RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 003602
(808 letters)
>gnl|CDD|178056 PLN02437, PLN02437, ribonucleoside--diphosphate reductase large
subunit.
Length = 813
Score = 1849 bits (4792), Expect = 0.0
Identities = 730/813 (89%), Positives = 770/813 (94%), Gaps = 5/813 (0%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELA 60
MYVVKRDG+QE VHFDKITARLKKLSYGLS +HCDPVLV+QKVC GVYKGVTTSQLDELA
Sbjct: 1 MYVVKRDGRQETVHFDKITARLKKLSYGLSQDHCDPVLVAQKVCAGVYKGVTTSQLDELA 60
Query: 61 AETAAAMTTNHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDV 120
AETAAAMTTNHPDYA LAARI VSNLHKNTKKSFSET+KDMYNH NERSGLKAPLIADDV
Sbjct: 61 AETAAAMTTNHPDYAILAARIAVSNLHKNTKKSFSETVKDMYNHVNERSGLKAPLIADDV 120
Query: 121 YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHK 180
YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKV GKVVERPQHMLMRV+VGIHK
Sbjct: 121 YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVNGKVVERPQHMLMRVSVGIHK 180
Query: 181 DDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAI 240
DDI+SAIKTYH+MSQRWFTHASPTLFNAGTPR QLSSCFL+CMKDDSIEGIYDTLKECA+
Sbjct: 181 DDIESAIKTYHLMSQRWFTHASPTLFNAGTPRPQLSSCFLICMKDDSIEGIYDTLKECAV 240
Query: 241 ISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVY 300
ISKSAGGIG+SVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFA+Y
Sbjct: 241 ISKSAGGIGLSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAIY 300
Query: 301 LEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLA 360
LEPWHADIFEFLDLRKNHGKEEHRARDLFYALW+PDLFMERVQSNG WSLFCPNEAPGLA
Sbjct: 301 LEPWHADIFEFLDLRKNHGKEEHRARDLFYALWIPDLFMERVQSNGDWSLFCPNEAPGLA 360
Query: 361 DCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNL 420
DCWG EFERLYTKYE+EGKAKKVVQAQ LWF IL+SQIETGTPYMLFKD+CN+KSNQQNL
Sbjct: 361 DCWGEEFERLYTKYEREGKAKKVVQAQQLWFAILESQIETGTPYMLFKDSCNRKSNQQNL 420
Query: 421 GTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYF 480
GTIKSSNLCTE+I+YTSPTETAVCNLASIALPR+VRE GVP+ESHPSKLVGS GSKNRYF
Sbjct: 421 GTIKSSNLCTEIIEYTSPTETAVCNLASIALPRFVREKGVPLESHPSKLVGSLGSKNRYF 480
Query: 481 DFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDS 540
DFEKLAEVT +VT NLNKIIDVNYYPVETARRSN+RHRPIGIGVQGLAD FILLGMPFDS
Sbjct: 481 DFEKLAEVTAVVTRNLNKIIDVNYYPVETARRSNMRHRPIGIGVQGLADAFILLGMPFDS 540
Query: 541 TEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDW 600
EAQQLNKDIFETIYYHAL+ SSE+AAREGPYETY GSPVSKGILQPDMWGV PS RWDW
Sbjct: 541 PEAQQLNKDIFETIYYHALKASSELAAREGPYETYAGSPVSKGILQPDMWGVTPSGRWDW 600
Query: 601 GGLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL 660
LR+MISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL
Sbjct: 601 AALREMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL 660
Query: 661 LHDLTEMGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCY 720
LHDLTEMGLW+P +KNKII ++GSVQKIP+IP++LKAIYKTVWEIKQ+TLVDMA DRGCY
Sbjct: 661 LHDLTEMGLWTPTLKNKIIAENGSVQKIPEIPDDLKAIYKTVWEIKQRTLVDMAADRGCY 720
Query: 721 IDHSQSLNIHMDQPNFGKLTSLHFHAWLRGLKTGMYYLRSRAAADAIKFTVDTSVLKENP 780
ID SQSLNIHMDQPNFGKLTSLHF+AW +GLKTGMYYLRSRAAADAIKFTVDT+ LK +
Sbjct: 721 IDQSQSLNIHMDQPNFGKLTSLHFYAWSKGLKTGMYYLRSRAAADAIKFTVDTASLKPSA 780
Query: 781 KVT-----DDDDAKMAQMVCSLTNREECMACGS 808
+D + KMAQMVCSL NREEC+ACGS
Sbjct: 781 TGVAAPEEEDVETKMAQMVCSLDNREECLACGS 813
>gnl|CDD|217257 pfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel
domain.
Length = 516
Score = 806 bits (2085), Expect = 0.0
Identities = 290/545 (53%), Positives = 372/545 (68%), Gaps = 30/545 (5%)
Query: 215 LSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVP 274
LSSCFL+ DDS++ IYDTLKE A++SKS GGIG+++ IRA GS IRGT G S+G+VP
Sbjct: 1 LSSCFLLPSVDDSLDSIYDTLKEAALLSKSGGGIGINLSKIRAKGSPIRGTGGVSSGVVP 60
Query: 275 MLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWV 334
L+VF+DTARYV+QGG KR+GA AVYLE WH DI EFLDL+KN+G EE RAR+L +WV
Sbjct: 61 FLKVFDDTARYVNQGG-KRRGAVAVYLEVWHPDIEEFLDLKKNNGDEERRARNLNLGVWV 119
Query: 335 PDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEIL 394
PDLFM+RV+++ W+LF P EAPGL D +G EFE Y K E GK KK V+A+ LWF+I+
Sbjct: 120 PDLFMKRVENDEDWTLFSPREAPGLEDLYGEEFEEEYEKLEANGKVKKTVKARELWFKIV 179
Query: 395 KSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAVCNLASIALPRY 454
+S ETG PY+LFKD N+ + Q++LGTIKSSNLCTE++Q TSP E AVCNLASI L ++
Sbjct: 180 ESAWETGEPYILFKDAVNRHNPQKHLGTIKSSNLCTEIVQPTSPGEDAVCNLASINLAKF 239
Query: 455 VREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSN 514
V + FDFE+L EV + L+ +ID+N YPV AR+SN
Sbjct: 240 VEN-------------------DFTFDFEELREVVRLAVRALDNVIDLNDYPVPEARKSN 280
Query: 515 LRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYET 574
RHR IG+GV GLAD LG+P+DS EA++L +IFETIYY+AL+ S+E+A +GP+
Sbjct: 281 KRHRSIGLGVMGLADALAKLGIPYDSEEARELADEIFETIYYYALKASNELAKEKGPFPG 340
Query: 575 YHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTSQILGNNE 634
+ GS +KG R DW LR+ I K+G+RNS L A PT S SQI G E
Sbjct: 341 FEGSKYAKG------EFHAIPLREDWEELREDIKKHGLRNSQLTAIAPTGSISQIAGTTE 394
Query: 635 CFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQKIPQIPEE 694
EP SN+YSRR SGEF+VVN +LL DL E LWS +KN++ Y +GSVQ IP+IPEE
Sbjct: 395 GIEPIFSNVYSRRSKSGEFLVVNPYLLRDLRE--LWSEEMKNELAY-NGSVQPIPEIPEE 451
Query: 695 LKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQ-PNFGKLTSLHFHAWLRGLKT 753
+KA+YKT ++I K +DMA R ++D S S + + + L SL+ +AW 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 (1907), Expect = 0.0
Identities = 285/600 (47%), Positives = 352/600 (58%), Gaps = 146/600 (24%)
Query: 167 PQHMLMRVAVGIHKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDD 226
PQ LMRVA+G+ D++ A + Y ++S++ FT A+PTLFNAGTPR QLSSCFL+ + DD
Sbjct: 1 PQDRLMRVALGLASGDLEWAKEFYDLLSKQRFTPATPTLFNAGTPRGQLSSCFLLTV-DD 59
Query: 227 SIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYV 286
S+E IYDT+KECA +SK GGIG+++ NIRATGS IRGTNG SNG++P L++ NDTARYV
Sbjct: 60 SLESIYDTIKECAQLSKIGGGIGLNLSNIRATGSPIRGTNGASNGVIPFLKLLNDTARYV 119
Query: 287 DQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNG 346
DQ GG+RKGA AVYLE WH DI EFLDL+KN+G E RARDLFY +W+PDLFMERV+
Sbjct: 120 DQ-GGQRKGAGAVYLEIWHPDIEEFLDLKKNNGDERRRARDLFYGVWIPDLFMERVE--- 175
Query: 347 LWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYML 406
++LW +IL+SQ ETG PY+L
Sbjct: 176 ----------------------------------------RDLWRKILESQFETGYPYIL 195
Query: 407 FKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPT-----ETAVCNLASIALPRYVREMGVP 461
