Sbjct: 400 FEAIYYYAIKASAELAKEKGPFPGFSGSKYAKGWLHPDTWEKTIDPKTSMAPTEEDWEAL 459
Query: 604 RDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHD 663
R+ I + G+RNS L A MPTAS+SQ+ G E EP SNI++++ LSGEF++ NK+L+ +
Sbjct: 460 RERIKEYGLRNSQLTALMPTASSSQLTGVTESIEPVFSNIFTKKTLSGEFLIPNKYLMKE 519
Query: 664 LTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQ 723
L E+G+W + I+ + GS Q I IPE LK YKT +E+ Q L+DMA DR ++DQ
Sbjct: 520 LEELGLWDADRRGDIVENVGSPQPIAAIPETLKYKYKTAYELDQEALIDMAADRQKFVDQ 579
Query: 724 SQSLNIHMD-QPNFKKVTSLHFRTWSRGLKTGMYYLRSR 761
S SLN+ + + K + L W +GLKT MYY RSR
Sbjct: 580 SISLNLFLTEEVTAKDLLKLLLLAWKKGLKT-MYYCRSR 617
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 643 bits (1660), Expect = 0.0
Identities = 317/845 (37%), Positives = 456/845 (53%), Gaps = 65/845 (7%)
Query: 1 MYVVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQKVCAGVYKGVTTSQLDELA 60
+ V DG + + ++ A +++ GL E D + + +Y GV ++ +
Sbjct: 149 LNVTLDDGVRRPLDMARLRALIEEACEGL--EAVDAEPILAETLKNLYDGVPMDEVYKAL 206
Query: 61 AETAAAMTTNHPDYASLAARIAVSNLHK----NTKKSFSETIKDMYNHYNE------RSG 110
A + P+Y+ + AR+ + L + T +M Y E + G
Sbjct: 207 ILAARTLIEKEPNYSYVTARLLLDTLRREALGFLGVPEEVTQAEMATRYAEYFPAFIKKG 266
Query: 111 LKAPLIADDIYEI-IMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQH 169
++A L+ + + + + A LD E RD + Y G +TL Y L V G +E PQ
Sbjct: 267 IEAELLDPKLAQFDLERLGAALDPE----RDLQFTYLGLQTLYDRYFLHVDGTRIELPQA 322
Query: 170 MLMRVSIGIHKDDIDS---AIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMKDD 226
MRV++G+ ++ID AI+ Y+++S F ++PTLFN+GT RPQLSSC+L + DD
Sbjct: 323 FFMRVAMGLALNEIDREARAIEFYNLLSSFDFMSSTPTLFNSGTLRPQLSSCYLTTVPDD 382
Query: 227 SIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYV 286
++GIYE +K+ A++SK AGG+G +RA GS+I+GTNG S G+VP L+V NDTA V
Sbjct: 383 -LDGIYEAIKDNALLSKFAGGLGNDWTPVRALGSHIKGTNGKSQGVVPFLKVVNDTAVAV 441
Query: 287 DQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNG 346
+QGG KRKGA YLE WH DI EFL L+KN G + R D+ A W+PDLFM+RV +G
Sbjct: 442 NQGG-KRKGAVCAYLETWHLDIEEFLELRKNTGDDRRRTHDMNTANWIPDLFMKRVMEDG 500
Query: 347 QWSLFCPNEASGLADCWGAEFEKLYTHYE---REGKAK--KVVQAQNLWFEILTSQIETG 401
+W+LF P+E L D +G FE+ YT YE G+ K K + A +LW ++L+ ETG
Sbjct: 501 EWTLFSPSEVPDLHDLFGKAFEEAYTAYEAKAARGEIKLFKKIPAVDLWRKMLSMLFETG 560
Query: 402 TPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKDVP 461
P++ FKD CN +S QQ++G + SSNLCTEI TS E AVCNL S+ L +++
Sbjct: 561 HPWITFKDPCNLRSPQQHVGVVHSSNLCTEITLNTSDDEIAVCNLGSVNLVAHIKDGAK- 619
Query: 462 VESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIG 521
D EKL + L+ +ID+NYY V AR SNLRHRP+G
Sbjct: 620 ------------------LDHEKLKRTVSTAMRMLDNVIDINYYAVPKARNSNLRHRPVG 661
Query: 522 IGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVS 581
+G+ G D LL + + S EA + E + Y+A+ S+E+A + G Y +Y S S
Sbjct: 662 LGIMGFQDALYLLRIPYASDEAVEFADRSMEAVSYYAIWASTELAEERGRYSSYEGSLWS 721
Query: 582 KGILQPD-----------MWNVIPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQIL 630
+GIL D V S DW LR I K+G+RNS +A PTA+ S I+
Sbjct: 722 RGILPIDSLKLLAEARGGYLEVDRSSTLDWDALRARIKKHGMRNSNCMAIAPTATISNII 781
Query: 631 GNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPE 690
G ++ EP N+Y + LSGEF VVN +L+ DL G+W + N + Y DGS+Q+I
Sbjct: 782 GVSQSIEPTYQNLYVKSNLSGEFTVVNPYLVRDLKARGLWDEVMVNDLKYFDGSLQRIDR 841
Query: 691 IPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLNIHMDQPNFKKVTSLHFRTWSRG 750
IP +LK +Y T +E+ LV+ A R +IDQ+QSLN++M + KK+ + W RG
Sbjct: 842 IPADLKALYATAFEVDPRWLVEAASRRQKWIDQAQSLNLYMAGASGKKLDETYKLAWLRG 901
Query: 751 LKTGMYYLRSRAAADAIKFTVDT----SVFKEKPEKPELVVDDETKMAQV--VCSLTNRE 804
LKT YYLR+ A K TV+T +V A CS+ +
Sbjct: 902 LKT-TYYLRTLGATHVEKSTVNTGALNAVSSGGGGAGGAAAAAAAPPAADPKACSIDD-P 959
Query: 805 ECMAC 809
+C AC
Sbjct: 960 DCEAC 964
>gnl|CDD|223287 COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide
transport and metabolism].
Length = 651
Score = 567 bits (1463), Expect = 0.0
Identities = 237/754 (31%), Positives = 352/754 (46%), Gaps = 128/754 (16%)
Query: 39 VSQKVCAGVYKGVTTSQLDELAAETAAAMTTNHPDYASLAARIAVSNLHKNTKKSFSETI 98
+ G Y G+T ++ LAA T + + PD LAAR+A S+L K + F
Sbjct: 1 RELRTVIGFYDGITIAENLILAALTV--IEEDDPDVQRLAARLAGSDLRKEAVRQF-GRF 57
Query: 99 KDMYNHYNERSGLKAPLIADDIYEIIMKN-AACLDSEIIYDRDFDYDYFGFKTLERSYLL 157
+ + + + + L+ +I+ +RD + Y K L YLL
Sbjct: 58 DVLDEKVFAL--VANGYYDQRLLRLYSREDLDDLNKKILLERDRQFSYAAAKVLYSRYLL 115
Query: 158 K--VQGKVVERPQHMLMRVSIGIHKDD-----IDSAIKTYHMMSQRWFTHASPTLFNAGT 210
K +++E PQ + MRV++ + +++ ++ A + Y +MS F A+PTL N GT
Sbjct: 116 KDEDGSEILELPQDLFMRVALLLAQNEAPERRLEWAKEFYDLMSSLRFMPATPTLLNGGT 175
Query: 211 PRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSN 270
PR QLSSCF++ ++DDS +
Sbjct: 176 PRGQLSSCFVLPVEDDS------------------------------------------S 193
Query: 271 GIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFY 330
G+VP +++ +D ++QGG R+GA AVYL+ WH DI EFL+ K+N+G E RA D+
Sbjct: 194 GVVPFMKLLDDAFDAINQGG-VRRGAQAVYLDIWHPDIEEFLDAKRNNGDEILRAFDISV 252
Query: 331 ALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGKAKKVVQAQNLW 390
+W+PDLFM+R + W+LF P + D +GAEFE+ + G KK ++A+ L+
Sbjct: 253 GVWIPDLFMKRAKEGEDWTLFSPRDGYEAPDVYGAEFEEYAEYEADPGIRKKRIKARELF 312
Query: 391 FEILTSQIETGTPYMLFKDTCNRKSNQ-QNLGTIKSSNLCTEIIEYTSPT-------ETA 442
++ + ETG PY++F DT NR++ + G I++SNLC+EI++ T P E A
Sbjct: 313 DKLAEAAFETGDPYLIFVDTLNRRNPNAEGGGAIRASNLCSEILQRTKPLSLEQPLGEDA 372
Query: 443 VCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDV 502
CNL SI L +FV+ D LAE+ A+ L+ +ID+
Sbjct: 373 SCNLGSINLAKFVKYGD------------------------GLAELVAVAVRALDNVIDL 408
Query: 503 NYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTS 562
N YPV A R+N R IG+GV GLAD LG+ + S EA + N +FE I Y+ALK S
Sbjct: 409 NPYPVPEAERANAESRAIGLGVMGLADLLAQLGIPYGSEEALKFNDRLFEYIAYYALKAS 468
Query: 563 SEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDR---WDWGVLRDMISKNGVRNSLLVA 619
+E+A + GPY + S ++GIL D P DW LR+ I K+G+RNS L A
Sbjct: 469 AELAKERGPYPYFEGSRWARGILPIDY----PRLFGITEDWEKLREDIKKHGLRNSYLTA 524
Query: 620 PMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKII 679
PT S S I G EP + +Y R G F V L DL
Sbjct: 525 IAPTGSISYIAGTTSGIEPIFALVYFRETKGGRFYYVVPPLFEDLLAY------------ 572
Query: 680 YDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLNIHMDQPN-FKK 738
Y +EI + +DM +IDQ S +++ K
Sbjct: 573 -------------------YGLAYEIDPLWHIDMQAAAQRWIDQGISKTLNLPNTATTKD 613
Query: 739 VTSLHFRTWSRGLKTGMYYLRSRAAADAIKFTVD 772
+ + W GLKT YY R+ AA + +D
Sbjct: 614 LNKAYLYAWKLGLKT-TYYRRTSQAAQVLTVVLD 646
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 520 bits (1340), Expect = e-170
Identities = 304/844 (36%), Positives = 448/844 (53%), Gaps = 73/844 (8%)
Query: 3 VVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQKVCAGVYKGVTTSQLDELAAE 62
V+ +DG + ++ A E D L++ A Y G+ S++
Sbjct: 238 VLSKDGSTYTMTKSQLLAHFAWACSRFP-ETTDAALLADMAFANFYSGIKESEVVLACIM 296
Query: 63 TAAAMTTNHPDYASLAARIAVSNLHKNT------KKSFSETIKDMYNHY---NERSGLKA 113
A A PDYA +AA + + ++K + E KD + Y + L
Sbjct: 297 AARANIEKEPDYAFVAAELLLDVVYKEALGKSKYDEDLEEAHKDHFKRYILEGDTYRLNP 356
Query: 114 PLIADDIYEIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMR 173
L D+ + A LD RD + Y G + L Y +G+ +E PQ MR
Sbjct: 357 ELKHYDLDAL----AEALD----LSRDLQFSYMGVQNLYDRYFNHHEGRRLETPQIFWMR 408
Query: 174 VSIGI----HKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMKDDSIE 229
VS+G+ +D AI Y+++S +T A+PTLFN+G QLSSC+L ++DD +
Sbjct: 409 VSMGLALNEGQDKTSWAITFYNLLSTFRYTPATPTLFNSGMRHSQLSSCYLSTVQDD-LV 467
Query: 230 GIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQG 289
IY+ + + A++SK AGGIG +RATG+ I+GTNG S G++P ++V NDTA V+QG
Sbjct: 468 HIYKVISDNAMLSKWAGGIGNDWTAVRATGALIKGTNGKSQGVIPFIKVANDTAVAVNQG 527
Query: 290 GGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWS 349
G KRKGA VYLE WH D +FL L+KN G E R D+ A W+PDLF +R+Q G W+
Sbjct: 528 G-KRKGAVCVYLEVWHLDYEDFLELRKNTGDERRRTHDINTASWIPDLFFKRLQQKGTWT 586
Query: 350 LFCPNEASGLADCWGAEFEKLYTHYER-----EGKAKKVVQAQNLWFEILTSQIETGTPY 404
LF P++ GL + +G EFEKLY YER E + K V+A++LW ++L+ ETG P+
Sbjct: 587 LFSPDDVPGLHEAYGEEFEKLYEEYERKVDTGEIRLYKKVEAEDLWRKMLSMLYETGHPW 646
Query: 405 MLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKDVPVES 464
M FKD N +S Q + G ++ SNLCTEI+ S TETAVCNL SI L + +
Sbjct: 647 MTFKDPSNIRSAQDHKGVVRCSNLCTEILLNCSETETAVCNLGSINLVEHIVNDGL---- 702
Query: 465 HPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGV 524
D EKL+E +I L+ +ID+N+YP + A+ +NL HR IG+GV
Sbjct: 703 ----------------DEEKLSETISIAIRILDNVIDINFYPTKEAKEANLAHRAIGLGV 746
Query: 525 QGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKGI 584
G D L +++ S EA + E I Y+A+ SS +A + G Y +Y S +G
Sbjct: 747 MGFQDALYKLNISYASQEAVEFADYSSELIAYYAILASSLLAKERGTYSSYKGSKWDRGY 806
Query: 585 LQPDMWNVIP------------SDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQILGN 632
L D ++ S R DW +R +I + G+RNS L+A PTA+ S I+G
Sbjct: 807 LPIDTIELLKEYRGEANLLMDTSSRKDWEPVRSLIKEYGMRNSQLMAIAPTATISNIIGV 866
Query: 633 NECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIP 692
+ EP +++ + LSGEF + N +L+ L ++GIW + + + Y DGS+ +I IP
Sbjct: 867 TQSIEPTYKHLFVKSNLSGEFTIPNVYLIEKLKKLGIWDADMLDDLKYFDGSLLEIERIP 926
Query: 693 EELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLNIHMDQPNFKKVTSLHFRTWSRGLK 752
+ LK I+ T +EI+ +++ A R +ID QSLN+++ +P+ KK+++++ W +GLK
Sbjct: 927 DHLKKIFLTAFEIEPEWIIECASRRQKWIDMGQSLNLYLAEPDGKKLSNMYLTAWKKGLK 986
Query: 753 TGMYYLRSRAAADAIKFTVDTSV-------FKEKPEKPELVVDDETKMAQVVCSLTNREE 805