FKDTCN+K+ Q++LGTIKSSNLCTE++Q TSP+ E AVCNLASI L +V
Sbjct: 196 FKDTCNRKNPQKHLGTIKSSNLCTEILQPTSPSEDEPGEDAVCNLASINLGNFV------ 249
Query: 462 MESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIG 521
FEKL EV + L+ +ID+NYYPV A+RSN+RHR IG
Sbjct: 250 -------------------TFEKLEEVVKLAVRALDNVIDLNYYPVPEAKRSNMRHRAIG 290
Query: 522 IGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVS 581
+GV GL D LL +P++S EA LN IFETI Y+AL+ S E+A G
Sbjct: 291 LGVMGLHDYLALLRIPYESEEALDLNDRIFETINYYALKASCELAKERG----------- 339
Query: 582 KGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTS 641
G+RNSLL+A PTAS SQILG EP TS
Sbjct: 340 -----------------------------GLRNSLLLAIAPTASISQILGATPSIEPITS 370
Query: 642 NIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKT 701
NIY RRVLSGEF VVN HL DL E GL YKT
Sbjct: 371 NIYVRRVLSGEFPVVNPHLEKDLWEYGL-----------------------------YKT 401
Query: 702 VWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQP-NFGKLTSLHFHAWLRGLKTGMYYLRS 760
+EI Q+ L+D+A DR +ID QSLN+ + P L SL+F+AW +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 = 706 bits (1823), Expect = 0.0
Identities = 288/639 (45%), Positives = 388/639 (60%), Gaps = 44/639 (6%)
Query: 145 YFGFKTLERSYLLKVQ--GKVVERPQHMLMRVAVGIH-----KDDIDSAIKTYHMMSQRW 197
Y G K L YLL+ G + E PQ MRVA+G+ + AI+ Y ++S+
Sbjct: 1 YMGLKELYNRYLLRNAATGAIYESPQEAYMRVAMGLASLEPKDTRLADAIRFYDLLSRLK 60
Query: 198 FTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRA 257
+ A+PTLFNAGTPR QLSSCFL+ + DD++E IY + + A +SK GGIG+++ +RA
Sbjct: 61 ISPATPTLFNAGTPRGQLSSCFLLDVTDDTLESIYKAIDDVAQLSKHGGGIGLNLTKLRA 120
Query: 258 TGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKN 317
GS IRGTN S GI+P L++ + + V+QGG KR GA AVYLE WH DI EFLDL+KN
Sbjct: 121 IGSPIRGTNNASKGIIPFLKLLDSSVEAVNQGG-KRPGAAAVYLEVWHPDIEEFLDLKKN 179
Query: 318 HGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKE 377
+G E R +LFY LW+PDLFM+RV+ + W LF P + PGL +G EFE Y + EK+
Sbjct: 180 NGDERRRCDNLFYGLWIPDLFMKRVEEDKDWYLFSPYDVPGLYGLYGEEFEEEYERLEKD 239
Query: 378 GKAKK---VVQAQNLWFEILKSQIETGTPYMLFKDTCNKK-SNQQNLGTIKSSNLCTEVI 433
+A+K V A++L +IL++++ETG PY+LFKD NK + G IK SNLCTE+
Sbjct: 240 VEARKKIRKVSARDLMKDILRTRVETGRPYILFKDAVNKHNPFKTGGGAIKMSNLCTEIT 299
Query: 434 QYTSP---TETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTG 490
Q T ETAVCNLAS+ L +V E FDF +L +
Sbjct: 300 QPTDDSHKGETAVCNLASVNLANFVME--------------------DKFDFSELEDAVR 339
Query: 491 IVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDI 550
I L+ +ID+ YP A +SN R R IGIGV GL D LG+P+DS EA+ LN I
Sbjct: 340 IAVRFLDNVIDLQNYPTAPAAKSNQRRRSIGIGVMGLHDVLAKLGLPYDSEEARDLNDRI 399
Query: 551 FETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRW-------DWGGL 603
FE IYY+A++ S+E+A +GP+ + GS +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 LTEMGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDH 723
L E+GLW + I+ + GS Q I IPE LK YKT +E+ Q+ L+DMA DR ++D
Sbjct: 520 LEELGLWDADRRGDIVENVGSPQPIAAIPETLKYKYKTAYELDQEALIDMAADRQKFVDQ 579
Query: 724 SQSLNIHMD-QPNFGKLTSLHFHAWLRGLKTGMYYLRSR 761
S SLN+ + + L L AW +GLKT MYY RSR
Sbjct: 580 SISLNLFLTEEVTAKDLLKLLLLAWKKGLKT-MYYCRSR 617
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 663 bits (1714), Expect = 0.0
Identities = 321/846 (37%), Positives = 461/846 (54%), Gaps = 70/846 (8%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELA 60
+ V DG + + ++ A +++ GL E D + + +Y GV ++ +
Sbjct: 149 LNVTLDDGVRRPLDMARLRALIEEACEGL--EAVDAEPILAETLKNLYDGVPMDEVYKAL 206
Query: 61 AETAAAMTTNHPDYASLAARIVVSNLHK----NTKKSFSETIKDMYNHYNE------RSG 110
A + P+Y+ + AR+++ L + T +M Y E + G
Sbjct: 207 ILAARTLIEKEPNYSYVTARLLLDTLRREALGFLGVPEEVTQAEMATRYAEYFPAFIKKG 266
Query: 111 LKAPLIADDV--YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQ 168
++A L+ + +D+ RL + + +RD + Y G +TL Y L V G +E PQ
Sbjct: 267 IEAELLDPKLAQFDL-----ERLGAALDPERDLQFTYLGLQTLYDRYFLHVDGTRIELPQ 321
Query: 169 HMLMRVAVGIHKDDIDS---AIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKD 225
MRVA+G+ ++ID AI+ Y+++S F ++PTLFN+GT R QLSSC+L + D
Sbjct: 322 AFFMRVAMGLALNEIDREARAIEFYNLLSSFDFMSSTPTLFNSGTLRPQLSSCYLTTVPD 381
Query: 226 DSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARY 285
D ++GIY+ +K+ A++SK AGG+G +RA GS+I+GTNG S G+VP L+V NDTA
Sbjct: 382 D-LDGIYEAIKDNALLSKFAGGLGNDWTPVRALGSHIKGTNGKSQGVVPFLKVVNDTAVA 440
Query: 286 VDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSN 345
V+QGG KRKGA YLE WH DI EFL+LRKN G + R D+ A W+PDLFM+RV +
Sbjct: 441 VNQGG-KRKGAVCAYLETWHLDIEEFLELRKNTGDDRRRTHDMNTANWIPDLFMKRVMED 499
Query: 346 GLWSLFCPNEAPGLADCWGTEFERLYTKYE---KEGKAK--KVVQAQNLWFEILKSQIET 400
G W+LF P+E P L D +G FE YT YE G+ K K + A +LW ++L ET
Sbjct: 500 GEWTLFSPSEVPDLHDLFGKAFEEAYTAYEAKAARGEIKLFKKIPAVDLWRKMLSMLFET 559
Query: 401 GTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGV 460
G P++ FKD CN +S QQ++G + SSNLCTE+ TS E AVCNL S+ L ++++
Sbjct: 560 GHPWITFKDPCNLRSPQQHVGVVHSSNLCTEITLNTSDDEIAVCNLGSVNLVAHIKDGAK 619
Query: 461 PMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPI 520
D EKL L+ +ID+NYY V AR SNLRHRP+
Sbjct: 620 -------------------LDHEKLKRTVSTAMRMLDNVIDINYYAVPKARNSNLRHRPV 660
Query: 521 GIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPV 580
G+G+ G D LL +P+ S EA + E + Y+A+ S+E+A G Y +Y GS
Sbjct: 661 GLGIMGFQDALYLLRIPYASDEAVEFADRSMEAVSYYAIWASTELAEERGRYSSYEGSLW 720
Query: 581 SKGILQPD-----------MWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTSQI 629
S+GIL D V+ S DW LR I K+G+RNS +A PTA+ S I
Sbjct: 721 SRGILPIDSLKLLAEARGGYLEVDRSSTLDWDALRARIKKHGMRNSNCMAIAPTATISNI 780
Query: 630 LGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQKIP 689
+G ++ EP N+Y + LSGEF VVN +L+ DL GLW ++ N + Y DGS+Q+I
Sbjct: 781 IGVSQSIEPTYQNLYVKSNLSGEFTVVNPYLVRDLKARGLWDEVMVNDLKYFDGSLQRID 840
Query: 690 QIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQPNFGKLTSLHFHAWLR 749
+IP +LKA+Y T +E+ + LV+ A R +ID +QSLN++M + KL + AWLR
Sbjct: 841 RIPADLKALYATAFEVDPRWLVEAASRRQKWIDQAQSLNLYMAGASGKKLDETYKLAWLR 900
Query: 750 GLKTGMYYLRSRAAADAIKFTVDTSVLKENPKVTDDDDAKMAQM---------VCSLTNR 800
GLKT YYLR+ A K TV+T L A CS+ +
Sbjct: 901 GLKT-TYYLRTLGATHVEKSTVNTGALNAVSSGGGGAGGAAAAAAAPPAADPKACSIDD- 958
Query: 801 EECMAC 806
+C AC
Sbjct: 959 PDCEAC 964
>gnl|CDD|223287 COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide
transport and metabolism].
Length = 651
Score = 556 bits (1436), Expect = 0.0
Identities = 232/752 (30%), Positives = 348/752 (46%), Gaps = 124/752 (16%)
Query: 39 VSQKVCTGVYKGVTTSQLDELAAETAAAMTTNHPDYASLAARIVVSNLHKNTKKSFSETI 98
+ G Y G+T ++ LAA T + + PD LAAR+ S+L K + F
Sbjct: 1 RELRTVIGFYDGITIAENLILAALTV--IEEDDPDVQRLAARLAGSDLRKEAVRQF-GRF 57
Query: 99 KDMYNHYNERSGLKAPLIADDVYDIIMKN-AARLDSEIIYDRDFDYDYFGFKTLERSYLL 157
+ + + + + L+ +I+ +RD + Y K L YLL
Sbjct: 58 DVLDEKVFAL--VANGYYDQRLLRLYSREDLDDLNKKILLERDRQFSYAAAKVLYSRYLL 115
Query: 158 K--VQGKVVERPQHMLMRVAVGIHKDD-----IDSAIKTYHMMSQRWFTHASPTLFNAGT 210
K +++E PQ + MRVA+ + +++ ++ A + Y +MS F A+PTL N GT
Sbjct: 116 KDEDGSEILELPQDLFMRVALLLAQNEAPERRLEWAKEFYDLMSSLRFMPATPTLLNGGT 175
Query: 211 PRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSN 270
PR QLSSCF++ ++DDS +
Sbjct: 176 PRGQLSSCFVLPVEDDS------------------------------------------S 193
Query: 271 GIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFY 330
G+VP +++ +D ++QGG R+GA AVYL+ WH DI EFLD ++N+G E RA D+
Sbjct: 194 GVVPFMKLLDDAFDAINQGG-VRRGAQAVYLDIWHPDIEEFLDAKRNNGDEILRAFDISV 252
Query: 331 ALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKVVQAQNLW 390
+W+PDLFM+R + W+LF P + D +G EFE G KK ++A+ L+
Sbjct: 253 GVWIPDLFMKRAKEGEDWTLFSPRDGYEAPDVYGAEFEEYAEYEADPGIRKKRIKARELF 312
Query: 391 FEILKSQIETGTPYMLFKDTCNKKSNQ-QNLGTIKSSNLCTEVIQYTSPT-------ETA 442
++ ++ ETG PY++F DT N+++ + G I++SNLC+E++Q T P E A
Sbjct: 313 DKLAEAAFETGDPYLIFVDTLNRRNPNAEGGGAIRASNLCSEILQRTKPLSLEQPLGEDA 372
Query: 443 VCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDV 502
CNL SI L ++V+ + LAE+ + L+ +ID+
Sbjct: 373 SCNLGSINLAKFVKY------------------------GDGLAELVAVAVRALDNVIDL 408
Query: 503 NYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTS 562
N YPV A R+N R IG+GV GLAD LG+P+ S EA + N +FE I Y+AL+ S
Sbjct: 409 NPYPVPEAERANAESRAIGLGVMGLADLLAQLGIPYGSEEALKFNDRLFEYIAYYALKAS 468
Query: 563 SEIAAREGPYETYHGSPVSKGILQPDM-WGVNPSDRWDWGGLRDMISKNGVRNSLLVAPM 621
+E+A GPY + GS ++GIL D + DW LR+ I K+G+RNS L A
Sbjct: 469 AELAKERGPYPYFEGSRWARGILPIDYPRLFGIT--EDWEKLREDIKKHGLRNSYLTAIA 526
Query: 622 PTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYD 681
PT S S I G EP + +Y R G F V L DL
Sbjct: 527 PTGSISYIAGTTSGIEPIFALVYFRETKGGRFYYVVPPLFEDLLAYYGL----------- 575
Query: 682 DGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQPNFGK-LT 740
+EI +DM +ID S +++ K L
Sbjct: 576 --------------------AYEIDPLWHIDMQAAAQRWIDQGISKTLNLPNTATTKDLN 615
Query: 741 SLHFHAWLRGLKTGMYYLRSRAAADAIKFTVD 772
+ +AW GLKT YY R+ AA + +D
Sbjct: 616 KAYLYAWKLGLKT-TYYRRTSQAAQVLTVVLD 646
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 519 bits (1339), Expect = e-170
Identities = 300/847 (35%), Positives = 456/847 (53%), Gaps = 82/847 (9%)
Query: 3 VVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELAAE 62
V+ +DG + ++ A E D L++ Y G+ S++
Sbjct: 238 VLSKDGSTYTMTKSQLLAHFAWACSRFP-ETTDAALLADMAFANFYSGIKESEVVLACIM 296
Query: 63 TAAAMTTNHPDYASLAARIVVSNLHKNT--KKSFSETIKDMYNHYNERSGLKAPLIADDV 120
A A PDYA +AA +++ ++K K + E +++ + + K ++ D
Sbjct: 297 AARANIEKEPDYAFVAAELLLDVVYKEALGKSKYDEDLEEAHKDH-----FKRYILEGDT 351
Query: 121 YDIIMKNAARLDSEII-YD-----------RDFDYDYFGFKTLERSYLLKVQGKVVERPQ 168
Y RL+ E+ YD RD + Y G + L Y +G+ +E PQ
Sbjct: 352 Y--------RLNPELKHYDLDALAEALDLSRDLQFSYMGVQNLYDRYFNHHEGRRLETPQ 403
Query: 169 HMLMRVAVGI----HKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMK 224
MRV++G+ +D AI Y+++S +T A+PTLFN+G +QLSSC+L ++
Sbjct: 404 IFWMRVSMGLALNEGQDKTSWAITFYNLLSTFRYTPATPTLFNSGMRHSQLSSCYLSTVQ 463
Query: 225 DDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTAR 284
DD + IY + + A++SK AGGIG +RATG+ I+GTNG S G++P ++V NDTA
Sbjct: 464 DD-LVHIYKVISDNAMLSKWAGGIGNDWTAVRATGALIKGTNGKSQGVIPFIKVANDTAV 522
Query: 285 YVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQS 344
V+QGG KRKGA VYLE WH D +FL+LRKN G E R D+ A W+PDLF +R+Q
Sbjct: 523 AVNQGG-KRKGAVCVYLEVWHLDYEDFLELRKNTGDERRRTHDINTASWIPDLFFKRLQQ 581
Query: 345 NGLWSLFCPNEAPGLADCWGTEFERLYTKYEK-----EGKAKKVVQAQNLWFEILKSQIE 399
G W+LF P++ PGL + +G EFE+LY +YE+ E + K V+A++LW ++L E
Sbjct: 582 KGTWTLFSPDDVPGLHEAYGEEFEKLYEEYERKVDTGEIRLYKKVEAEDLWRKMLSMLYE 641
Query: 400 TGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMG 459
TG P+M FKD N +S Q + G ++ SNLCTE++ S TETAVCNL SI L ++ G
Sbjct: 642 TGHPWMTFKDPSNIRSAQDHKGVVRCSNLCTEILLNCSETETAVCNLGSINLVEHIVNDG 701
Query: 460 VPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRP 519
+ D EKL+E I L+ +ID+N+YP + A+ +NL HR
Sbjct: 702 L--------------------DEEKLSETISIAIRILDNVIDINFYPTKEAKEANLAHRA 741
Query: 520 IGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSP 579
IG+GV G D L + + S EA + E I Y+A+ SS +A G Y +Y GS
Sbjct: 742 IGLGVMGFQDALYKLNISYASQEAVEFADYSSELIAYYAILASSLLAKERGTYSSYKGSK 801
Query: 580 VSKGILQPDMWG------------VNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTS 627
+G L D ++ S R DW +R +I + G+RNS L+A PTA+ S
Sbjct: 802 WDRGYLPIDTIELLKEYRGEANLLMDTSSRKDWEPVRSLIKEYGMRNSQLMAIAPTATIS 861
Query: 628 QILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQK 687
I+G + EP +++ + LSGEF + N +L+ L ++G+W + + + Y DGS+ +
Sbjct: 862 NIIGVTQSIEPTYKHLFVKSNLSGEFTIPNVYLIEKLKKLGIWDADMLDDLKYFDGSLLE 921
Query: 688 IPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQPNFGKLTSLHFHAW 747
I +IP+ LK I+ T +EI+ + +++ A R +ID QSLN+++ +P+ KL++++ AW
Sbjct: 922 IERIPDHLKKIFLTAFEIEPEWIIECASRRQKWIDMGQSLNLYLAEPDGKKLSNMYLTAW 981
Query: 748 LRGLKTGMYYLRSRAAADAIKFTVDTSVLKENPKVTDDDDAKMAQM--------VCSLTN 799
+GLKT YYLRS AA K VD + P+ + A + + VCSL
Sbjct: 982 KKGLKT-TYYLRSSAATSVEKSFVDINKRGIQPRWMKNKSASTSIVVERAKKTPVCSL-- 1038
Query: 800 REECMAC 806
E C +C
Sbjct: 1039 EEGCESC 1045
>gnl|CDD|180610 PRK06539, PRK06539, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 822
Score = 463 bits (1193), Expect = e-151
Identities = 263/806 (32%), Positives = 416/806 (51%), Gaps = 76/806 (9%)
Query: 3 VVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELAAE 62
VVKRDG +E +K+ A ++ + GL ++ ++ ++ G+TT QLDE +