T YYLRS AA K VD + K K +VV+ K VCSL E
Sbjct: 987 T-TYYLRSSAATSVEKSFVDINKRGIQPRWMKNKSASTSIVVERAKKTP--VCSL--EEG 1041
Query: 806 CMAC 809
C +C
Sbjct: 1042 CESC 1045
>gnl|CDD|180610 PRK06539, PRK06539, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 822
Score = 464 bits (1195), Expect = e-152
Identities = 258/806 (32%), Positives = 413/806 (51%), Gaps = 76/806 (9%)
Query: 3 VVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQKVCAGVYKGVTTSQLDELAAE 62
VVKRDG +E +K+ A ++ + GL ++ ++ ++ G+TT QLDE +
Sbjct: 5 VVKRDGSKEPYDANKVNAAIEDAARGLDDAITWVTQLASELEITLFDGITTQQLDEAVIQ 64
Query: 63 TAAAMTTNHPDYASLAARIAVSNLHKNTKKSFS--ETIKDMYNHYNERSGLKAPLIADDI 120
A + P + ++AAR+ + ++K + E ++D+ H N +A+ +
Sbjct: 65 VALQNVKDDPAFDTVAARLLLKKIYKRVLGDYDSPEELQDL--HANHFRRTIEKGVAEGL 122
Query: 121 YEIIMKNAACLDSEIIYDRDFDYD---------------YFGFKTLERSYLLKVQ-GKVV 164
LDS + FD + Y G TL Y ++ + G +
Sbjct: 123 ----------LDSRL--GGLFDLERLAAALDPTRDELLKYIGVVTLNNRYGIRARNGDAL 170
Query: 165 ERPQHMLMRVSIGI---HKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLV 221
E PQ+ MR+++G+ D SA+ Y MS+ + A TL NAGTP PQLS+CF++
Sbjct: 171 EVPQYFWMRIAMGLSLNEDDPTSSALAFYEKMSKLEYLAAGSTLVNAGTPYPQLSNCFVM 230
Query: 222 CMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFND 281
M+DD IE I +T ++ ++K GGIG+SV +RA GS IR N TS G +P + +
Sbjct: 231 EMQDD-IEHIAKTTRDVMWLTKGTGGIGLSVSKLRAQGSPIRSNNTTSTGPIPFMHTIDS 289
Query: 282 TARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMER 341
R V +GG K+ GA Y+E WH D EFL+L++N G R R A+W+ D FM+R
Sbjct: 290 VLRAVSRGG-KKFGALCFYMENWHMDFPEFLDLRQNSGDPYRRTRTANTAVWISDEFMKR 348
Query: 342 VQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGKAKKV-----VQAQNLWFEILTS 396
VQ + W LF P E L + +G F K Y Y + +A ++ + A+ + IL S
Sbjct: 349 VQNDEDWYLFDPLETPDLNELYGKAFSKRYAQYVEQAEAGRIRMFKRITAREQFRAILMS 408
Query: 397 QIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVR 456
T P++ +KDT N ++ N GTI SNLCTEI +VCNLASI L R +
Sbjct: 409 LQTTSHPWLTWKDTINNRALNNNTGTIHLSNLCTEICLPQDRDNVSVCNLASINLSRHLA 468
Query: 457 EKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLR 516
+ ++ D+ +L E T + L+ +ID+ V+ A SN +
Sbjct: 469 DGEL--------------------DWAQLEESTRLAVRQLDNLIDITASSVKEADFSNQQ 508
Query: 517 HRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYH 576
+R IG+GV G D LG ++ES EA L I E I Y A+ S+++AA+ G Y +
Sbjct: 509 NRAIGLGVMGFTDMVERLGYSYESEEAYDLIDRIMEHISYAAIDESADLAAERGAYPNFE 568
Query: 577 NSPVSKGILQPDMWNVIPSD-----------RWDWGVLRDMISKNGVRNSLLVAPMPTAS 625
S S+G++ D ++ +D R DW LR + + G+RN+ L+A PTAS
Sbjct: 569 GSRWSRGMVPVDSIALLEADRGVPVDVNRTTRLDWDALRAKV-RGGMRNATLMAIAPTAS 627
Query: 626 TSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSV 685
+ G +P S I+SR SG+F+ VN++L+ DL E+G+W T++ +I+ G +
Sbjct: 628 IGLVAGTTPGLDPQFSQIFSRSTSSGKFLEVNRNLVADLKELGLWE-TVREEILRSQGDI 686
Query: 686 QKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLNIHMDQPNFKKVTSLHFR 745
Q+I IP+E+K +Y+T +++ +++A ++DQ+ S N++++ + + ++
Sbjct: 687 QEIAAIPDEIKALYRTSFQLSPYAFLEVAARAQKWVDQAISRNMYLESRDIGDMMDIYTA 746
Query: 746 TWSRGLKTGMYYLRSRAAADAIKFTV 771
W G+KT YYL + A + TV
Sbjct: 747 AWEMGVKT-TYYLHMKPRHTAEQSTV 771
>gnl|CDD|236266 PRK08447, PRK08447, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 789
Score = 454 bits (1171), Expect = e-148
Identities = 281/858 (32%), Positives = 413/858 (48%), Gaps = 159/858 (18%)
Query: 1 MYVVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQ-KVCAGVY--KGVTTSQLD 57
+ VVKR+GR E + KI +K + + E + V S+ +V A + G+TT ++
Sbjct: 2 ITVVKRNGRIEPLDISKI----QKYTSD-AVEGLEGVSQSELEVDAKIQFRDGITTEEIQ 56
Query: 58 ELAAETAA-AMTTNHPDYASLAARIAVSNLHKNTKKSFSETIKDMYNHYNE--RSGLKAP 114
+ +TA + + P++ +AAR+ + +L+ + YNH E G K
Sbjct: 57 QTLIKTAVDKIDIDRPNWTFVAARLFLYDLYHKV------SGFTGYNHLKEYFEKGEKEG 110
Query: 115 LIADDIYEIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLK-VQGKVVERPQHMLMR 173
I + E + L++ I +RD ++Y G KTL YL+K +E PQHM M
Sbjct: 111 RILLGLKE--KYDLDDLNAYIKPERDLQFNYLGIKTLYDRYLIKDRNNNPIELPQHMFMA 168
Query: 174 VSIGIHKDDIDS---AIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMKDDSIEG 230
+++ + ++++D A K Y ++S+ A+PTL NA T R QLSSC++ D+ IEG
Sbjct: 169 IAMFLAQNELDPQKWAKKFYDVISKFEVMLATPTLSNARTTRHQLSSCYIGSTPDN-IEG 227
Query: 231 IYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGG 290
I+++ KE A++SK GGIG +RA GSYI G + GI+P L++ ND A VDQ G
Sbjct: 228 IFDSYKEMALLSKYGGGIGWDWSKVRAMGSYIDGHKNAAGGIIPFLKITNDIAIAVDQLG 287
Query: 291 GKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSL 350
RKGA AVYLEPWH DI +F++L+KN G+E RA DLF ALW+ DLFM+RV+ + W+L
Sbjct: 288 -TRKGAIAVYLEPWHMDISDFIDLRKNSGEERRRAHDLFPALWINDLFMKRVEEDAMWTL 346
Query: 351 FCPNEASGLADCWGAEFEKLYTHYE-REGKAKKVVQAQNLWFEILTSQIETGTPYMLFKD 409
F P E L + +G EFEK Y YE E K+ + A+ LW +ILT+ ETG P++ FKD
Sbjct: 347 FDPYECKDLTELYGEEFEKRYLEYEKDEKIIKEYINAKELWKKILTNYFETGLPFLCFKD 406
Query: 410 TCNRKSNQQNLGTIKSSNLCTEI------------IEYTSPTE----------------- 440
NR + + G I+SSNLCTEI IE+ +
Sbjct: 407 NANRANPNAHAGIIRSSNLCTEIFQNTAPNHYKIKIEFEDGSIEFFEEEELVTVDSGITK 466
Query: 441 ---------------------------TAVCNLASIALPRFVREKDVPVESHPSRIVGSR 473
TAVCNLASI L S+I
Sbjct: 467 KAKKITSLDSLKGKKIYIVEKEKKDGKTAVCNLASINL---------------SKI---- 507
Query: 474 GSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFIL 533
+K E + V I L+ +ID+N+YP + +NL+ R IG+GV G A
Sbjct: 508 NTK------EDIERVVPIAIRMLDNVIDLNFYPNRKVKATNLKSRAIGLGVMGEAQMLAE 561
Query: 534 LGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNV- 592
+A+ S E + +I E I Y+A+ SS +A ++G Y + S SKGI D N
Sbjct: 562 HKIAWGSKEHLEKIDEIMEQISYNAIDASSNLALEKGVYPDFEGSNWSKGIFPIDKANEE 621
Query: 593 ---------IPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNI 643
+ DW LR+ + K+G+RN L+A PT+S S ++G + EP +
Sbjct: 622 AKKLVERGGLFDSACDWEGLREKVKKDGMRNGYLMAIAPTSSISILVGTTQTIEP----V 677
Query: 644 YSRRV----LSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIY 699
Y R+ LSG VV +P + E Y
Sbjct: 678 YKRKWFEENLSGLIPVV-------------------------------VPNLSPETWQYY 706
Query: 700 KTVWEIKQMTLVDMAVDRGCYIDQSQSLNIHM--DQPNFKKVTSLHFRTWSRGLKTGMYY 757
+++ Q L+ A R +IDQ QSLNI + D+ + K + ++ W GLK+ YY
Sbjct: 707 TPAYDLDQKDLIKAAAVRQKWIDQGQSLNIFLSLDKASGKYLNEIYTLAWKLGLKS-TYY 765
Query: 758 LRSRAAADAIKFTVDTSV 775
LRS + D S+
Sbjct: 766 LRSESPESEEVSVADRSI 783
>gnl|CDD|236378 PRK09102, PRK09102, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 601
Score = 392 bits (1009), Expect = e-127
Identities = 221/677 (32%), Positives = 331/677 (48%), Gaps = 113/677 (16%)
Query: 146 FGFKTLERSYLLKVQGKVVERPQHMLMRVSIGIHKDDIDSAIKTYHMMSQRWFTHASPTL 205
FG TL YLL+ G E Q + R++ D + A + Y MS+ WF A+P L
Sbjct: 24 FGKATLRDRYLLE--G---ESYQDLFARIAEAYADIDPEHAQRFYDYMSRGWFMPATPVL 78
Query: 206 FNAGTPRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGT 265
N GT R SCFL + +DS+EGI T E ++K GGIG N+R+ G IR
Sbjct: 79 SNGGTDRGLPISCFLNYV-EDSLEGIVNTWNENVWLAKRGGGIGSYWGNVRSIGEPIRN- 136
Query: 266 NGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRA 325
NG S+GI+P ++V D+ G R+G+FAVYL+ H +I EFL+++K G +A
Sbjct: 137 NGKSSGIIPFIKVM-DSLTLAISQGSLRRGSFAVYLDIEHPEIEEFLDIRKPTGDPNRKA 195
Query: 326 RDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGKAKKVVQ 385
+L + + V D FME V+ +W L P ++ + V+
Sbjct: 196 LNLHHGVCVTDEFMEAVEDGDEWDLISP----------------------KDKSVIRTVK 233
Query: 386 AQNLWFEILTSQIETGTPYMLFKDTCNRK--SNQQNLG-TIKSSNLCTEI-----IEYTS 437
A++LW +IL ++IETG PY+LF D NR ++LG +K+SNLC+EI I++
Sbjct: 234 ARDLWAKILETRIETGEPYLLFIDNVNRALPEVYKDLGLKVKASNLCSEITLPTGIDHLG 293
Query: 438 PTETAVCNLASIALPRFVREKDVP--VESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTEN 495
TAVC L+S+ L + KD +E ++ RF D ++ +
Sbjct: 294 EDRTAVCCLSSLNLEYYDEWKDTDAFIED----LM-------RFLD--------NVLQDF 334
Query: 496 LNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIY 555
++K D +E A+ S +R R +G+GV G + FES A+Q NK IF+ I
Sbjct: 335 IDKAPDE----MERAKYSAMRERSVGLGVMGFHSYLQSKMIPFESVMAKQWNKKIFKHIR 390
Query: 556 YHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDWGVLRDMISKNGVRNS 615
A K S E+A ++G D +GV+R R S
Sbjct: 391 EQADKASKELAKEKGE----------------------CPDAAGYGVMR--------RFS 420
Query: 616 LLVAPMPTASTSQILGN-NECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTI 674
+A PTAS S ILGN + EP +N Y+ + L G F V NK+L L E G + +
Sbjct: 421 TKMAIAPTASISIILGNTSPGIEPIAANYYTHKTLKGSFTVKNKYLEKLLEEKGKDTDEV 480
Query: 675 KNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLN--IHMD 732
+ I+ ++GSVQ + + EE K ++KT +EI Q ++++A DR YIDQ+QSLN + +
Sbjct: 481 WSSILTNEGSVQHLDFLSEEEKDVFKTAFEIDQRWIIELAADRQKYIDQAQSLNLFLPAN 540
Query: 733 QPNFKKVTSLHFRTWSRGLKTGMYYLRSRAAADAIKFTVDTSVFKEKPEKPELVVDDETK 792
P + + LHF W +G+K+ +YY RS++ A +K L K
Sbjct: 541 VPK-RDLNKLHFEAWKKGVKS-LYYQRSKSVQRA-----------DKVSHDVLKKRLVEK 587
Query: 793 MAQVVCSLTNREECMAC 809
A + +EC+AC
Sbjct: 588 SAFN----RDYDECLAC 600
>gnl|CDD|181700 PRK09209, PRK09209, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 761
Score = 365 bits (940), Expect = e-115
Identities = 238/829 (28%), Positives = 366/829 (44%), Gaps = 159/829 (19%)
Query: 3 VVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQKVCAGVYKG--VTTSQLDELA 60
V + R+ +++ + ++ D ++V V + VT L +
Sbjct: 12 VKEAGNRKLPFDKERLDRYIDQIHAEFP--QLDVEDYKRRVFNFVERKESVTADDLVDYL 69
Query: 61 AETAAAMTTNH-PDYASLAARIAVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADD 119
A A P++ AAR+ ++ L+K ++ + Y + GL+ L
Sbjct: 70 IREAEARVDLEEPEWTFFAARLYLNRLYKRASRNRFYDASEKYGSF---VGLQESLAERG 126
Query: 120 IY----------EIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLK-VQGKVVERPQ 168
IY E +++ +D E RD + Y G L YL V E PQ
Sbjct: 127 IYSNDLLKRYSKEELIEAGKMIDPE----RDKLFTYIGLYLLADRYLATDSDRNVYELPQ 182
Query: 169 HMLMRVSIGIHKDD-----IDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCM 223
+ +++ + +++ + + Y +S + T A+PTL NAG QLSSCF+ +
Sbjct: 183 ERWLTIALYLMQNEPRERRMQLVKEAYWALSNLYMTVATPTLANAGKVGGQLSSCFIDTV 242
Query: 224 KDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTA 283
DDS++GIY++ + A +SK GG+G + +R+ GS IRG G S+G++P ++ N+TA
Sbjct: 243 -DDSLQGIYDSNTDVARVSKHGGGVGAYLGKVRSRGSDIRGFKGVSSGVIPWIKQLNNTA 301
Query: 284 RYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQ 343
VDQ G +RKGA AVYL+ WH DI FL+L+ N+G E RA D+F + +PDLFME V+
Sbjct: 302 VSVDQLG-QRKGAIAVYLDVWHKDIESFLDLRLNNGDERLRAHDVFTGVCIPDLFMEAVE 360
Query: 344 TNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGK--------------AKKVVQAQNL 389
G W LF P+E + G E Y + +G ++K V+A ++
Sbjct: 361 RRGDWYLFDPHEVKKVM---GWYLEDFYDEKKGDGSFREKYEECVADERLSRKTVKAIDI 417
Query: 390 WFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTET-------- 441
I+ SQ+ETG P+M ++D NR + ++ G I SSNLCTEI++ SPT
Sbjct: 418 MKRIMVSQLETGNPFMFYRDEVNRMNPNKHEGMIYSSNLCTEIMQNMSPTVMIQEIISGG 477
Query: 442 -----------AVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTA 490
VCNL+SI L R V DV L +
Sbjct: 478 QIVITKQPGDFVVCNLSSINLGRAVTA-DV------------------------LERLIP 512
Query: 491 IVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDI 550
I L+ +ID+N PV A +N ++R IG+G G L G+A+ES EA Q ++
Sbjct: 513 IQVRMLDNVIDLNQLPVPQATITNQKYRAIGLGTFGWHHLLALKGIAWESEEAVQYADEL 572
Query: 551 FETIYYHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRW------------ 598
+E I Y ++ S E+A ++G Y PV KG SD W
Sbjct: 573 YERINYLTIQASMELAKEKGAY------PVFKG-----------SD-WQTGEYFERRGYN 614
Query: 599 --DWGVLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVV 656
W L +++NGVRN+ L+A P ST+QI G+ +P S Y V
Sbjct: 615 SPQWDELAAQVAENGVRNAYLMAVAPNMSTAQIAGSTASIDPIYSAFYYEEKKDYRRPVT 674
Query: 657 NKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVD 716
DL+ Y+ K +++ Q +
Sbjct: 675 ----APDLSLDTWP--------YYE------------------KGAYKVDQFWSIRQNAA 704
Query: 717 RGCYIDQSQSLNIHMDQPN---FKKVTSLHFRTWSRGLKTGMYYLRSRA 762
R ++DQS S N ++ P+ ++ LH W GLKT YY+RS
Sbjct: 705 RQRHVDQSISFNFYV--PSTIRASELLDLHMTAWKEGLKT-TYYVRSTD 750
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 364 bits (937), Expect = e-113
Identities = 241/760 (31%), Positives = 364/760 (47%), Gaps = 121/760 (15%)
Query: 53 TSQLDELAAETAAAM---TTNHPDYASLAARIAVSNLHKNTKKSFSE-TIKDMYNH--YN 106
S+ + LAA AA+ T PD+ +AAR+ + K KS + I Y+ Y
Sbjct: 143 MSEGESLAALIKAAVELTTQEAPDWEFIAARLLMLQFSKKLGKSLEKLGIHSFYDKIKYL 202
Query: 107 ERSGLKAPLI-----ADDIYEIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLKV-Q 160
GL I ++I E I +RD + Y G L + Y+++
Sbjct: 203 TEEGLYGSYILEHYSREEIEE--------AAGFIDPERDKLFTYSGLDLLLKRYVIRTHS 254
Query: 161 GKVVERPQHMLMRVSIGIH------KDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQ 214
+ +E PQ M + I +H +D + + Y M+S+ T A+PTL NA P Q
Sbjct: 255 HEPLESPQEMFL--GIALHLAMPEKQDRMGWVKRFYDMLSKLKVTMATPTLSNARKPFHQ 312
Query: 215 LSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVP 274
LSSCF+ + D S++GIY ++ A +SK GG+G+ +RA GS IRG G + G++
Sbjct: 313 LSSCFIDTVPD-SLDGIYRSIDNFAQVSKFGGGMGLYFGKVRAVGSNIRGFQGVAGGVIR 371
Query: 275 MLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWV 334
+++ NDTA VDQ G R+GA AVYL+ WH DI EFL L+ N+G + +A D+F A+
Sbjct: 372 WIKLANDTAVAVDQLG-MRQGAVAVYLDVWHKDIPEFLQLRTNNGDDRMKAHDVFPAVCY 430
Query: 335 PDLF--MERVQTNGQWSLFCPNEAS-----GLADCWGAEFEKLYTHYEREGK-AKKVVQA 386
PDLF M R N W LFCP+E L D +G E+EK Y + + +K+ +
Sbjct: 431 PDLFWKMVRDDINQSWYLFCPHEILTVKGYALEDYYGEEWEKRYLDCVNDARISKRSIPI 490
Query: 387 QNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTET----- 441
++L IL S +ETGTP+ +DT NR + ++ G I SNLCTEI + S ET
Sbjct: 491 KDLVRLILKSAVETGTPFTFNRDTVNRANPNKHKGMIYCSNLCTEIAQNMSAIETVSTEI 550
Query: 442 ------------------AVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFE 483
VCNLAS++L + +E D E
Sbjct: 551 ETEDGDTVVVTTTRPGDFVVCNLASLSLGN------IDLE-----------------DEE 587
Query: 484 KLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEA 543
+L EV V L+ +ID+N+YPV A+ +N R+R IG+GV G G+ +ES E
Sbjct: 588 ELEEVVRTVVRALDNVIDLNFYPVPYAQITNKRYRSIGLGVSGYHHALAKNGIRWESEEH 647
Query: 544 QQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDWGVL 603
+ +FE I Y A+K S EIA ++G Y + S G +W L
Sbjct: 648 LEFADRVFERINYAAIKASMEIAKEKGAYGYFEGSDWQTGAYFRKRGYTSE----EWQRL 703
Query: 604 RDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHD 663
+++NG+RN+ L+A PT+STS I G +P V+ ++ L +
Sbjct: 704 AREVAENGMRNAYLLAVAPTSSTSIIAGTTAGVDP----------------VMKRYFLEE 747
Query: 664 LTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQ 723
+ G P + PE+ ++ +YK I Q + A R +IDQ
Sbjct: 748 --KKGALMPRVA-------------PELSDKTFWLYKNAHLIDQKWSIRAAGVRQRHIDQ 792
Query: 724 SQSLNIHMDQP-NFKKVTSLHFRTWSRGLKTGMYYLRSRA 762
+QS+N+++ ++V L+ W G+KT +YY+RS++
Sbjct: 793 AQSVNLYITNEFTMRQVLDLYLLAWEEGVKT-IYYVRSKS 831
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 362 bits (931), Expect = e-113
Identities = 241/824 (29%), Positives = 379/824 (45%), Gaps = 143/824 (17%)
Query: 5 KRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQKVCAGVYKGVTTSQLDELAAETA 64
KRDG+ E + +K +K GL CDP+ + G+TT ++ + +TA
Sbjct: 7 KRDGQYEPLQVEKTKKMVKLACEGLYG--CDPLELELDSRIQFRDGMTTKEIQKSLIQTA 64
Query: 65 -------------AAMTTNHPDYASLAARIAVSNLHKNTKKSF---SETIKDMYNHYNE- 107
+P++ +AAR+ V +L+K + + S D Y +
Sbjct: 65 IEKVIQNSKDNNGNNTKKTNPNWQYVAARLYVFDLYKEARINRHYNSFGYGDYYELVKKL 124
Query: 108 -RSGLKAPLI-----ADDIYEIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLK-VQ 160
L + ++I E L+ I +RDF ++Y G K L YL+K
Sbjct: 125 VEEKLYGEYLLQNYSKEEIKE--------LEKYIKPERDFLFNYEGLKLLADRYLVKGFN 176
Query: 161 GKVVERPQHMLMRVSIGIH-------KDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRP 213
+++E PQ M I +H + + A K Y ++S+ T A+PTL NAGTP
Sbjct: 177 REILELPQERFM--GIAMHLAIPEGKEKRVYYAKKFYDLLSELKATVATPTLSNAGTPFY 234
Query: 214 QLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIV 273
QLSSCF+ + DD++ IY+ ++ A +SK G +G+ IRA S IRG S G++
Sbjct: 235 QLSSCFISVV-DDNLWSIYDVNQKFAQVSKHGGALGIYTGKIRALNSEIRGFKNASGGVI 293
Query: 274 PMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALW 333
P ++++NDTA VDQ G KRKG A+ L+ WH DI EFL+LK N+G + +A D+F +
Sbjct: 294 PWIKLYNDTAIAVDQLG-KRKGGAAITLDIWHKDIPEFLDLKTNNGDDRRKAHDIFPGVS 352
Query: 334 VPDLFMERVQTNGQWSLFCPNEAS-----GLADCWG----AEFEKLYTHYEREGK-AKKV 383
PDLFM+R++ WSLF P+E L D + EF K Y E + ++
Sbjct: 353 YPDLFMKRLEKRENWSLFDPHEIKKVKGYSLEDYYDEEDRKEFTKKYLECEEDTNIPRRT 412
Query: 384 VQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETA- 442
V ++ +I+ S +ETGTP++ F+DT N+ + ++ G I SSNLC EI + S +E
Sbjct: 413 VPVLDIMKKIMKSAVETGTPFIFFRDTVNKANPNKHKGMIYSSNLCHEIAQNMSESELLE 472
Query: 443 ----------------------VCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFF 480
CNL SI L
Sbjct: 473 EEIIDENGYYEVVQKIKAGDMVTCNLNSIVLGN--------------------------V 506
Query: 481 DFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFES 540
D E+L EV L+ +I +NYYPV A ++ ++R IG+G G + +ES
Sbjct: 507 DDEELEEVIPTQIRMLDNVISLNYYPVPEAEITSDKYRAIGLGTSGYHHMLANNKIRWES 566
Query: 541 PEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKG-ILQPDMWNVIPSDRWD 599
E + I+E I Y+A+K S E+A ++G Y + S G + +N S+RW
Sbjct: 567 DEHIKFADKIYEEIAYYAIKASMELAKEKGSYPAFKGSEWETGKYFERRGYN---SERWK 623
Query: 600 WGVLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKH 659
L++ I K G+RN + A PT STS I +P V +
Sbjct: 624 --KLKEEIKKYGMRNGYITAVAPTGSTSNIANTTAGIDP----------------VFKRF 665
Query: 660 LLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGC 719
+ + + G ++P P++ EE YK I Q + R
Sbjct: 666 FMEE--KKGSFTPKTA-------------PDLNEENFWYYKEAHTIDQQWSIKACGVRQR 710
Query: 720 YIDQSQSLNIHMD-QPNFKKVTSLHFRTWSRGLKTGMYYLRSRA 762
+IDQ+QS N+++ + K++ +L+ W +G+KT +YY+R+++
Sbjct: 711 HIDQAQSFNLYITPEYKAKQILNLYIEAWKQGVKT-IYYVRNKS 753
>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 = 317 bits (814), Expect = 3e-98
Identities = 193/621 (31%), Positives = 298/621 (47%), Gaps = 67/621 (10%)
Query: 151 LERSYLLKVQ-GKVVERPQHMLMRVSIGI-HKDDIDSAIKT-------YHMMSQRWFTHA 201
L YL K + G ++E P+ + RV+ + +D ++ Y +M F
Sbjct: 2 LAARYLRKDEDGNILESPEDLFRRVARALAAAEDKYNSPVWKQLYERFYDLMVNLGFMPN 61
Query: 202 SPTLFN-AGTPRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGS 260
SPTL N GT QLS+CF V +D +E I+E KE A+I K GG+G + +R G
Sbjct: 62 SPTLMNAGGTRLGQLSACF-VLPVEDDMESIFEAAKEAALIFKRGGGVGYNFSTLRPKGD 120
Query: 261 YIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGK 320
+ GT G ++G V +RVF+ A + Q GG R+GA L+ WH DI EF+ KK GK
Sbjct: 121 KVSGTGGVASGPVSFMRVFDAAAGVIKQ-GGTRRGAQMGILDVWHPDIEEFIEAKKKEGK 179
Query: 321 EEHRARDLF-YALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGK 379
+ F ++ V D FME V+ + ++ L P G E E+L E +
Sbjct: 180 LTN-----FNISVGVTDAFMEAVEADEEYKLRNPRT--------GEEIEELAEKREPKLV 226
Query: 380 AKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEI--IEYTS 437
K V A+ LW +I+ + ++ P +LF DT N+ +N LG I ++N C E + Y S
Sbjct: 227 VYKEVPARELWDKIVEAAWKSAEPGLLFIDTINKWNNLPYLGRINATNPCGEQPLLPYES 286
Query: 438 PTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLN 497
CNL SI L +FV+ FDFE+L EV + T L+
Sbjct: 287 ------CNLGSINLAKFVKN----------------DFGGASFDFERLREVVRLATRFLD 324