Sbjct: 5 VVKRDGSKEPYDANKVNAAIEDAARGLDDAITWVTQLASELEITLFDGITTQQLDEAVIQ 64
Query: 63 TAAAMTTNHPDYASLAARIVVSNLHKNTKKSFS--ETIKDMYNHYNERSGLKAPLIADDV 120
A + P + ++AAR+++ ++K + E ++D++ ++ R+ I V
Sbjct: 65 VALQNVKDDPAFDTVAARLLLKKIYKRVLGDYDSPEELQDLHANHFRRT------IEKGV 118
Query: 121 YDIIMKNAARLDSEIIYDRDFDYD---------------YFGFKTLERSYLLKVQ-GKVV 164
+ + LDS + FD + Y G TL Y ++ + G +
Sbjct: 119 AEGL------LDSRL--GGLFDLERLAAALDPTRDELLKYIGVVTLNNRYGIRARNGDAL 170
Query: 165 ERPQHMLMRVAVGI---HKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLV 221
E PQ+ MR+A+G+ D SA+ Y MS+ + A TL NAGTP QLS+CF++
Sbjct: 171 EVPQYFWMRIAMGLSLNEDDPTSSALAFYEKMSKLEYLAAGSTLVNAGTPYPQLSNCFVM 230
Query: 222 CMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFND 281
M+DD IE I T ++ ++K GGIG+SV +RA GS IR N TS G +P + +
Sbjct: 231 EMQDD-IEHIAKTTRDVMWLTKGTGGIGLSVSKLRAQGSPIRSNNTTSTGPIPFMHTIDS 289
Query: 282 TARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMER 341
R V +GG K+ GA Y+E WH D EFLDLR+N G R R A+W+ D FM+R
Sbjct: 290 VLRAVSRGG-KKFGALCFYMENWHMDFPEFLDLRQNSGDPYRRTRTANTAVWISDEFMKR 348
Query: 342 VQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKV-----VQAQNLWFEILKS 396
VQ++ W LF P E P L + +G F + Y +Y ++ +A ++ + A+ + IL S
Sbjct: 349 VQNDEDWYLFDPLETPDLNELYGKAFSKRYAQYVEQAEAGRIRMFKRITAREQFRAILMS 408
Query: 397 QIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVR 456
T P++ +KDT N ++ N GTI SNLCTE+ +VCNLASI L R+
Sbjct: 409 LQTTSHPWLTWKDTINNRALNNNTGTIHLSNLCTEICLPQDRDNVSVCNLASINLSRH-- 466
Query: 457 EMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLR 516
L D+ +L E T + L+ +ID+ V+ A SN +
Sbjct: 467 ------------LADGE------LDWAQLEESTRLAVRQLDNLIDITASSVKEADFSNQQ 508
Query: 517 HRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYH 576
+R IG+GV G D LG ++S EA L I E I Y A+ S+++AA G Y +
Sbjct: 509 NRAIGLGVMGFTDMVERLGYSYESEEAYDLIDRIMEHISYAAIDESADLAAERGAYPNFE 568
Query: 577 GSPVSKGILQPDMWG-----------VNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTAS 625
GS S+G++ D VN + R DW LR + + G+RN+ L+A PTAS
Sbjct: 569 GSRWSRGMVPVDSIALLEADRGVPVDVNRTTRLDWDALRAKV-RGGMRNATLMAIAPTAS 627
Query: 626 TSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSV 685
+ G +P S I+SR SG+F+ VN++L+ DL E+GLW ++ +I+ G +
Sbjct: 628 IGLVAGTTPGLDPQFSQIFSRSTSSGKFLEVNRNLVADLKELGLWET-VREEILRSQGDI 686
Query: 686 QKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQPNFGKLTSLHFH 745
Q+I IP+E+KA+Y+T +++ +++A ++D + S N++++ + G + ++
Sbjct: 687 QEIAAIPDEIKALYRTSFQLSPYAFLEVAARAQKWVDQAISRNMYLESRDIGDMMDIYTA 746
Query: 746 AWLRGLKTGMYYLRSRAAADAIKFTV 771
AW G+KT YYL + A + TV
Sbjct: 747 AWEMGVKT-TYYLHMKPRHTAEQSTV 771
>gnl|CDD|236266 PRK08447, PRK08447, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 789
Score = 453 bits (1168), Expect = e-148
Identities = 280/834 (33%), Positives = 422/834 (50%), Gaps = 111/834 (13%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQ-KVCTGVY--KGVTTSQLD 57
+ VVKR+G+ E + KI +K + ++E + V S+ +V + G+TT ++
Sbjct: 2 ITVVKRNGRIEPLDISKI----QKYTSD-AVEGLEGVSQSELEVDAKIQFRDGITTEEIQ 56
Query: 58 ELAAETAA-AMTTNHPDYASLAARIVVSNL-HKNTKKSFSETIKDMYNHYNERSGLKAPL 115
+ +TA + + P++ +AAR+ + +L HK + + +K+ Y E+ G
Sbjct: 57 QTLIKTAVDKIDIDRPNWTFVAARLFLYDLYHKVSGFTGYNHLKE-YFEKGEKEGRILLG 115
Query: 116 IADDVYDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLK-VQGKVVERPQHMLMRV 174
+ + YD+ L++ I +RD ++Y G KTL YL+K +E PQHM M +
Sbjct: 116 LKEK-YDL-----DDLNAYIKPERDLQFNYLGIKTLYDRYLIKDRNNNPIELPQHMFMAI 169
Query: 175 AVGIHKDDIDS---AIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGI 231
A+ + ++++D A K Y ++S+ A+PTL NA T R QLSSC++ D+ IEGI
Sbjct: 170 AMFLAQNELDPQKWAKKFYDVISKFEVMLATPTLSNARTTRHQLSSCYIGSTPDN-IEGI 228
Query: 232 YDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGG 291
+D+ KE A++SK GGIG +RA GSYI G + GI+P L++ ND A VDQ G
Sbjct: 229 FDSYKEMALLSKYGGGIGWDWSKVRAMGSYIDGHKNAAGGIIPFLKITNDIAIAVDQLG- 287
Query: 292 KRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLF 351
RKGA AVYLEPWH DI +F+DLRKN G+E RA DLF ALW+ DLFM+RV+ + +W+LF
Sbjct: 288 TRKGAIAVYLEPWHMDISDFIDLRKNSGEERRRAHDLFPALWINDLFMKRVEEDAMWTLF 347
Query: 352 CPNEAPGLADCWGTEFERLYTKYEK-EGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDT 410
P E L + +G EFE+ Y +YEK E K+ + A+ LW +IL + ETG P++ FKD
Sbjct: 348 DPYECKDLTELYGEEFEKRYLEYEKDEKIIKEYINAKELWKKILTNYFETGLPFLCFKDN 407
Query: 411 CNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAV---CNLASIALPRYVREMGVPMES--- 464
N+ + + G I+SSNLCTE+ Q T+P + SI + E V ++S
Sbjct: 408 ANRANPNAHAGIIRSSNLCTEIFQNTAPNHYKIKIEFEDGSIEF--FEEEELVTVDSGIT 465
Query: 465 HPSKLVGSRGSKN--RYFDFEKLAE-----VTGIVTENLNKI------------------ 499
+K + S S + + EK + V + + NL+KI
Sbjct: 466 KKAKKITSLDSLKGKKIYIVEKEKKDGKTAVCNLASINLSKINTKEDIERVVPIAIRMLD 525
Query: 500 --IDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYH 557
ID+N+YP + +NL+ R IG+GV G A + + S E + +I E I Y+
Sbjct: 526 NVIDLNFYPNRKVKATNLKSRAIGLGVMGEAQMLAEHKIAWGSKEHLEKIDEIMEQISYN 585
Query: 558 ALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNP----------SDRWDWGGLRDMI 607
A+ SS +A +G Y + GS SKGI D DW GLR+ +
Sbjct: 586 AIDASSNLALEKGVYPDFEGSNWSKGIFPIDKANEEAKKLVERGGLFDSACDWEGLREKV 645
Query: 608 SKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRV----LSGEFVVVNKHLLHD 663
K+G+RN L+A PT+S S ++G + EP +Y R+ LSG VV
Sbjct: 646 KKDGMRNGYLMAIAPTSSISILVGTTQTIEP----VYKRKWFEENLSGLIPVV------- 694
Query: 664 LTEMGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDH 723
+P + E Y +++ QK L+ A R +ID
Sbjct: 695 ------------------------VPNLSPETWQYYTPAYDLDQKDLIKAAAVRQKWIDQ 730
Query: 724 SQSLNIHM--DQPNFGKLTSLHFHAWLRGLKTGMYYLRSRAAADAIKFTVDTSV 775
QSLNI + D+ + L ++ AW GLK+ YYLRS + D S+
Sbjct: 731 GQSLNIFLSLDKASGKYLNEIYTLAWKLGLKS-TYYLRSESPESEEVSVADRSI 783
>gnl|CDD|236378 PRK09102, PRK09102, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 601
Score = 386 bits (994), Expect = e-125
Identities = 226/698 (32%), Positives = 331/698 (47%), Gaps = 116/698 (16%)