Query: 498 KIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYH 557
+ID+N +P+ + + R IG+G+ GLAD I LG+ ++S EA+ +++ I
Sbjct: 325 NVIDLNRFPLPEIAEATKKTRRIGLGIMGLADLLIKLGIPYDSEEARAFAEELMRFIADA 384
Query: 558 ALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDWGVLRDMISKNGVRNSLL 617
A + S+E+A + G + + S LR+ I+K G+RN+ L
Sbjct: 385 AYRASAELAKERGAFPLFEAS------KYLMGKVARIPSALPA-ELREAIAKYGIRNAQL 437
Query: 618 VAPMPTASTSQILGNNECFEPYTSNIYSRRVL-SGEFVVVNKHLLHDLTEMGIWSPTIKN 676
PT + S I G + EP + +Y R V GE + VN + L E+G +S I
Sbjct: 438 TTIAPTGTISLIAGTSSGIEPVFALVYFRNVTVGGELLEVNPLVELALRELGYYSDEIVK 497
Query: 677 KIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDM--AVDRGCYIDQSQSLNIHMDQP 734
+ + G+V+ P++PEEL ++ T +I V M A+ ++D S S I+M P
Sbjct: 498 IEVAEKGTVEGAPDLPEELPKVFVTANDISPEDHVLMQAAIQP--WVDSSISKTINM--P 553
Query: 735 N---FKKVTSLHFRTWSRGLK 752
+ + V +++ W GLK
Sbjct: 554 SDATVEDVKAVYLEAWKLGLK 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 = 287 bits (736), Expect = 2e-88
Identities = 147/453 (32%), Positives = 221/453 (48%), Gaps = 53/453 (11%)
Query: 190 YHMMSQRWFTHASPTLFNAGT-PRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGI 248
++++ + F SPTL NAGT QLS+CF++ ++DDSIEGI++ LKE A+I K GG+
Sbjct: 5 FYLLLSQGFIPNSPTLMNAGTGELGQLSACFVLPVEDDSIEGIFDALKEAALIFKRGGGV 64
Query: 249 GVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADI 308
G + +R G ++ T G ++G V +RVF+ + QGG R+GA L+ H DI
Sbjct: 65 GYNFSRLRPKGDIVKSTGGVASGPVSFMRVFDAATGVIKQGG-TRRGANMGVLDVDHPDI 123
Query: 309 FEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFE 368
EF++ K K ++ ++ V D FME V+ + W L P E
Sbjct: 124 EEFIDAKMKEEKTVV-LQNFNISVAVTDAFMEAVENDEPWELRNPRE------------- 169
Query: 369 KLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNL 428
GK + V A+ LW +I+ + ++ P +LF DT NR + LG I ++N
Sbjct: 170 ------PDTGKVYRTVPARELWDKIVEAAWDSADPGVLFIDTINRWNPLPGLGRINATNP 223
Query: 429 CTEI--IEYTSPTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLA 486
C E + Y S CNL SI L +FV+ FDFE+L
Sbjct: 224 CGEQPLLPYES------CNLGSINLSKFVKN----------------PFGGASFDFERLR 261
Query: 487 EVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQL 546
E + L+ +IDVN YP+ R IG+GV GLAD I LG+ ++S EA++L
Sbjct: 262 EAVRLAVRFLDNVIDVNRYPLPEIAEETKATRRIGLGVMGLADMLIKLGIPYDSEEAREL 321
Query: 547 NKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDWGVLRDM 606
+ I I A + S+E+A + GP+ + S + M VI + + + +
Sbjct: 322 AERIMSFIRDAAYRASAELAKERGPFPLFDAS-------RYLMLKVIVNAKELPDDVLEE 374
Query: 607 ISKNGVRNSLLVAPMPTASTSQILGNNECFEPY 639
I K G+RN+ L PT + S I G + EP
Sbjct: 375 IEKYGIRNAHLTTIAPTGTISLIAGTSSGIEPI 407
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 285 bits (732), Expect = 7e-85
Identities = 198/673 (29%), Positives = 317/673 (47%), Gaps = 81/673 (12%)
Query: 1 MYVVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQKVCAGVYKGVTTSQLDELA 60
+ V+K G + +KI K L + DP + + + G+TT + E+
Sbjct: 4 INVIKSSGVSQPFDLEKI---HKVLEWACEGTGVDPSELEENSKIQLRDGMTTKDIQEIL 60
Query: 61 AETAA-AMTTNHPDYASLAARIAVSNLHKNTKKSFSETIKDMYNHYNERSGLK--APLIA 117
++AA ++ PDY +AAR+ + L K +Y + S + + +
Sbjct: 61 IKSAADLISVEEPDYQYVAARLLMFALRK-----------QVYGQFEPPSFIDHISKCVN 109
Query: 118 DDIY--EIIMKNAA----CLDSEIIYDRDFDYDYFGFKTLERSYLLK--VQGKVVERPQH 169
+ Y EI+ K +A L+S I +DRDF++ Y G L+ YL++ G++ E PQ
Sbjct: 110 EGKYDPEILSKYSAEEITYLESFIDHDRDFEFTYAGAMQLKEKYLVQDRSTGEIYETPQF 169
Query: 170 MLMRVSIGIHKDD-----IDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMK 224
M +++ +H+D+ ++ I+ Y+ +S R + +P + TP Q SSC ++
Sbjct: 170 AYMLIAMALHQDEPKEDRLEHVIRFYNAVSTRKISLPTPIMAGVRTPTRQFSSCVVI-ES 228
Query: 225 DDSIEGIYETLKECA-VISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTA 283
DS++ I +T ISK AG IG++ IRA GS IRG G++P + F
Sbjct: 229 GDSLDSINKTAMAIVKYISKRAG-IGINAGMIRAEGSKIRGGEVRHTGVIPFWKHFQTAV 287
Query: 284 RYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQ 343
+ QGG R GA Y WH ++ + L LK N G EE+R R L Y + + DL ER
Sbjct: 288 KSCSQGG-IRGGAATAYYPIWHLEVEDLLVLKNNKGVEENRIRHLDYGVQINDLMYERFI 346
Query: 344 TNGQWSLFCPNEASG-LADCWGA---EFEKLYTHYEREGKA-KKVVQAQNLWFEILTSQI 398
N +LF P++ G L D + A F +LY E++ KK ++AQ L+ +L +
Sbjct: 347 KNDYITLFSPHDVGGELYDAYFADQDRFRELYEALEKDPSVRKKRIKAQELFLLLLKERS 406
Query: 399 ETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSP-------TETAVCNLASIAL 451
ETG Y++F D CN S I+ SNLC EI T P E A+C L++I L
Sbjct: 407 ETGRIYIMFIDHCNNHSP--FKDPIRQSNLCCEIALPTKPLNHIDGEGEIALCTLSAIVL 464
Query: 452 PRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETAR 511
F D +++ E+ + L+ ++D YPV A
Sbjct: 465 -------------------------GNFEDQDEIEELAEVAVRALDNLLDYQDYPVPAAL 499
Query: 512 RSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGP 571
++ R R +G+GV A ++E A L ++FE + Y+ +K S+++A ++G
Sbjct: 500 KAKKR-RSLGVGVTNYAHYLAKNFASYEDANA-DLVHELFERLQYYLIKASNKLAKEKGA 557
Query: 572 YETYHNSPVSKGILQPDMWN------VIPSDRWDWGVLRDMISKNGVRNSLLVAPMPTAS 625
E + ++ S+G L D + V P DW LR+ + K G+RNS L A MP S
Sbjct: 558 CEYFSDTKYSRGELPIDWYKKKVDELVAPKYNCDWESLREDLKKYGIRNSTLSALMPCES 617
Query: 626 TSQILGNNECFEP 638
+SQ+ + EP
Sbjct: 618 SSQVSNSTNGIEP 630
>gnl|CDD|236330 PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 752
Score = 253 bits (649), Expect = 4e-73
Identities = 171/568 (30%), Positives = 264/568 (46%), Gaps = 92/568 (16%)
Query: 151 LERSYLLK-VQGKVVERPQHMLMRVSIGI--------HKDDIDS-AIKTYHMMSQRWFTH 200
LE+ YL K GK +E P+ M RV+ I K D+++ A + Y +M+ F
Sbjct: 20 LEKRYLKKDEDGKPIETPEDMFRRVARTIAAAELIYDSKADVEALADRFYDLMTSLEFLP 79
Query: 201 ASPTLFNAGTPRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGS 260
SPTL NAG QLS+CF V DSIE I++ +K A+I KS GG G S +R
Sbjct: 80 NSPTLMNAGRELGQLSACF-VLPVGDSIEEIFDAVKHAALIHKSGGGTGFSFSRLRPKND 138
Query: 261 YIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGK 320
+ T G ++G V +RVF+ + QGG R+GA L H DI EF+ K+++G+
Sbjct: 139 RVGSTGGVASGPVSFMRVFDAATEAIKQGG-TRRGANMGILRVDHPDIMEFITCKEDNGE 197
Query: 321 EEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGKA 380
+ ++ + + FME V+ + ++ L P R G+
Sbjct: 198 ----LTNFNISVAITEAFMEAVEADEEYDLINP----------------------RTGEV 231
Query: 381 KKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTE--IIEYTSP 438
+ A+ ++ I+ E G P ++F D NR + +LG I+S+N C E ++ Y S
Sbjct: 232 VGRLNAREVFDLIVEMAWENGEPGIVFIDRINRDNPTPHLGEIESTNPCGEQPLLPYES- 290
Query: 439 TETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNK 498
CNL SI L + V+ DV D+EKL EV + L+
Sbjct: 291 -----CNLGSINLSKMVKNGDV--------------------DWEKLREVVHLAVRFLDN 325
Query: 499 IIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHA 558
+ID N YP+ +R IG+GV G AD I LG+ ++S EA +L + + + I A
Sbjct: 326 VIDANKYPLPQIEEMTKGNRKIGLGVMGWADMLIQLGIPYDSEEAVELAEKVMKFIQDEA 385
Query: 559 LKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDWGVLRDMISKNGVRNSLLV 618
S E+A + GP+ Y S +D +D + +RN+ +
Sbjct: 386 HAASRELAEERGPFPNYEGS------------------IYD----KDGLGP--MRNATVT 421
Query: 619 APMPTASTSQILGNNECFEPYTSNIYSRRVLSGE-FVVVNKHLLHDLTEMGIWSPTIKNK 677
PT + S I G + EP + ++R V+ GE V VN E G +S + K
Sbjct: 422 TIAPTGTISIIAGCSSGIEPLFALSFTRNVMDGERLVEVNPVFEAAAKEEGFYSEELMEK 481
Query: 678 IIYDDGSVQKIPEIPEELKMIYKTVWEI 705
I + GS+Q I E+PE+++ ++ T +I
Sbjct: 482 IA-EKGSIQDIDEVPEDVRRVFVTAHDI 508
>gnl|CDD|181649 PRK09103, PRK09103, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 758
Score = 250 bits (641), Expect = 5e-72
Identities = 236/816 (28%), Positives = 367/816 (44%), Gaps = 132/816 (16%)
Query: 1 MYVVKRDGRQEAVHFDKITARLKKLSYGLSTEHCDPVLVSQ---KVCAGVYKGVTTSQLD 57
+ V KRDGR E ++ DKI + + GL V VSQ + Y G+ TS +
Sbjct: 2 LLVTKRDGRTERINLDKIHRVITWAAEGL-----HNVSVSQVELRSHIQFYDGIKTSDIH 56
Query: 58 ELAAETAAAM-TTNHPDYASLAARIAVSNLHKNTKKSFSETIKDMYNHYN---ERSGLKA 113
E + AA + + + PDY LAAR+A+ +L K F +Y+H E
Sbjct: 57 ETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQF--EPPALYDHVVKMVEMGKYDK 114
Query: 114 PLIADDIYEIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLL--KVQGKVVERPQHML 171
L+ D E + +D+ I + RD ++ Y K LE YL+ +V G++ E Q +
Sbjct: 115 HLLEDYTEEEFDQ----MDTFIDHWRDMNFSYAAVKQLEGKYLVQNRVTGEIYESAQFLY 170
Query: 172 MRVSI----GIHKDDIDSAIKT-YHMMSQRWFTHASPTLFNAG--TPRPQLSSCFLV-CM 223
+ V+ K+ +K Y +S F + PT +G TP Q SSC L+ C
Sbjct: 171 ILVAACLFSNYPKETRLDYVKRFYDAVST--FKISLPTPIMSGVRTPTRQFSSCVLIEC- 227
Query: 224 KDDSIEGIYETLKECAVI---SKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFN 280
DS++ I T A++ S+ AG IG++ IRA GS IRG G +P + F
Sbjct: 228 -GDSLDSINAT--SSAIVKYVSQRAG-IGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQ 283
Query: 281 DTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFME 340
+ QGG R GA ++ WH ++ L LK N G EE+R R + Y + + L +
Sbjct: 284 TAVKSCSQGG-VRGGAATLFYPIWHLEVESLLVLKNNRGVEENRVRHMDYGVQINKLMYQ 342
Query: 341 RVQTNGQWSLFCPNEASGLADCWGA---EFEKLYTHYEREGKA-KKVVQAQNLWFEILTS 396
R+ G +LF P++ GL D + A EFE+LYT YE++ KK V+A L+ ++
Sbjct: 343 RLIKGGDITLFSPSDVPGLYDAFFADQDEFERLYTKYEQDDSIRKKRVKAVELFSLMMQE 402
Query: 397 QIETGTPYMLFKDTCNRKSN-QQNLGTIKSSNLCTEIIEYTSPT--------ETAVCNLA 447
+ TG Y+ D CN S + ++ SNLC EI T P E A+C L+
Sbjct: 403 RASTGRIYIQNVDHCNTHSPFDPKVAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLS 462
Query: 448 SIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPV 507
+ L G+ N + E+LA+ + L+ ++D YP+
Sbjct: 463 AFNL----------------------GAINSLDELEELAD---LAVRALDALLDYQDYPI 497
Query: 508 ETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAA 567
A+R + R +GIGV A G+ + A L FE I Y+ LK S+E+A