Query: 125 MKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHKDDID 184
M+N I RD FG TL YLL+ G E Q + R+A D +
Sbjct: 3 MQNKLVFQINIDRSRDAWLTEFGKATLRDRYLLE--G---ESYQDLFARIAEAYADIDPE 57
Query: 185 SAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKS 244
A + Y MS+ WF A+P L N GT R SCFL + +DS+EGI +T E ++K
Sbjct: 58 HAQRFYDYMSRGWFMPATPVLSNGGTDRGLPISCFLNYV-EDSLEGIVNTWNENVWLAKR 116
Query: 245 AGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPW 304
GGIG N+R+ G IR NG S+GI+P ++V D+ G R+G+FAVYL+
Sbjct: 117 GGGIGSYWGNVRSIGEPIRN-NGKSSGIIPFIKVM-DSLTLAISQGSLRRGSFAVYLDIE 174
Query: 305 HADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWG 364
H +I EFLD+RK G +A +L + + V D FME V+ W L P
Sbjct: 175 HPEIEEFLDIRKPTGDPNRKALNLHHGVCVTDEFMEAVEDGDEWDLISP----------- 223
Query: 365 TEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKK--SNQQNLG- 421
K+ + V+A++LW +IL+++IETG PY+LF D N+ ++LG
Sbjct: 224 -----------KDKSVIRTVKARDLWAKILETRIETGEPYLLFIDNVNRALPEVYKDLGL 272
Query: 422 TIKSSNLCTEV-----IQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSK 476
+K+SNLC+E+ I + TAVC L+S+ L Y L+
Sbjct: 273 KVKASNLCSEITLPTGIDHLGEDRTAVCCLSSLNLEYYDEWKDTDA--FIEDLM------ 324
Query: 477 NRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGM 536
R+ D ++ + ++K D +E A+ S +R R +G+GV G +
Sbjct: 325 -RFLD--------NVLQDFIDKAPDE----MERAKYSAMRERSVGLGVMGFHSYLQSKMI 371
Query: 537 PFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSD 596
PF+S A+Q NK IF+ I A + S E+A +G D
Sbjct: 372 PFESVMAKQWNKKIFKHIREQADKASKELAKEKGE----------------------CPD 409
Query: 597 RWDWGGLRDMISKNGVRNSLLVAPMPTASTSQILGN-NECFEPYTSNIYSRRVLSGEFVV 655
+G +R R S +A PTAS S ILGN + EP +N Y+ + L G F V
Sbjct: 410 AAGYGVMR--------RFSTKMAIAPTASISIILGNTSPGIEPIAANYYTHKTLKGSFTV 461
Query: 656 VNKHLLHDLTEMGL-----WSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTL 710
NK+L L E G WS I+ N +GSVQ + + EE K ++KT +EI Q+ +
Sbjct: 462 KNKYLEKLLEEKGKDTDEVWSSILTN-----EGSVQHLDFLSEEEKDVFKTAFEIDQRWI 516
Query: 711 VDMAVDRGCYIDHSQSLN--IHMDQPNFGKLTSLHFHAWLRGLKTGMYYLRSRAAADAIK 768
+++A DR YID +QSLN + + P L LHF AW +G+K+ +YY RS
Sbjct: 517 IELAADRQKYIDQAQSLNLFLPANVPK-RDLNKLHFEAWKKGVKS-LYYQRS-------- 566
Query: 769 FTVDTSVLKENPKVTDDDDAKMAQMVCSLTNREECMAC 806
SV + + D ++ + + +EC+AC
Sbjct: 567 ----KSVQRADKVSHDVLKKRLVEKSAFNRDYDECLAC 600
>gnl|CDD|181700 PRK09209, PRK09209, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 761
Score = 371 bits (955), Expect = e-117
Identities = 236/797 (29%), Positives = 359/797 (45%), Gaps = 128/797 (16%)
Query: 16 DKITARLKKLSYGLSIEHCDPVLVSQKVCTG--VYKGVTTSQLDELAAETAAAMTTNHPD 73
D+I A +L + ++ T + + + E P+
Sbjct: 32 DQIHAEFPQLDVEDYKRRVFNFVERKESVTADDLVDYLIREAEARVDLEE--------PE 83
Query: 74 YASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDVYDI-IMKNAAR-- 130
+ AAR+ ++ L+K ++ + Y + GL+ L +Y ++K ++
Sbjct: 84 WTFFAARLYLNRLYKRASRNRFYDASEKYGSF---VGLQESLAERGIYSNDLLKRYSKEE 140
Query: 131 ---LDSEIIYDRDFDYDYFGFKTLERSYLLK-VQGKVVERPQHMLMRVAVGIHKDD---- 182
I +RD + Y G L YL V E PQ + +A+ + +++
Sbjct: 141 LIEAGKMIDPERDKLFTYIGLYLLADRYLATDSDRNVYELPQERWLTIALYLMQNEPRER 200
Query: 183 -IDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAII 241
+ + Y +S + T A+PTL NAG QLSSCF+ + DDS++GIYD+ + A +
Sbjct: 201 RMQLVKEAYWALSNLYMTVATPTLANAGKVGGQLSSCFIDTV-DDSLQGIYDSNTDVARV 259
Query: 242 SKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYL 301
SK GG+G + +R+ GS IRG G S+G++P ++ N+TA VDQ G +RKGA AVYL
Sbjct: 260 SKHGGGVGAYLGKVRSRGSDIRGFKGVSSGVIPWIKQLNNTAVSVDQLG-QRKGAIAVYL 318
Query: 302 EPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAP---- 357
+ WH DI FLDLR N+G E RA D+F + +PDLFME V+ G W LF P+E
Sbjct: 319 DVWHKDIESFLDLRLNNGDERLRAHDVFTGVCIPDLFMEAVERRGDWYLFDPHEVKKVMG 378
Query: 358 -GLADCW-----GTEFERLYTKYEK----EGKAKKVVQAQNLWFEILKSQIETGTPYMLF 407
L D + F KYE+ E ++K V+A ++ I+ SQ+ETG P+M +
Sbjct: 379 WYLEDFYDEKKGDGSFRE---KYEECVADERLSRKTVKAIDIMKRIMVSQLETGNPFMFY 435
Query: 408 KDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTET-------------------AVCNLAS 448
+D N+ + ++ G I SSNLCTE++Q SPT VCNL+S
Sbjct: 436 RDEVNRMNPNKHEGMIYSSNLCTEIMQNMSPTVMIQEIISGGQIVITKQPGDFVVCNLSS 495
Query: 449 IALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVE 508
I L R V V E+L I L+ +ID+N PV
Sbjct: 496 INLGRAVTA-DV---------------------LERLIP---IQVRMLDNVIDLNQLPVP 530
Query: 509 TARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAR 568
A +N ++R IG+G G L G+ ++S EA Q +++E I Y ++ S E+A
Sbjct: 531 QATITNQKYRAIGLGTFGWHHLLALKGIAWESEEAVQYADELYERINYLTIQASMELAKE 590
Query: 569 EGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTSQ 628
+G Y + GS G + + + W L +++NGVRN+ L+A P ST+Q
Sbjct: 591 KGAYPVFKGSDWQTG----EYFERRGYNSPQWDELAAQVAENGVRNAYLMAVAPNMSTAQ 646
Query: 629 ILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQKI 688
I G+ +P S Y V DL+ Y + K+
Sbjct: 647 IAGSTASIDPIYSAFYYEEKKDYRRPVT----APDLSLDTWP---------YYEKGAYKV 693
Query: 689 PQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQPN---FGKLTSLHFH 745
Q W I+Q R ++D S S N ++ P+ +L LH
Sbjct: 694 DQF-----------WSIRQ------NAARQRHVDQSISFNFYV--PSTIRASELLDLHMT 734
Query: 746 AWLRGLKTGMYYLRSRA 762
AW GLKT YY+RS
Sbjct: 735 AWKEGLKT-TYYVRSTD 750
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 362 bits (931), Expect = e-113
Identities = 239/817 (29%), Positives = 386/817 (47%), Gaps = 129/817 (15%)
Query: 5 KRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELAAETA 64
KRDG+ E + +K +K GL CDP+ + G+TT ++ + +TA
Sbjct: 7 KRDGQYEPLQVEKTKKMVKLACEGL--YGCDPLELELDSRIQFRDGMTTKEIQKSLIQTA 64
Query: 65 -------------AAMTTNHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGL 111
+P++ +AAR+ V +L+K + + ++Y L
Sbjct: 65 IEKVIQNSKDNNGNNTKKTNPNWQYVAARLYVFDLYKEARINRHYNSFGYGDYYE----L 120
Query: 112 KAPLIADDVY-DIIMKNAARLD-----SEIIYDRDFDYDYFGFKTLERSYLLK-VQGKVV 164
L+ + +Y + +++N ++ + I +RDF ++Y G K L YL+K +++
Sbjct: 121 VKKLVEEKLYGEYLLQNYSKEEIKELEKYIKPERDFLFNYEGLKLLADRYLVKGFNREIL 180
Query: 165 ERPQHMLMRVAVGI-----HKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCF 219
E PQ M +A+ + + + A K Y ++S+ T A+PTL NAGTP QLSSCF
Sbjct: 181 ELPQERFMGIAMHLAIPEGKEKRVYYAKKFYDLLSELKATVATPTLSNAGTPFYQLSSCF 240
Query: 220 LVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVF 279
+ + DD++ IYD ++ A +SK G +G+ IRA S IRG S G++P ++++
Sbjct: 241 ISVV-DDNLWSIYDVNQKFAQVSKHGGALGIYTGKIRALNSEIRGFKNASGGVIPWIKLY 299
Query: 280 NDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFM 339
NDTA VDQ G KRKG A+ L+ WH DI EFLDL+ N+G + +A D+F + PDLFM
Sbjct: 300 NDTAIAVDQLG-KRKGGAAITLDIWHKDIPEFLDLKTNNGDDRRKAHDIFPGVSYPDLFM 358
Query: 340 ERVQSNGLWSLFCPNEAP-----GLADCWGTEFERLYTK-----YEKEGKAKKVVQAQNL 389
+R++ WSLF P+E L D + E + +TK E ++ V ++
Sbjct: 359 KRLEKRENWSLFDPHEIKKVKGYSLEDYYDEEDRKEFTKKYLECEEDTNIPRRTVPVLDI 418
Query: 390 WFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETA------- 442
+I+KS +ETGTP++ F+DT NK + ++ G I SSNLC E+ Q S +E
Sbjct: 419 MKKIMKSAVETGTPFIFFRDTVNKANPNKHKGMIYSSNLCHEIAQNMSESELLEEEIIDE 478
Query: 443 ----------------VCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLA 486
CNL SI L D E+L
Sbjct: 479 NGYYEVVQKIKAGDMVTCNLNSIVLGN--------------------------VDDEELE 512
Query: 487 EVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQL 546
EV L+ +I +NYYPV A ++ ++R IG+G G + ++S E +
Sbjct: 513 EVIPTQIRMLDNVISLNYYPVPEAEITSDKYRAIGLGTSGYHHMLANNKIRWESDEHIKF 572
Query: 547 NKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDM 606
I+E I Y+A++ S E+A +G Y + GS G + G N S+RW L++
Sbjct: 573 ADKIYEEIAYYAIKASMELAKEKGSYPAFKGSEWETGKYF-ERRGYN-SERWK--KLKEE 628
Query: 607 ISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTE 666
I K G+RN + A PT STS I +P V + + + +
Sbjct: 629 IKKYGMRNGYITAVAPTGSTSNIANTTAGIDP----------------VFKRFFMEE--K 670
Query: 667 MGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQS 726
G ++P + P + EE YK I Q+ + R +ID +QS
Sbjct: 671 KGSFTP-------------KTAPDLNEENFWYYKEAHTIDQQWSIKACGVRQRHIDQAQS 717
Query: 727 LNIHMD-QPNFGKLTSLHFHAWLRGLKTGMYYLRSRA 762
N+++ + ++ +L+ AW +G+KT +YY+R+++
Sbjct: 718 FNLYITPEYKAKQILNLYIEAWKQGVKT-IYYVRNKS 753
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 360 bits (926), Expect = e-112
Identities = 239/757 (31%), Positives = 368/757 (48%), Gaps = 115/757 (15%)
Query: 53 TSQLDELAAETAAAM---TTNHPDYASLAARIVVSNLHKNTKKSFSE-TIKDMYNH--YN 106
S+ + LAA AA+ T PD+ +AAR+++ K KS + I Y+ Y
Sbjct: 143 MSEGESLAALIKAAVELTTQEAPDWEFIAARLLMLQFSKKLGKSLEKLGIHSFYDKIKYL 202
Query: 107 ERSGLKAPLIADDVYDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKV-QGKVVE 165
GL I + ++ AA I +RD + Y G L + Y+++ + +E
Sbjct: 203 TEEGLYGSYILEHYSREEIEEAA---GFIDPERDKLFTYSGLDLLLKRYVIRTHSHEPLE 259
Query: 166 RPQHMLMRVAVGI----HKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLV 221
PQ M + +A+ + +D + + Y M+S+ T A+PTL NA P QLSSCF+
Sbjct: 260 SPQEMFLGIALHLAMPEKQDRMGWVKRFYDMLSKLKVTMATPTLSNARKPFHQLSSCFID 319
Query: 222 CMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFND 281
+ D S++GIY ++ A +SK GG+G+ +RA GS IRG G + G++ +++ ND
Sbjct: 320 TVPD-SLDGIYRSIDNFAQVSKFGGGMGLYFGKVRAVGSNIRGFQGVAGGVIRWIKLAND 378
Query: 282 TARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLF--M 339
TA VDQ G R+GA AVYL+ WH DI EFL LR N+G + +A D+F A+ PDLF M
Sbjct: 379 TAVAVDQLG-MRQGAVAVYLDVWHKDIPEFLQLRTNNGDDRMKAHDVFPAVCYPDLFWKM 437
Query: 340 ERVQSNGLWSLFCPNE-----APGLADCWGTEFERLYTKYEKEGK-AKKVVQAQNLWFEI 393
R N W LFCP+E L D +G E+E+ Y + + +K+ + ++L I
Sbjct: 438 VRDDINQSWYLFCPHEILTVKGYALEDYYGEEWEKRYLDCVNDARISKRSIPIKDLVRLI 497
Query: 394 LKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTET------------ 441
LKS +ETGTP+ +DT N+ + ++ G I SNLCTE+ Q S ET
Sbjct: 498 LKSAVETGTPFTFNRDTVNRANPNKHKGMIYCSNLCTEIAQNMSAIETVSTEIETEDGDT 557
Query: 442 -----------AVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTG 490
VCNLAS++L + +E D E+L EV
Sbjct: 558 VVVTTTRPGDFVVCNLASLSLGN------IDLE-----------------DEEELEEVVR 594
Query: 491 IVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDI 550
V L+ +ID+N+YPV A+ +N R+R IG+GV G G+ ++S E + +
Sbjct: 595 TVVRALDNVIDLNFYPVPYAQITNKRYRSIGLGVSGYHHALAKNGIRWESEEHLEFADRV 654
Query: 551 FETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKN 610
FE I Y A++ S EIA +G Y + GS G + +W L +++N
Sbjct: 655 FERINYAAIKASMEIAKEKGAYGYFEGSDWQTG----AYFRKRGYTSEEWQRLAREVAEN 710
Query: 611 GVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLW 670
G+RN+ L+A PT+STS I G +P V+ ++ L +
Sbjct: 711 GMRNAYLLAVAPTSSTSIIAGTTAGVDP----------------VMKRYFLEEK------ 748
Query: 671 SPIIKNKIIYDDGSVQKIPQIPEELKA----IYKTVWEIKQKTLVDMAVDRGCYIDHSQS 726
K + +P++ EL +YK I QK + A R +ID +QS
Sbjct: 749 ----KGAL---------MPRVAPELSDKTFWLYKNAHLIDQKWSIRAAGVRQRHIDQAQS 795
Query: 727 LNIHMDQP-NFGKLTSLHFHAWLRGLKTGMYYLRSRA 762
+N+++ ++ L+ AW G+KT +YY+RS++
Sbjct: 796 VNLYITNEFTMRQVLDLYLLAWEEGVKT-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 = 318 bits (817), Expect = 9e-99
Identities = 197/619 (31%), Positives = 304/619 (49%), Gaps = 63/619 (10%)
Query: 151 LERSYLLKVQ-GKVVERPQHMLMRVAVGI-HKDDIDSAIKT-------YHMMSQRWFTHA 201
L YL K + G ++E P+ + RVA + +D ++ Y +M F
Sbjct: 2 LAARYLRKDEDGNILESPEDLFRRVARALAAAEDKYNSPVWKQLYERFYDLMVNLGFMPN 61
Query: 202 SPTLFN-AGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGS 260
SPTL N GT QLS+CF V +D +E I++ KE A+I K GG+G + +R G
Sbjct: 62 SPTLMNAGGTRLGQLSACF-VLPVEDDMESIFEAAKEAALIFKRGGGVGYNFSTLRPKGD 120
Query: 261 YIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGK 320
+ GT G ++G V +RVF+ A + QGG R+GA L+ WH DI EF++ +K GK
Sbjct: 121 KVSGTGGVASGPVSFMRVFDAAAGVIKQGG-TRRGAQMGILDVWHPDIEEFIEAKKKEGK 179
Query: 321 EEHRARDLF-YALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGK 379
+ F ++ V D FME V+++ + L P G E E L K E +
Sbjct: 180 LTN-----FNISVGVTDAFMEAVEADEEYKLRNPRT--------GEEIEELAEKREPKLV 226
Query: 380 AKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPT 439
K V A+ LW +I+++ ++ P +LF DT NK +N LG I ++N C E P
Sbjct: 227 VYKEVPARELWDKIVEAAWKSAEPGLLFIDTINKWNNLPYLGRINATNPCGEQPLL--PY 284