Sbjct: 498 PAAKRGAMGRRTLGIGVINFAYYLAKNGVRYSDGSANNLTHKTFEAIQYYLLKASNELAK 557
Query: 568 KEGPYETYHNSPVSKGILQPDMW----NVIPSD--RWDWGVLRDMISKNGVRNSLLVAPM 621
++G ++ + ++GIL D + + I ++ +DW LR+ I +G+RNS L A M
Sbjct: 558 EQGACPWFNETTYAQGILPIDTYKKDLDAICNEPLHYDWETLREEIKTHGLRNSTLSALM 617
Query: 622 PTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYD 681
P+ ++SQI EP R +S + +K
Sbjct: 618 PSETSSQISNATNGIEP------PRGYVS---IKASK----------------------- 645
Query: 682 DGSV-QKIPEIPEELKMIYKTVWEIKQM----TLVDMAVDRGCYIDQSQSLNIHMDQPNF 736
DG + Q +P+ E LK Y+ +WE+ LV + ++DQS S N + D F
Sbjct: 646 DGILKQVVPDY-ERLKDAYELLWEMPNNDGYLQLVGIMQK---FVDQSISANTNYDPSRF 701
Query: 737 -------KKVTSLHFRTWSRGLKTGMYYLRSRAAAD 765
K++ + G+KT +YY +R A+
Sbjct: 702 PSGKVPMKQLLKDLLTAYKFGVKT-LYYHNTRDGAE 736
>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 = 234 bits (598), Expect = 7e-68
Identities = 171/626 (27%), Positives = 266/626 (42%), Gaps = 114/626 (18%)
Query: 151 LERSYLLK---VQGKVVERPQHMLMRVSIGIHKDDIDSAIKTYHMMSQRWFTHASPTLFN 207
R YLLK V+G+V E + + +++ ++ A+P N
Sbjct: 14 FRRGYLLKGETVEGRVREIASTA------EKLDIRPGFEERFFEYLARGKYSLATPVWAN 67
Query: 208 AGTPRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNG 267
G R SC + DS+ I E E +++K+ GG + +IR G+ I TNG
Sbjct: 68 TGLDRGLPISCAGSYV-GDSVLDILEGQAEVGMMAKNGGGTSSYLGDIRPRGADIS-TNG 125
Query: 268 TSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHRARD 327
TSNG +F++ QG +R G +A Y++ H D E+L ++ + +H
Sbjct: 126 TSNGADGFAPLFDNFINVKTQGATRR-GEWAGYVDFEHPDFEEWLGIQLENPASQH---- 180
Query: 328 LFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYEREGKAKKVVQAQ 387
+ + + V D + E++ G +K +
Sbjct: 181 VGWGVEVGDDWYEKM---------------------------------IAGDPEK----R 203
Query: 388 NLWFEILTSQIETGTPYMLFKDTCNRKSNQ--QNLG-TIKSSNLCTEIIEYTSPTETAVC 444
W +++ S+ TG PYM F+ N + Q +N G I++SNLCTEI + E+ VC
Sbjct: 204 ARWAKLMYSRARTGIPYMWFRWNANELAPQVIKNSGIPIRASNLCTEIALPSDDMESFVC 263
Query: 445 NLASIALPRFVREKDV-PVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVN 503
L+S+ + + KD VE+ RF D ++ +E + K ++
Sbjct: 264 CLSSLNVLHYDEWKDTDAVET-----------LVRFLD--------SVCSEFIAKAKGLS 304
Query: 504 YYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSS 563
Y + A R R R IG+G G + FES EA LN +I++TI A + S
Sbjct: 305 Y--MHRAVRFAERARAIGLGTLGWHSYLQSNRIPFESGEAHILNAEIYKTIKERAEEASR 362
Query: 564 EIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDWGVLRDMISKNGVRNSLLVAPMPT 623
E+A E Y V +G G RN+ L+A PT
Sbjct: 363 ELA------ERYGEPEVCEG--------------------------TGRRNATLIAIAPT 390
Query: 624 ASTSQILGN-NECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDD 682
S++ ILG + EP SN + + G+ V N L L E G + + I Y +
Sbjct: 391 KSSAFILGQVSPSIEPLVSNYFIQDSNKGDVVRKNPVLAKVLKEKGTDQELVWDIITYHN 450
Query: 683 GSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLN--IHMDQPNFKKVT 740
GSVQ + + +E K ++KT +EI QM ++ +A R +IDQ+QSLN I D+
Sbjct: 451 GSVQHLDFLTDEEKSVFKTFYEISQMAIIRLAAARQKHIDQAQSLNLFISPDEKPSVDAN 510
Query: 741 SLHFRTWSRGLKTGMYYLRSRAAADA 766
L W GLK+ +YY RS A A
Sbjct: 511 VLRAFAWDPGLKS-LYYQRSERGAQA 535
>gnl|CDD|235796 PRK06406, PRK06406, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 771
Score = 235 bits (601), Expect = 2e-66
Identities = 164/549 (29%), Positives = 253/549 (46%), Gaps = 87/549 (15%)
Query: 188 KTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGG 247
K +MS F SPTL NAGT QLS+CF++ + DSIEGI+ LK A+I KS GG
Sbjct: 222 KFEEVMSNLKFVPNSPTLMNAGTKLGQLSACFVLPV-PDSIEGIFNALKYTAMIHKSGGG 280
Query: 248 IGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHAD 307
G S +R + T G ++G + +R+F+ T + QGG KR+GA L H D
Sbjct: 281 TGFSFSRLRPKDDIVASTKGVASGPLSFMRIFDVTTDVIKQGG-KRRGANMGILSYHHPD 339
Query: 308 IFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEF 367
I EF+ K + K + ++ V D F +++ + + L P
Sbjct: 340 IMEFITSKDSENKV---LSNFNISVAVTDEFFDKLDNDDYYPLRNP-------------- 382
Query: 368 EKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSN 427
R GK K ++A+ +W I+T +TG P ++F D NRK+ +NLG I+S+N
Sbjct: 383 --------RNGKEVKRIKARQVWDLIITQAWKTGDPGVIFLDEINRKNPVKNLGEIESTN 434
Query: 428 LCTE--IIEYTSPTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKL 485
C E ++ Y S CNL SI L +FV +N D+++L
Sbjct: 435 PCGEQPLLPYES------CNLGSINLSKFV--------------------ENGKIDWDRL 468
Query: 486 AEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQ 545
E I T L+ +ID N +PV + R IG+GV G AD I LG+ + S EA +
Sbjct: 469 RETVHIATRFLDNVIDANKFPVPQIKEMTRMTRKIGLGVMGFADMLIKLGIPYNSEEALE 528
Query: 546 LNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKGILQPDMWNVIPSDRWDWGVLRD 605
+ + + + I + + S ++A + G + ++ S +W
Sbjct: 529 IAEKVMKFINEESHRASQKLAEERGVFPAWYGS--------------------EW----- 563
Query: 606 MISKNGV--RNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSG-EFVVVNKHLLH 662
K G+ RNS PT + S I G + EP + + R VL+G E + VN
Sbjct: 564 --EKKGIKMRNSTTTTIAPTGTISIIAGCSSSIEPLFAIAFVRHVLNGQELLEVNPLFEE 621
Query: 663 DLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYID 722
+ G++S + K+ + G++Q I ++PE++K I+ T EI V M Y D
Sbjct: 622 ITRKRGLYSEELMRKVA-ETGNLQNI-DVPEDIKRIFVTAHEIDPQWHVLMQATFQRYCD 679
Query: 723 QSQSLNIHM 731
S I++
Sbjct: 680 SGVSKTINL 688
Score = 31.4 bits (71), Expect = 2.6
Identities = 42/183 (22%), Positives = 69/183 (37%), Gaps = 43/183 (23%)
Query: 1 MYVVKRDGRQEAVHFDKITARLKK--LSYGLSTEHCDPVLVSQKVCAGV--YKGVTTSQL 56
V+KRDG KI + K LS + D ++ KV + Y+ T Q+
Sbjct: 5 KEVIKRDGTVVPFDKKKIAMAIYKAMLSVKNGSME-DAEELTDKVVERLKKYERPTVEQI 63
Query: 57 DELAAETAAAMTTNHPDYASLAARIAVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLI 116
++ + N D+ +A L++ ++ E + + G+K
Sbjct: 64 QDIVEKVLMTKKINGKDFTDVAKSYI---LYREKRRKIREEKELI--------GVK---- 108
Query: 117 ADDIYEIIMKNAACLDSEIIYDRDFDYDYFGFKTLERSYLLKVQ-GKVVERPQHMLMRVS 175
DD+ + NA K LE YLLK + GK++E P+ M RV+
Sbjct: 109 -DDLK--LTLNA-------------------IKVLEARYLLKDEDGKIIETPRQMFRRVA 146
Query: 176 IGI 178
I
Sbjct: 147 RHI 149
>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 = 197 bits (502), Expect = 2e-53
Identities = 182/677 (26%), Positives = 290/677 (42%), Gaps = 114/677 (16%)
Query: 134 EIIYDRDFDYDYF--GFKTLERSYLLKV--QGKVVERPQHMLMRVSIGIHKDDIDSAIK- 188
E Y F + F FK SY LK + +ER + + V++ + D + A +
Sbjct: 76 EHAYASKFRFPSFMGAFK-FYTSYALKTNDGKRYLERYEDRVCMVALTLANGDEELAKQL 134
Query: 189 TYHMMSQRWFTHASPTLFNAGTP-RPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGG 247
M+SQR + A+PT NAG R +L SCFL+ + +D++ I + +SK GG
Sbjct: 135 VDEMISQR-YQPATPTFLNAGRARRGELVSCFLLRV-EDNMNSIGRAINSALQLSKRGGG 192
Query: 248 IGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHAD 307
+ +++ N+R G+ I+G S+G++P++++ D Y +Q G +R+GA AVYL +H D
Sbjct: 193 VALNLSNLREAGAPIKGIENQSSGVIPVMKLLEDAFSYANQLG-QRQGAGAVYLNAFHPD 251
Query: 308 IFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEF 367
I FL+ KK + E+ R + L + +PD F E + N LF P + + +G F
Sbjct: 252 ILRFLDTKKENADEKIRIKTLSLGVVIPDKFFELAKENKDMYLFSPYD---VEREYGVPF 308
Query: 368 EKL-YTHYEREGKA-----KKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLG 421
+ + T E A KK + A++ + + Q E+G PY++F+DT NR +G
Sbjct: 309 DDIDITEKYDEMVANPRIRKKKINARDFFQTLAEIQFESGYPYIMFEDTVNRA--NPIIG 366
Query: 422 TIKSSNLCTEIIEYTSPT------------ETAVCNLASIALPRFVREKDVPVESHPSRI 469
IK SNLC+EI++ + + CNL S+ + V P
Sbjct: 367 RIKMSNLCSEILQVSEASLYNDYLEYDEIGHDISCNLGSLNI--------ANVMDSP--- 415
Query: 470 VGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDV-NYYPVETARRSNLRHRPIGIGVQGLA 528
DF + E TAI L + D+ + V + R+ N IG+G L
Sbjct: 416 -----------DFGRTVE-TAI--RALTAVSDMSHIRNVPSIRKGNAASHAIGLGQMNLH 461
Query: 529 DTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSK------ 582
G+A+ SPEA F T+ Y++L+ S EIA + G ET+ S
Sbjct: 462 GYLAREGIAYGSPEALDFTNIYFMTVNYYSLRRSMEIARERG--ETFAGFEQSDYASGEY 519
Query: 583 ------GILQPDMWNV--------IPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQ 628
P V IP+ R DW L+D + + G+ + +A PT S S
Sbjct: 520 FDKYVSQEFAPKTEKVRELFEGIHIPT-REDWAELKDDVMEYGLYHQNRLAVAPTGSISY 578
Query: 629 ILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKI 688
I + P S I R E I ++ Y
Sbjct: 579 INHSTSSIHPIVSKIEIR------------------KEGKI------GRVYY------PA 608
Query: 689 PEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLNIHM-DQPNFKKVTSLHFRTW 747
P + E Y+ ++I ++D ++DQ SL + D + + W
Sbjct: 609 PFLTNENLEYYQDAYDIDMEKIIDTYATATQHVDQGLSLTLFFKDTATTRDLNRAQIYAW 668
Query: 748 SRGLKTGMYYLRSRAAA 764
+G+KT +YY+R R A
Sbjct: 669 HKGIKT-LYYIRLRQLA 684
>gnl|CDD|236069 PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 699
Score = 182 bits (463), Expect = 3e-48
Identities = 174/718 (24%), Positives = 302/718 (42%), Gaps = 97/718 (13%)
Query: 85 NLHKNTK--KSFSETIKDMYNHYNERSGLKAPLIADDIYEIIMKNAACLD----SEIIYD 138
L K+ + + E IKD ++ L+ +D Y + + D ++ Y
Sbjct: 26 QLEKDQEALVVYLEEIKDNTIFFDTEIERLRYLVDNDFYFNVFDIYSEEDLIEVTDYAYS 85
Query: 139 RDFDY-DYFGFKTLERSYLLKVQGK--VVERPQHMLMRVSIGIHKDDIDSAIKTYHMMSQ 195
F++ Y + Y LK K +E + + V++ + D A + M +
Sbjct: 86 IKFNFASYMSASKFYKDYALKTNDKKQYLEDYEDHVAIVALYLANGDKAKAKQFISAMVE 145
Query: 196 RWFTHASPTLFNAGTPRP-QLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGVSVHN 254
+ + A+PT NAG R +L SCFL+ + DDS+ I +SK GG+ +++
Sbjct: 146 QRYQPATPTFLNAGRARRGELVSCFLLEV-DDSLNSINFIDSTAKQLSKIGGGVAINLSK 204
Query: 255 IRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNL 314
+RA G I+G G + G++P+ ++ Y DQ G +R GA AVYL +H D+ EFL+
Sbjct: 205 LRARGEAIKGIKGAAKGVLPVAKLLEGGFSYADQLG-QRPGAGAVYLNIFHYDVEEFLDT 263