Query: 440 ETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKI 499
E CNL SI L ++V+ FDFE+L EV + T L+ +
Sbjct: 285 E--SCNLGSINLAKFVKN----------------DFGGASFDFERLREVVRLATRFLDNV 326
Query: 500 IDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHAL 559
ID+N +P+ + + R IG+G+ GLAD I LG+P+DS EA+ +++ I A
Sbjct: 327 IDLNRFPLPEIAEATKKTRRIGLGIMGLADLLIKLGIPYDSEEARAFAEELMRFIADAAY 386
Query: 560 RTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVA 619
R S+E+A G + + S L + + + + LR+ I+K G+RN+ L
Sbjct: 387 RASAELAKERGAFPLFEAS----KYLMGKVARIPSALPAE---LREAIAKYGIRNAQLTT 439
Query: 620 PMPTASTSQILGNNECFEPYTSNIYSRRVL-SGEFVVVNKHLLHDLTEMGLWSPIIKNKI 678
PT + S I G + EP + +Y R V GE + VN + L E+G +S I
Sbjct: 440 IAPTGTISLIAGTSSGIEPVFALVYFRNVTVGGELLEVNPLVELALRELGYYSDEIVKIE 499
Query: 679 IYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDM--AVDRGCYIDHSQSLNIHMDQPN- 735
+ + G+V+ P +PEEL ++ T +I + V M A+ ++D S S I+M P+
Sbjct: 500 VAEKGTVEGAPDLPEELPKVFVTANDISPEDHVLMQAAIQP--WVDSSISKTINM--PSD 555
Query: 736 --FGKLTSLHFHAWLRGLK 752
+ +++ AW GLK
Sbjct: 556 ATVEDVKAVYLEAWKLGLK 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 = 288 bits (740), Expect = 4e-89
Identities = 148/453 (32%), Positives = 221/453 (48%), Gaps = 53/453 (11%)
Query: 190 YHMMSQRWFTHASPTLFNAGT-PRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGI 248
++++ + F SPTL NAGT QLS+CF++ ++DDSIEGI+D 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 FEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFE 368
EF+D + K ++ ++ V D FME V+++ W L P E
Sbjct: 124 EEFIDAKMKEEKTVV-LQNFNISVAVTDAFMEAVENDEPWELRNPRE------------- 169
Query: 369 RLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNL 428
GK + V A+ LW +I+++ ++ P +LF DT N+ + LG I ++N
Sbjct: 170 ------PDTGKVYRTVPARELWDKIVEAAWDSADPGVLFIDTINRWNPLPGLGRINATNP 223
Query: 429 CTEVIQ--YTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLA 486
C E Y S CNL SI L ++V+ FDFE+L
Sbjct: 224 CGEQPLLPYES------CNLGSINLSKFVKN----------------PFGGASFDFERLR 261
Query: 487 EVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQL 546
E + L+ +IDVN YP+ R IG+GV GLAD I LG+P+DS EA++L
Sbjct: 262 EAVRLAVRFLDNVIDVNRYPLPEIAEETKATRRIGLGVMGLADMLIKLGIPYDSEEAREL 321
Query: 547 NKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDM 606
+ I I A R S+E+A GP+ + S + M V + + + +
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 = 288 bits (738), Expect = 1e-85
Identities = 211/722 (29%), Positives = 333/722 (46%), Gaps = 94/722 (13%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELA 60
+ V+K G + +KI L+ G + DP + + + G+TT + E+
Sbjct: 4 INVIKSSGVSQPFDLEKIHKVLEWACEGTGV---DPSELEENSKIQLRDGMTTKDIQEIL 60
Query: 61 AETAA-AMTTNHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLK--APLIA 117
++AA ++ PDY +AAR+++ L K +Y + S + + +
Sbjct: 61 IKSAADLISVEEPDYQYVAARLLMFALRK-----------QVYGQFEPPSFIDHISKCVN 109
Query: 118 DDVYD--IIMKNAA----RLDSEIIYDRDFDYDYFGFKTLERSYLLK--VQGKVVERPQH 169
+ YD I+ K +A L+S I +DRDF++ Y G L+ YL++ G++ E PQ
Sbjct: 110 EGKYDPEILSKYSAEEITYLESFIDHDRDFEFTYAGAMQLKEKYLVQDRSTGEIYETPQF 169
Query: 170 MLMRVAVGIHKDD-----IDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMK 224
M +A+ +H+D+ ++ I+ Y+ +S R + +P + TP Q SSC ++
Sbjct: 170 AYMLIAMALHQDEPKEDRLEHVIRFYNAVSTRKISLPTPIMAGVRTPTRQFSSCVVI-ES 228
Query: 225 DDSIEGIYDTLKECAI---ISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFND 281
DS++ I T AI ISK AG IG++ IRA GS IRG G++P + F
Sbjct: 229 GDSLDSINKTAM--AIVKYISKRAG-IGINAGMIRAEGSKIRGGEVRHTGVIPFWKHFQT 285
Query: 282 TARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMER 341
+ QGG R GA Y WH ++ + L L+ N G EE+R R L Y + + DL ER
Sbjct: 286 AVKSCSQGG-IRGGAATAYYPIWHLEVEDLLVLKNNKGVEENRIRHLDYGVQINDLMYER 344
Query: 342 VQSNGLWSLFCPNEAPG-LADCWG---TEFERLYTKYEKEGKA-KKVVQAQNLWFEILKS 396
N +LF P++ G L D + F LY EK+ KK ++AQ L+ +LK
Sbjct: 345 FIKNDYITLFSPHDVGGELYDAYFADQDRFRELYEALEKDPSVRKKRIKAQELFLLLLKE 404
Query: 397 QIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSP-------TETAVCNLASI 449
+ ETG Y++F D CN S I+ SNLC E+ T P E A+C L++I
Sbjct: 405 RSETGRIYIMFIDHCNNHSP--FKDPIRQSNLCCEIALPTKPLNHIDGEGEIALCTLSAI 462
Query: 450 ALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVET 509
L + D +++ E+ + L+ ++D YPV
Sbjct: 463 VL-------------------------GNFEDQDEIEELAEVAVRALDNLLDYQDYPVPA 497
Query: 510 ARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAARE 569
A ++ R R +G+GV A ++ A L ++FE + Y+ ++ S+++A +
Sbjct: 498 ALKAKKR-RSLGVGVTNYAHYLAKNFASYEDANA-DLVHELFERLQYYLIKASNKLAKEK 555
Query: 570 GPYETYHGSPVSKGILQPDMWG------VNPSDRWDWGGLRDMISKNGVRNSLLVAPMPT 623
G E + + S+G L D + V P DW LR+ + K G+RNS L A MP
Sbjct: 556 GACEYFSDTKYSRGELPIDWYKKKVDELVAPKYNCDWESLREDLKKYGIRNSTLSALMPC 615
Query: 624 ASTSQILGNNECFEP---YTSNIYSRRVLSGEF--VVVNKHLLHDLTEMGLWSPIIKNKI 678
S+SQ+ + EP S S+ G F VV N L DL ++ LW K
Sbjct: 616 ESSSQVSNSTNGIEPPRGPVSIKKSKE---GPFNQVVPNVETLKDLYDL-LWDLAKKGNK 671
Query: 679 IY 680
Y
Sbjct: 672 GY 673
>gnl|CDD|236330 PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 752
Score = 256 bits (656), Expect = 3e-74
Identities = 179/587 (30%), Positives = 269/587 (45%), Gaps = 100/587 (17%)
Query: 151 LERSYLLK-VQGKVVERPQHMLMRVAVGI--------HKDDIDS-AIKTYHMMSQRWFTH 200
LE+ YL K GK +E P+ M RVA I K D+++ A + Y +M+ F
Sbjct: 20 LEKRYLKKDEDGKPIETPEDMFRRVARTIAAAELIYDSKADVEALADRFYDLMTSLEFLP 79
Query: 201 ASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGS 260
SPTL NAG QLS+CF V DSIE I+D +K A+I KS GG G S +R
Sbjct: 80 NSPTLMNAGRELGQLSACF-VLPVGDSIEEIFDAVKHAALIHKSGGGTGFSFSRLRPKND 138
Query: 261 YIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGK 320
+ T G ++G V +RVF+ + QGG R+GA L H DI EF+ ++++G+
Sbjct: 139 RVGSTGGVASGPVSFMRVFDAATEAIKQGG-TRRGANMGILRVDHPDIMEFITCKEDNGE 197
Query: 321 EEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKA 380
+ ++ + + FME V+++ + L P + G+
Sbjct: 198 ----LTNFNISVAITEAFMEAVEADEEYDLINP----------------------RTGEV 231