Query: 315 KKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPN---EASG--LADCWGAEFEK 369
KK + E+ R + L VP F E + + +F P+ + G L D + E+
Sbjct: 264 KKVNADEDLRLSTISTGLIVPSKFFELAKEGKDFYMFAPHTVYKEYGVTLDD---IDLEE 320
Query: 370 LYTHYEREGKA-KKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNL 428
+Y KK A+ + +I +Q+++G PY++FKD N+ N+G IK SNL
Sbjct: 321 MYDDLVANPNVKKKKKNAREMLNKIAQTQLQSGYPYLMFKDNANKVHPNSNIGQIKMSNL 380
Query: 429 CTEIIEYTSPTETAVCNLASIALPRFVREKDVPVESHPSR-IVGSRGSKN--RFFDFEKL 485
CTEI + ET++ N D +E R I + GS N + +K
Sbjct: 381 CTEIFQL---QETSIIN-------------DYGIEDEIKRDISCNLGSLNIVNVMESKKF 424
Query: 486 AEVTAIVTENLNKIIDV-NYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQ 544
+ + L + DV N R++N +G+GV L + +ES EA+
Sbjct: 425 RDSVHSGMDALTVVSDVANIQNAPGVRKANSELHSVGLGVMNLHGYLAKNKIGYESEEAK 484
Query: 545 QLNKDIFETIYYHALKTSSEIAAKEGPYETYHN--------------------SPVSKGI 584
F + +++++ S EIA + G ETY + P + +
Sbjct: 485 DFANTFFMMMNFYSIERSMEIAKERG--ETYQDFEKSDYANGKYFEKYTTQDFEPKFEKV 542
Query: 585 LQPDMWNVIPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIY 644
+ IP+ DW L+ + + G+ ++ +A PT S S + P I
Sbjct: 543 RELFEGMHIPTKE-DWKKLQQDVEQYGLYHAYRLAIAPTQSISYVQNATSSVMPIVDQIE 601
Query: 645 SRRVLSGEFVVVNKHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWE 704
R T N + +P + + YK+ +
Sbjct: 602 RR--------------------------TYGNAETF-----YPMPFLSPQTMWYYKSAFN 630
Query: 705 IKQMTLVDMAVDRGCYIDQSQSLNIHM-DQPNFKKVTSLHFRTWSRGLKTGMYYLRSR 761
QM L+D+ +IDQ S +++ + + +++ L+ +GLK+ +YY R++
Sbjct: 631 TDQMKLIDLIATIQTHIDQGISTILYVNSEISTRELARLYVYAHHKGLKS-LYYTRNK 687
>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 720
Score = 169 bits (430), Expect = 6e-44
Identities = 146/502 (29%), Positives = 228/502 (45%), Gaps = 90/502 (17%)
Query: 192 MMSQRWFTHASPTLFNAG-TPRPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGV 250
M+ QR + A+P+ NAG R +L SCFL+ + DD + I ++ +S+ GG+G+
Sbjct: 146 MIHQR-YQPATPSFLNAGRARRGELVSCFLIQVTDD-MNSIGRSINSALQLSRIGGGVGI 203
Query: 251 SVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFE 310
++ N+R G+ I+G G ++G+VP++++F D+ Y +Q G +R+GA VYL +H DI
Sbjct: 204 NLSNLREAGAPIKGYEGAASGVVPVMKLFEDSFSYSNQLG-QRQGAGVVYLNVFHPDIIA 262
Query: 311 FLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWG------ 364
FL+ KK + E+ R + L + VPD F E + N LF P + +G
Sbjct: 263 FLSTKKENADEKVRVKTLSLGVTVPDKFYELARKNEDMYLFSP---YSVEKEYGVPFNYV 319
Query: 365 ---AEFEKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLG 421
E+++L + K ++A++L EI Q E+G PY++ DT NR +N + G
Sbjct: 320 DITKEYDELVANPNIR---KTKIKARDLETEISKLQQESGYPYIINIDTANR-ANPID-G 374
Query: 422 TIKSSNLCTEIIEYTSPTE-----------TAV-CNLASIALPRFVREKDVPVESHPSRI 469
I SNLC+EI++ +P+ T + CNL S + + D
Sbjct: 375 KIIMSNLCSEILQVQTPSLINDAQEYVKMGTDISCNLGSTNIVNMMTSPD---------- 424
Query: 470 VGSRGSKNRFFDFEKLAEVTAI--VTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGL 527
F V A+ VT++ N ID V + + N + IG+G GL
Sbjct: 425 ----------FGRSIETMVRALTFVTDSSN--IDA----VPSIKHGNSQAHTIGLGAMGL 468
Query: 528 ADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSK----- 582
+ + SPE+ + F + Y L S+ IA + G ET+HN SK
Sbjct: 469 HSYLAQNHIEYGSPESLEFTSIYFMLLNYWTLVASNNIARERG--ETFHNFEKSKYADGS 526
Query: 583 -------GILQPDMWNV--------IPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTS 627
G P V IP+ DW LRD + K+G+ + +A P S S
Sbjct: 527 YFDKYVTGDFVPKSDKVKELFKGIFIPTAA-DWAALRDAVMKDGLYHQNRLAVAPNGSIS 585
Query: 628 QILGNNEC---FEPYTSNIYSR 646
I N+ P T I R
Sbjct: 586 YI---NDTSASIHPITQRIEER 604
>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 721
Score = 167 bits (426), Expect = 2e-43
Identities = 126/477 (26%), Positives = 217/477 (45%), Gaps = 71/477 (14%)
Query: 192 MMSQRWFTHASPTLFNAGTP-RPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIGV 250
++ R F A+PT NAG R + SC+L+ + +D++E I + +SK GG+ +
Sbjct: 144 ILLGR-FQPATPTFLNAGKKRRGEYISCYLLRV-EDNMESISRAISTSLQLSKRGGGVAL 201
Query: 251 SVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFE 310
+ N+R G+ I+G + GI+P++++ D+ Y +Q G +R+GA AVYL H D+
Sbjct: 202 CLTNLREIGAPIKGIENQATGIIPVMKLLEDSFSYANQLG-QRQGAGAVYLHAHHPDVLT 260
Query: 311 FLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEF--- 367
FL+ K+ + E+ R + L L +PD+ E + N +LF P + + +G
Sbjct: 261 FLDTKRENADEKIRIKSLSLGLVIPDITFELAKENKDMALFSPYD---IKREYGKPMSDI 317
Query: 368 ---EKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIK 424
E+ Y K + A+ L+ I E+G PY+LF DT N+++ G I
Sbjct: 318 SITEEYYNLLANPAIKKTYISARKLFQTIAELHFESGYPYLLFDDTVNKRNPHAKKGRIV 377
Query: 425 SSNLCTEIIEYTSPT------------ETAVCNLASIALPRFVREKDVPVESHPSRIVGS 472
SNLC+EI + ++P+ E CNL S+ + +ES P
Sbjct: 378 MSNLCSEIAQVSTPSTFNEDLSFKKIGEDICCNLGSLNI-------AKAMESGP------ 424
Query: 473 RGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFI 532
+FE+L + + ++++ D++ P + + N + +G+G L
Sbjct: 425 --------EFEQLIYTSIRALDRVSRVSDLSCAP--SIEKGNAANHAVGLGAMNLHGFLA 474
Query: 533 LLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKG-------IL 585
+ ++S EA F T+ Y+A K S+++A ++G + + S + G
Sbjct: 475 TNHIYYDSKEAVDFTDLFFYTMAYYAFKASNQLAKEKGAFAGFELSKYADGSYFDKYTKE 534
Query: 586 QPDMWN---------------VIPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTS 627
W IP+ + DW L + I K G+ NS L+A PT S S
Sbjct: 535 DAKKWTPKTAKVKELLQKYGVTIPT-QADWQELVEDIKKTGLANSHLLAVAPTGSIS 590
>gnl|CDD|236179 PRK08188, PRK08188, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 714
Score = 157 bits (399), Expect = 6e-40
Identities = 188/695 (27%), Positives = 295/695 (42%), Gaps = 141/695 (20%)
Query: 137 YDRDF-----DYDY---FGFKTL------ERSYLLKV-QGK-VVERPQHMLMRVSIGIHK 180
Y R+F D+ Y F F+T SY LK GK +ER + + V++ + +
Sbjct: 80 YSRNFVKTLFDHAYAKKFRFQTFLGAFKYYTSYTLKTFDGKRYLERFEDRVCMVALTLAQ 139
Query: 181 DDIDSAIK-TYHMMSQRWFTHASPTLFNAGTP-RPQLSSCFLVCMKDDSIEGIYETLKEC 238
D A + ++S R F A+PT N G R +L SCFL+ + +D++E I ++
Sbjct: 140 GDETLARQLVDEIISGR-FQPATPTFLNCGKKQRGELVSCFLLRI-EDNMESIGRSINSA 197
Query: 239 AVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFA 298
+SK GG+ + + N+R G+ I+ S+G++P++++ D Y +Q G R+GA A
Sbjct: 198 LQLSKRGGGVALLLSNLREAGAPIKRIENQSSGVIPVMKLLEDAFSYANQLGA-RQGAGA 256
Query: 299 VYLEPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASG 358
VYL H DI FL+ K+ + E+ R + L + +PD+ E + N LF P +
Sbjct: 257 VYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFELAKENEDMYLFSPYDVER 316
Query: 359 LADCWGAEF------EKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCN 412
+ +G F EK E KK + A+ + + Q E+G PY++F+DT N
Sbjct: 317 V---YGKPFADISVTEKYDEMVADERIRKKKINAREFFQTLAEIQFESGYPYIMFEDTVN 373
Query: 413 RKSNQQNLGTIKSSNLCTEIIEYTSPTETA------------VCNLAS--IALPRFVREK 458
R + G I SNLC+EI++ S +E CNL S IA
Sbjct: 374 RANPIA--GRINMSNLCSEILQVNSASEYNEDLSYAHIGKDISCNLGSLNIA-----HTM 426
Query: 459 DVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNY-YPVETARRSNLRH 517
D P DF + E TAI L + D+++ V + + N
Sbjct: 427 DSP-------------------DFGRTVE-TAI--RALTAVSDMSHIRSVPSIEKGNAAS 464
Query: 518 RPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHN 577
IG+G L G+ + S EA F T+ YHAL+ S+ +A + G ET+
Sbjct: 465 HAIGLGQMNLHGYLAREGIFYGSEEALDFTNIYFYTVTYHALRASNLLARERG--ETFAG 522
Query: 578 SPVSK------------GILQPDMWNV----------IPSDRWDWGVLRDMISKNGVRNS 615
SK QP V IP + DW LRD + ++G+ N
Sbjct: 523 FEQSKYASGEYFDKYTQQDWQPKTAKVRELFARAGITIP-TQEDWAQLRDDVMRHGIYNQ 581
Query: 616 LLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWSPTIK 675
L A PT S S I N+ TS+I+ I
Sbjct: 582 NLQAVPPTGSISYI--NHS-----TSSIHP----------------------------IV 606
Query: 676 NKI-IYDDGSVQKI----PEIPEELKMIYKTVWEIKQMTLVDMAVDRGCYIDQSQSLNIH 730
+KI I +G + ++ P + + Y+ +EI ++D ++DQ SL +
Sbjct: 607 SKIEIRKEGKIGRVYYPAPYMTNDNLEYYQDAYEIGPEKIIDTYAAATQHVDQGLSLTLF 666
Query: 731 M-DQPNFKKVTSLHFRTWSRGLKTGMYYLRSRAAA 764
D + + W +G+KT +YY+R R A
Sbjct: 667 FPDTATTRDINKAQIYAWRKGIKT-LYYIRLRQMA 700
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 148 bits (375), Expect = 1e-36
Identities = 104/408 (25%), Positives = 170/408 (41%), Gaps = 73/408 (17%)
Query: 191 HMMSQRWFTHASPTLFNAGTP-RPQLSSCFLVCMKDDSIEGIYETLKECAVISKSAGGIG 249
++ + F+ SP FN GT Q+S+CF++ + DDS+E I KE ++ K G G
Sbjct: 124 WLLLHQKFSFNSPVWFNVGTESPQQVSACFILSV-DDSMESILNWYKEEGMLFKGGSGTG 182
Query: 250 VSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIF 309
++ IR++ + G GT++G V +R + +A + GG R+ A V L+ H DI
Sbjct: 183 TNLSRIRSSKELLSG-GGTASGPVSFMRGADASAGTIKSGGATRRAAKMVILDVDHPDIE 241
Query: 310 EFLNLKKNHGKEEHRARDL-----------------FY-----ALWVPDLFMERVQTNGQ 347
EF+ K KEE + R L Y ++ V D FM V+ +G+
Sbjct: 242 EFIETK---AKEEDKIRALRDAGYDMDLGGEAYSSVQYQNANNSVRVSDEFMRAVENDGE 298
Query: 348 WSLFCPNEASGLADCWGAEFEKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLF 407
+ L +G+ + V A+ L+ +I + E P + +
Sbjct: 299 FGL----------------------RARTDGEVIETVDAKELFRKIAEAAWECADPGIQY 336
Query: 408 KDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKDVPVESHPS 467
DT N G I +SN C+ EY ++ CNLAS+ L +F+R+
Sbjct: 337 DDTINDWHTCPESGRINASNPCS---EYMFLDNSS-CNLASLNLMKFLRDDGT------- 385
Query: 468 RIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGL 527
FD E +V + I +P E R+ R +G+G L
Sbjct: 386 ------------FDVESFRHAVELVITAMEISICFADFPTEKIARNTRAFRQLGLGYANL 433
Query: 528 ADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETY 575
+ G+ ++S + L I + A + S+E+A GP+E Y
Sbjct: 434 GALLMATGLPYDSDGGRALAAAITSLMTGEAYRRSAELAGVVGPFEGY 481
>gnl|CDD|180772 PRK06948, PRK06948, ribonucleotide reductase-like protein;
Provisional.
Length = 595
Score = 135 bits (342), Expect = 3e-33
Identities = 118/470 (25%), Positives = 191/470 (40%), Gaps = 69/470 (14%)
Query: 201 ASPTLFNAGTPRPQ-LSSCFL--------VCMKDDSIEGIYETLKECAVISKSAGGIGVS 251
A + NAG Q + +CF+ + +++ L + + GGIG
Sbjct: 70 AGRIMANAGAAPDQTMVNCFVHPIRAPAALTAVHPNLD---RALDDARLTLLMGGGIGYD 126
Query: 252 VHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEF 311
I + + S G+ L F+ + G+R AV L H D+ F
Sbjct: 127 FSAIPPADARPDADHPDSPGVCAALDRFDRICAALPFRDGRRGAQMAV-LRCDHPDLLAF 185
Query: 312 LNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLY 371
+ K+ R ++ V D FM+ V + W+L A GA
Sbjct: 186 VAAKRGRA----RWTTFNLSVAVTDAFMQAVAQDLPWALRHRAPPRRAAG--GA------ 233
Query: 372 THYEREGK-AKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCT 430
+G V A++LW EI+++ ++ P +LF DT + + + I ++N C
Sbjct: 234 -LRGADGAWTYATVPARHLWREIVSAARDSAEPGLLFVDTIDAANPLREHERIDATNPCG 292
Query: 431 E--IIEYTSPTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEV 488
E + Y S C L I L RFVR HP + G + RF DF LA
Sbjct: 293 EQPLPPYGS------CVLGPIDLSRFVR--------HPFGV----GGEPRF-DFAALATA 333
Query: 489 TAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNK 548
I L+ +D+ +P+ R + R IG+GV GLAD ++ + ++SP A+++ +
Sbjct: 334 VRIQVRMLDNALDLTRWPLAAHAREARQKRRIGVGVTGLADALTMMRLRYDSPAAREMAR 393
Query: 549 DIFETIYYHALKTSSEIAAKEGPYETY----HNSPVSKGILQPDMWNVIPSDRWDWGVLR 604
I + +HA S+ +AA+ G Y H + G P +
Sbjct: 394 YIASDLRHHAYAASAALAAERGAYPLCDPAAHLDALRAGPPLP-------------HAVC 440
Query: 605 DMISKNGVRNSLLVAPMPTASTSQILGNNEC---FEPYTSNIYSRRVLSG 651
I+++G+RNS L++ P S S G+N C EP + I R V +G
Sbjct: 441 HAIARHGLRNSHLLSFAPVGSVSLAFGDN-CSPGIEPARAWIEHRPVRAG 489
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 137 bits (346), Expect = 5e-33
Identities = 94/314 (29%), Positives = 151/314 (48%), Gaps = 35/314 (11%)
Query: 426 SNLCTE--IIEYTSPTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFE 483
S+ C E + EY S CNLASI L +FV+ + P +FD++
Sbjct: 1294 SHNCGEEPLYEYES------CNLASINLAKFVKYDE---NGKP------------YFDWD 1332
Query: 484 KLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEA 543
+ A V V + L+ IDVN +P+ + R IG+G+ GLAD LG+ + S E
Sbjct: 1333 EYAYVIQKVAKYLDNAIDVNKFPLPEIDYNTKLTRRIGVGMMGLADALFKLGIPYNSEEG 1392
Query: 544 QQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPVSKGIL------QPDMWNVIPSDR 597
+ + + E + ++A K S E A K G + Y + KG L P++WN+
Sbjct: 1393 FKFMRKVTEYLTFYAYKYSVEAAKKRGTFPLYEKTEYPKGELPVEGFYHPEIWNL----- 1447
Query: 598 WDWGVLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVN 657
W L + I K GVRN+++ PT S S I + EP + +Y + V GEF V+
Sbjct: 1448 -PWDKLVEEIKKYGVRNAMVTTCPPTGSVSMIADTSSGIEPIFALVYKKSVTVGEFYYVD 1506
Query: 658 KHLLHDLTEMGIWSPTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMAVDR 717
+L + G++S + KI + GSVQ + EIPE+++ ++ T +I + + +
Sbjct: 1507 PVFEAELKKRGLYSEELLKKISDNYGSVQGLEEIPEDMQRVFVTALDIHWLDHILAQANI 1566
Query: 718 GCYIDQSQSLNIHM 731
++ S S I+M
Sbjct: 1567 QMWLTDSASKTINM 1580
Score = 47.5 bits (112), Expect = 3e-05
Identities = 25/78 (32%), Positives = 45/78 (57%), Gaps = 4/78 (5%)
Query: 170 MLMRVSIGIHKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRPQLSSCFLVCMKDDSIE 229
ML R ++ +I+ + + +M+ + F +P L N+G P LS+CF+V ++DD +E
Sbjct: 228 MLERGEFDKYEKEIE---EYFRLMTNQIFMPNTPALINSGRPLGMLSACFVVPIEDD-ME 283
Query: 230 GIYETLKECAVISKSAGG 247
I + + A+I K+ GG
Sbjct: 284 SIMKAAHDVAMIQKAGGG 301
Score = 46.7 bits (110), Expect = 5e-05
Identities = 43/184 (23%), Positives = 80/184 (43%), Gaps = 28/184 (15%)
Query: 249 GVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADI 308
G++ +R G + T G ++G V + + + + + QGG R+GA LE WH DI
Sbjct: 757 GLNFSKLRPEGDIVGTTTGAASGPVSFMHLIDAVSDVIKQGG-VRRGANMGILEIWHPDI 815
Query: 309 FEFLNLK-KNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEF 367
+F++ K KN G ++ +W + F E ++ ++ L P
Sbjct: 816 EKFIHAKEKNIGTNVLSNFNISVGIW--EDFWEALKEGKKYPLINP-------------- 859
Query: 368 EKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKS--NQQNLGTIKS 425
R G+ K + ++L+ E+ P ++F D NR++ + G I++
Sbjct: 860 --------RTGEVVKEIDPKSLFEELAYMAWAKADPGVIFFDVINRRNVLKEAKGGPIRA 911
Query: 426 SNLC 429
+N C
Sbjct: 912 TNPC 915
>gnl|CDD|215855 pfam00317, Ribonuc_red_lgN, Ribonucleotide reductase, all-alpha
domain.
Length = 79
Score = 96.5 bits (241), Expect = 3e-24
Identities = 31/79 (39%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 141 FDYDYFGFKTLERSYLLKV-QGKVVERPQHMLMRVSIGIH-----KDDIDSAIKTYHMMS 194
Y K LE YLLK G+V+E PQ M MRV++ + +D ++ A + Y ++S
Sbjct: 1 RFLTYLAAKVLEDRYLLKDEDGEVLETPQDMFMRVALALAGAEPPEDRLELAEEFYDLLS 60
Query: 195 QRWFTHASPTLFNAGTPRP 213
F A+PTL NAGTP
Sbjct: 61 SLKFLPATPTLMNAGTPLG 79
>gnl|CDD|236152 PRK08115, PRK08115, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 858
Score = 107 bits (269), Expect = 7e-24
Identities = 104/428 (24%), Positives = 175/428 (40%), Gaps = 66/428 (15%)
Query: 379 KAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNLG-TIKSSNLCTEIIEYTS 437
+ + ++A+ LW I + P + F D N +N + G + ++N C E + +
Sbjct: 428 RTYRKIKAKELWNLINICATYSAEPGIFFIDNANEMTNAKAYGQKVVATNPCGE--QPLA 485
Query: 438 PTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLN 497
P +VCNLA+I L ++ + D+EKL + +
Sbjct: 486 PY--SVCNLAAINLANMADKE------------------TKTVDYEKLKRTVEVGVRMQD 525
Query: 498 KIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYH 557
+ID Y +E ++ L R +G+GV GL D I + S E QL IFETI
Sbjct: 526 NVIDATPYFLEENKKQALGERRVGLGVMGLHDLLIYCETVYGSEEGNQLVDQIFETIATT 585
Query: 558 ALKTSSEIAAKEG--PYETYHNSPVSKGI----LQPDMWNVIPSDRWDWGVLRDMISKNG 611
A +TS E+A ++G P+ + + + +P D +R+ I K G
Sbjct: 586 AYRTSIELAKEKGSFPFLVGQTEEETAKLREAFINTGYMKKMPED------IREDILKYG 639
Query: 612 VRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGIWS 671
+RNS L+ PT ST ++G + EPY S Y R G+F+ V ++ + +
Sbjct: 640 IRNSHLLTVAPTGSTGTMVGVSTGLEPYFSFSYYRSGRLGKFIEVKADIVQEYLD----- 694
Query: 672 PTIKNKIIYDDGSVQKIPEIPEELKMIYKTVWEIKQMTLVDMA-VDRGCYIDQ--SQSLN 728
+ + +PE W I M L A D C I + SL+
Sbjct: 695 -------KHPEADENHLPE------------WFISAMELKPEAHADVQCIIQRWVDSSLS 735
Query: 729 IHMDQP---NFKKVTSLHFRTWSRGLKTGMYYLRSRAAADAIKFTVDTSVFKEKPE-KPE 784
++ P ++V ++ R + G K G Y+ A + + + E+ PE
Sbjct: 736 KTVNAPKGYTVEQVQKVYERLYRGGAKGGTVYVDGSRDAQVLTLKAEENDLDEQLLLLPE 795
Query: 785 LVVDDETK 792
+ ++ETK
Sbjct: 796 ELEEEETK 803
Score = 63.3 bits (154), Expect = 4e-10
Identities = 42/128 (32%), Positives = 63/128 (49%), Gaps = 6/128 (4%)
Query: 188 KTYHMMSQRWFTHASPTLFNAGTPRP-QLSSCFLVCMKDDSIEGIYETLKECAVISKSAG 246
K Y + F A L+ AG+ +C+++ DS EGI E K+ I G
Sbjct: 158 KFYQELVNMNFVPAGRVLYGAGSKTDVTYFNCYVMPFVKDSREGISEHRKQVMEIMSRGG 217
Query: 247 GIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTAR--YVDQGGGKRKGAFAVYLEPW 304
G+G + +R + RG NG S+G V L +D A+ ++ + GG R+GA + L W
Sbjct: 218 GVGTNGSTLRPRNTLARGVNGKSSGSVSWL---DDIAKLTHLVEQGGSRRGAQMIMLADW 274
Query: 305 HADIFEFL 312
H DI EF+
Sbjct: 275 HPDILEFI 282
>gnl|CDD|217585 pfam03477, ATP-cone, ATP cone domain.
Length = 88
Score = 66.9 bits (164), Expect = 1e-13
Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 7/91 (7%)
Query: 1 MYVVKRDGRQEAVHFDKITARLKKLSYGLSTE-HCDPVLVSQKVCAGVYKG--VTTSQLD 57
M V+KRDGR+E +KI ++K + L ++++V + G ++T ++
Sbjct: 1 MKVIKRDGRREPFDREKIRRAIEKAARALRPVDPEQAEEIAEEVEEELRDGGEISTEEIQ 60
Query: 58 ELAAETAAAMTTNHPDYASLAARIAVSNLHK 88
+L +T HPDYA A I NL K
Sbjct: 61 DLVEKTLME----HPDYAVARAYILYRNLRK 87
>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1220
Score = 58.4 bits (142), Expect = 1e-08
Identities = 61/248 (24%), Positives = 99/248 (39%), Gaps = 56/248 (22%)
Query: 334 VPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKLYTHYER-EGKAKKVVQAQNLWFE 392
V D F+ V+ +G W+L R +GK K ++A++LW +
Sbjct: 403 VTDEFLRAVENDGDWNL-----------------------TARTDGKVAKTLKARDLWEK 439
Query: 393 ILTSQIETGTPYMLFKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALP 452
I + + P + F T N G I++SN C+ EY +TA CNLAS+ L
Sbjct: 440 IGYAAWASADPGLQFNTTINDWHTCPASGPIRASNPCS---EYMFLDDTA-CNLASLNLL 495
Query: 453 RFVREKDVPVESHPSRIVGSRGSKNRF--FDFEKLAEVTAIVTENLNKIIDV--NYYPV- 507
F E RF +E + +V E I V +P
Sbjct: 496 TFRDED-----------------TKRFDVEAYEHACRLWTVVLE-----ISVLMAQFPSK 533
Query: 508 ETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIYYHALKTSSEIAA 567
E A S R +G+G + + +G+ ++S E + + + + A TS+E+A
Sbjct: 534 EIAELS-YEFRTLGLGYANIGGLLMTMGIPYDSDEGRAICGALSAIMTGVAYATSAEMAK 592
Query: 568 KEGPYETY 575
+ GP+ Y
Sbjct: 593 ELGPFPGY 600
Score = 35.7 bits (83), Expect = 0.13
Identities = 35/115 (30%), Positives = 58/115 (50%), Gaps = 6/115 (5%)
Query: 212 RPQLSSCFLVCMKDDSIE--GIYETLKECAVISKSAGGIGVSVHNIRATGSYIRGTNGTS 269
PQ +CF+ ++DD + GI + A + K G G + N+R G + G G S
Sbjct: 193 HPQPHACFIQSVEDDLVNEGGIMDLWVREARLFKYGSGTGSNFSNLRGEGEKLSG-GGKS 251
Query: 270 NGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLNLKKNHGKEEHR 324
+G++ L++ + A + GG R+ A V ++ H DI EF++ K KEE +
Sbjct: 252 SGLMSFLKIGDRAAGAIKSGGTTRRAAKMVIVDIDHPDIEEFIDWKV---KEEQK 303
>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 = 50.2 bits (120), Expect = 3e-06
Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 6/172 (3%)
Query: 462 VESHPSRIVGSRGSKNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIG 521
V + +RI+ + + E+L E+ + L+ +ID + + T R +G
Sbjct: 203 VSLNLARIMEKAINGSMDVVLEELEELAFLAVRALDCVIDSHDERIPTIELGGDERRTVG 262
Query: 522 IGVQGLADTFILLGMAF-ESPEAQQLNKDIFETIYYHALKTSSEIAAKEGPYETYHNSPV 580
+G+ G+AD I LG+ PEA L ++ + + H +K ++E + S
Sbjct: 263 LGIAGVADLLIKLGLEKVGDPEADDLAAELVDQLKKHLVKATNERGFNFLLGLSPSESNS 322
Query: 581 SKGILQPDMWNVIPSDRWDWGVLRDMISKNGVRNSLLVAPMPTASTSQILGN 632
S + PS VL I S VA + + + I
Sbjct: 323 SGAPATNGVS---PSRGXIAIVLNGDIGPEESLAS--VAILQFYADNGISDT 369
Score = 45.6 bits (108), Expect = 8e-05
Identities = 37/194 (19%), Positives = 55/194 (28%), Gaps = 31/194 (15%)
Query: 205 LFNAGTPRPQLSSCFLVC---MKDDSIEGIYETLKEC-------------AVISKSAGGI 248
+ G P + C LV D I+G+ ET K A +++ GG+
Sbjct: 12 VITVGRPDLPFTGCVLVDYGDSLDPGIKGVNETAKSINEAIQKTYQIIALAASNQNGGGV 71
Query: 249 GVSVH--NIRATGSYIRG-TNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVY----L 301
+ + GS +GT V FN + V QG G+ A
Sbjct: 72 SFARASSILSPYGSRDYAKGSGTETDAVEAADAFNLALKEVGQGNGRTGAATGFIGGVHK 131
Query: 302 EPWHADIFEFLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLAD 361
EFLNL +G E ++ V + + EA
Sbjct: 132 GKGDKISQEFLNLALANGGEGIPLNFPNLSVRVSSDKPGILVKAVELKQLIAEEARKTGS 191
Query: 362 --------CWGAEF 367
C
Sbjct: 192 PGIFNDELCNLVSL 205
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 36.4 bits (85), Expect = 0.060
Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 1/84 (1%)
Query: 482 FEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLG-MAFES 540
FE+L + + ++I P L + + IG+ GL + LG E
Sbjct: 301 FEELDRYDLAKRKLIEELIAAGLLPFYKQYLWRLDNHFLTIGINGLNEALANLGGTDIED 360
Query: 541 PEAQQLNKDIFETIYYHALKTSSE 564
E ++ + + I A + E
Sbjct: 361 EEGKKFGLRVLDFIREKAREAQEE 384
>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription
elongation factor TFIIS [Transcription].
Length = 113
Score = 32.0 bits (73), Expect = 0.29
Identities = 12/44 (27%), Positives = 20/44 (45%)
Query: 768 KFTVDTSVFKEKPEKPELVVDDETKMAQVVCSLTNREECMACGS 811
K SV + +K E+V+ E + T +E+C CG+
Sbjct: 37 KKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGN 80
>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 = 33.0 bits (75), Expect = 0.80
Identities = 46/295 (15%), Positives = 88/295 (29%), Gaps = 73/295 (24%)
Query: 252 VHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYV-DQGGGKRKGAFAVYLEPWHADIFE 310
+ +IR G+ ++G GT++G VP+ ++ D A + ++ GG+ A +
Sbjct: 214 LSDIRPAGAELKGFGGTASGPVPLAKMLTDVAEILSNKAGGRLTAVDAADICNLIGKAVV 273
Query: 311 FLNLKKNHGKEEHRARDLFYALWVPDLFMERVQTNGQWSLFCPNEASGLADCWGAEFEKL 370
N++++ + F + +
Sbjct: 274 AGNVRRS-----AEMALFSNDDPEFESFKQAKEKLM------------------------ 304
Query: 371 YTHYEREGKAKKVVQAQNLW--FEILTSQIETGTPYMLFKDTC-------NRKSNQQNLG 421
+ R V +E G P + D N + G
Sbjct: 305 ---HHRWASNNSVAVDSAFSGLARSAADILENGEPGQVNLDLSKSEGRIVNGRYQAGEDG 361
Query: 422 TIKSSNLCTEI-IEYTSPTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGSKNRFF 480
++ +N C EI + P CNL + L F +
Sbjct: 362 DVEGTNPCGEILLANGEP-----CNLFEVNLLAFEEDGW--------------------- 395
Query: 481 DFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLG 535
L A+ ++ Y E +R ++R IG+ + G+ D +L G
Sbjct: 396 ---GLQRAFALAARYAKRVTFSP-YDDEISREIIQKNRRIGVSMSGIQDFLLLRG 446
>gnl|CDD|226741 COG4291, COG4291, Predicted membrane protein [Function unknown].
Length = 228
Score = 30.9 bits (70), Expect = 2.2
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 1/51 (1%)
Query: 505 YPVETARRSNLRHRPIGIGVQGLADTFILLGMAFESPEAQQLNKDIFETIY 555
P R + RHR I G LL +A P A + ++F Y
Sbjct: 9 EPTAMQRFAVRRHRLFAIAALGGVLAL-LLALALSRPLAILIGANLFFLAY 58
>gnl|CDD|148412 pfam06791, TMP_2, Prophage tail length tape measure protein. This
family represents a conserved region located towards the
N-terminal end of prophage tail length tape measure
protein (TMP). TMP is important for assembly of phage
tails and involved in tail length determination. Mutated
forms TMP cause tail fibres to be shortened.
Length = 210
Score = 30.4 bits (69), Expect = 2.8
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 15/70 (21%)
Query: 46 GVYKGVTTSQLDELAAETAAAMTTNHPDYASLAARI---------------AVSNLHKNT 90
G GVT SQL ++A + T +L A A + + + T
Sbjct: 109 GNAAGVTASQLADMARAISDVGGTQGAAAEALTALAAAGKFAGEQLEAVAQAAAKMSEAT 168
Query: 91 KKSFSETIKD 100
+S ET+KD
Sbjct: 169 GQSVDETVKD 178
>gnl|CDD|233269 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 250
Score = 30.4 bits (69), Expect = 3.1
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 12/64 (18%)
Query: 147 GFKTLERSYLLKVQGKVVERPQHMLMRVSIGIHKDD------IDSAIK------TYHMMS 194
GF K G V ++ IG+ K D + A+ TY +S
Sbjct: 187 GFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADGTYQKIS 246
Query: 195 QRWF 198
++WF
Sbjct: 247 KKWF 250
>gnl|CDD|177979 PLN02345, PLN02345, endoglucanase.
Length = 469
Score = 30.5 bits (69), Expect = 3.7
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 52 TTSQLDELAAETAAAMT-------TNHPDYASLAARIA--VSNLHKNTKKSFSETIKDMY 102
T+S E+AAETAAAM ++ Y+ + A + N + S+SE+I ++
Sbjct: 136 TSSPGSEVAAETAAAMAAASLVFKSSDSTYSDTLLKHAKQLFNFADKYRGSYSESIPEVQ 195
Query: 103 NHYN 106
++YN
Sbjct: 196 DYYN 199
>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 = 30.6 bits (69), Expect = 4.0
Identities = 52/334 (15%), Positives = 96/334 (28%), Gaps = 86/334 (25%)
Query: 255 IRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFL-- 312
IR G ++G G ++G P+ ++ A ++ GK + + D+ +
Sbjct: 200 IRPAGERLKGFGGIASGPEPLKKLHKAIAAILNDRSGKPLTSVDI------VDLMNLIGV 253
Query: 313 -----NLKKNHGKEEHRARDLFYA-----LWVPDLFMERVQTNGQWSLFCPNEASGLADC 362
N++++ + D +A W P +N S+
Sbjct: 254 CVVSGNVRRSAEIAFGQPEDEDFADLKQYQWNPGRREHGWASNN--SVV----------- 300
Query: 363 WGAEFEKLYTHYEREGKAKKVVQAQNLWFEILTSQIETGTPYMLFKDTCNRKSNQQNL-- 420
FE E G P + + D + L
Sbjct: 301 ----FESKPDRLEYS--------------FACMLIRGNGEPGIAWLDNMKAYARMVLLTT 342
Query: 421 ----GTIKSSNLCTEII-EYTSPTETAVCNLASIALPRFVREKDVPVESHPSRIVGSRGS 475
K N C EI E CNL VE P +
Sbjct: 343 PYHDLRAKGGNPCGEISLESYEL-----CNL---------------VEVFPLKH------ 376
Query: 476 KNRFFDFEKLAEVTAIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLG 535
+ D ++ + K + + E LR+R IG+ + G+AD + G
Sbjct: 377 EGDLEDLQETLYLAGR----YAKTVTLLPLHWEITNEIILRNRRIGVSMSGIADFIVRAG 432
Query: 536 MAFESPEAQQLNKDIFETIYYHALKTSSEIAAKE 569
+ ++ +E +Y + + S +
Sbjct: 433 GDLTLHDLKRWRNIGYEAVYQYDERLSKWLGIPL 466
>gnl|CDD|237339 PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
Length = 394
Score = 30.2 bits (69), Expect = 5.2
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 54 SQLD-ELAAETAAAMTTNHPDYASLAARIAV 83
SQL +L ET AM T P L +I+V
Sbjct: 167 SQLGFDLETETFEAMKTQAP----LLEKISV 193
>gnl|CDD|235937 PRK07111, PRK07111, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 735
Score = 30.3 bits (69), Expect = 5.7
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 2 YVVKRDGRQEAVHFDKITARLKK 24
Y+VKRDGR+ +KIT + K
Sbjct: 4 YIVKRDGREVPFDEEKITNAIFK 26
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 0.134 0.400
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: 41,061,814
Number of extensions: 4039317
Number of successful extensions: 3314
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3101
Number of HSP's successfully gapped: 74
Length of query: 811
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 706
Effective length of database: 6,280,432
Effective search space: 4433984992
Effective search space used: 4433984992
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 (27.9 bits)