Query: 381 KKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTE 440
+ A+ ++ I++ E G P ++F D N+ + +LG I+S+N C E Q P E
Sbjct: 232 VGRLNAREVFDLIVEMAWENGEPGIVFIDRINRDNPTPHLGEIESTNPCGE--QPLLPYE 289
Query: 441 TAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKII 500
CNL SI L + V+ V D+EKL EV + L+ +I
Sbjct: 290 --SCNLGSINLSKMVKNGDV--------------------DWEKLREVVHLAVRFLDNVI 327
Query: 501 DVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALR 560
D N YP+ +R IG+GV G AD I LG+P+DS EA +L + + + I A
Sbjct: 328 DANKYPLPQIEEMTKGNRKIGLGVMGWADMLIQLGIPYDSEEAVELAEKVMKFIQDEAHA 387
Query: 561 TSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVAP 620
S E+A GP+ Y GS +D GL M RN+ +
Sbjct: 388 ASRELAEERGPFPNYEGS------------------IYDKDGLGPM------RNATVTTI 423
Query: 621 MPTASTSQILGNNECFEPYTSNIYSRRVLSGE-FVVVNKHLLHDLTEMGLWSPIIKNKII 679
PT + S I G + EP + ++R V+ GE V VN E G +S + KI
Sbjct: 424 APTGTISIIAGCSSGIEPLFALSFTRNVMDGERLVEVNPVFEAAAKEEGFYSEELMEKIA 483
Query: 680 YDDGSVQKIPQIPEELKAIYKT------VWEIK-----QKTLVDMAV 715
+ GS+Q I ++PE+++ ++ T W ++ QK D AV
Sbjct: 484 -EKGSIQDIDEVPEDVRRVFVTAHDISPEWHVRMQAAFQKH-TDNAV 528
>gnl|CDD|181649 PRK09103, PRK09103, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 758
Score = 247 bits (633), Expect = 8e-71
Identities = 201/671 (29%), Positives = 315/671 (46%), Gaps = 89/671 (13%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQ---KVCTGVYKGVTTSQLD 57
+ V KRDG+ E ++ DKI + + GL V VSQ + Y G+ TS +
Sbjct: 2 LLVTKRDGRTERINLDKIHRVITWAAEGL-----HNVSVSQVELRSHIQFYDGIKTSDIH 56
Query: 58 ELAAETAAAM-TTNHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLI 116
E + AA + + + PDY LAAR+ + +L K F +Y+H + ++
Sbjct: 57 ETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQF--EPPALYDHVVK-------MV 107
Query: 117 ADDVYDI-IMKNAAR-----LDSEIIYDRDFDYDYFGFKTLERSYLL--KVQGKVVERPQ 168
YD ++++ +D+ I + RD ++ Y K LE YL+ +V G++ E Q
Sbjct: 108 EMGKYDKHLLEDYTEEEFDQMDTFIDHWRDMNFSYAAVKQLEGKYLVQNRVTGEIYESAQ 167
Query: 169 HMLMRVAV----GIHKDDIDSAIKT-YHMMSQRWFTHASPTLFNAG--TPRAQLSSCFLV 221
+ + VA K+ +K Y +S F + PT +G TP Q SSC L+
Sbjct: 168 FLYILVAACLFSNYPKETRLDYVKRFYDAVST--FKISLPTPIMSGVRTPTRQFSSCVLI 225
Query: 222 -CMKDDSIEGIYDTLKECAII---SKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLR 277
C DS++ I T AI+ S+ AG IG++ IRA GS IRG G +P +
Sbjct: 226 EC--GDSLDSINAT--SSAIVKYVSQRAG-IGINAGRIRALGSPIRGGEAFHTGCIPFYK 280
Query: 278 VFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDL 337
F + QGG R GA ++ WH ++ L L+ N G EE+R R + Y + + L
Sbjct: 281 HFQTAVKSCSQGG-VRGGAATLFYPIWHLEVESLLVLKNNRGVEENRVRHMDYGVQINKL 339
Query: 338 FMERVQSNGLWSLFCPNEAPGLADCW---GTEFERLYTKYEKEGKA-KKVVQAQNLWFEI 393
+R+ G +LF P++ PGL D + EFERLYTKYE++ KK V+A L+ +
Sbjct: 340 MYQRLIKGGDITLFSPSDVPGLYDAFFADQDEFERLYTKYEQDDSIRKKRVKAVELFSLM 399
Query: 394 LKSQIETGTPYMLFKDTCNKKSN-QQNLGTIKSSNLCTEVIQYTSPT--------ETAVC 444
++ + TG Y+ D CN S + ++ SNLC E+ T P E A+C
Sbjct: 400 MQERASTGRIYIQNVDHCNTHSPFDPKVAPVRQSNLCLEIALPTKPLNDVNDENGEIALC 459
Query: 445 NLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNY 504
L++ L G+ N + E+LA+ + L+ ++D
Sbjct: 460 TLSAFNL----------------------GAINSLDELEELAD---LAVRALDALLDYQD 494
Query: 505 YPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSE 564
YP+ A+R + R +GIGV A G+ + A L FE I Y+ L+ S+E
Sbjct: 495 YPIPAAKRGAMGRRTLGIGVINFAYYLAKNGVRYSDGSANNLTHKTFEAIQYYLLKASNE 554
Query: 565 IAAREGPYETYHGSPVSKGILQPDMWG------VNPSDRWDWGGLRDMISKNGVRNSLLV 618
+A +G ++ + ++GIL D + N +DW LR+ I +G+RNS L
Sbjct: 555 LAKEQGACPWFNETTYAQGILPIDTYKKDLDAICNEPLHYDWETLREEIKTHGLRNSTLS 614
Query: 619 APMPTASTSQI 629
A MP+ ++SQI
Sbjct: 615 ALMPSETSSQI 625
>gnl|CDD|235796 PRK06406, PRK06406, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 771
Score = 241 bits (616), Expect = 2e-68
Identities = 164/545 (30%), Positives = 257/545 (47%), Gaps = 79/545 (14%)
Query: 188 KTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGG 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 IFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEF 367
I EF+ K+ E + ++ V D F +++ ++ + L P
Sbjct: 340 IMEFI-TSKD--SENKVLSNFNISVAVTDEFFDKLDNDDYYPLRNP-------------- 382
Query: 368 ERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSN 427
+ GK K ++A+ +W I+ +TG P ++F D N+K+ +NLG I+S+N
Sbjct: 383 --------RNGKEVKRIKARQVWDLIITQAWKTGDPGVIFLDEINRKNPVKNLGEIESTN 434
Query: 428 LCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAE 487
C E Q P E+ CNL SI L ++V +N D+++L E
Sbjct: 435 PCGE--QPLLPYES--CNLGSINLSKFV--------------------ENGKIDWDRLRE 470
Query: 488 VTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLN 547
I T L+ +ID N +PV + R IG+GV G AD I LG+P++S EA ++
Sbjct: 471 TVHIATRFLDNVIDANKFPVPQIKEMTRMTRKIGLGVMGFADMLIKLGIPYNSEEALEIA 530
Query: 548 KDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMI 607
+ + + I + R S ++A G + ++GS W+ G++
Sbjct: 531 EKVMKFINEESHRASQKLAEERGVFPAWYGS------------------EWEKKGIK--- 569
Query: 608 SKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSG-EFVVVNKHLLHDLTE 666
+RNS PT + S I G + EP + + R VL+G E + VN +
Sbjct: 570 ----MRNSTTTTIAPTGTISIIAGCSSSIEPLFAIAFVRHVLNGQELLEVNPLFEEITRK 625
Query: 667 MGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQS 726
GL+S + K+ + G++Q I +PE++K I+ T EI + V M Y D S
Sbjct: 626 RGLYSEELMRKVA-ETGNLQNI-DVPEDIKRIFVTAHEIDPQWHVLMQATFQRYCDSGVS 683
Query: 727 LNIHM 731
I++
Sbjct: 684 KTINL 688
Score = 34.1 bits (78), Expect = 0.39
Identities = 42/184 (22%), Positives = 60/184 (32%), Gaps = 45/184 (24%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELA 60
V+KRDG KI + K LS+ K + +EL
Sbjct: 5 KEVIKRDGTVVPFDKKKIAMAIYKAM--LSV-----------------KNGSMEDAEELT 45
Query: 61 AETAAAMTTNHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDV 120
VV L K ++ E I+D+ + D
Sbjct: 46 -------------------DKVVERL-KKYERPTVEQIQDIVEKVLMTKKINGKDFTDVA 85
Query: 121 YDIIM----KNAARLDSEII-YDRDFDYDYFGFKTLERSYLLKVQ-GKVVERPQHMLMRV 174
I+ + R + E+I D K LE YLLK + GK++E P+ M RV
Sbjct: 86 KSYILYREKRRKIREEKELIGVKDDLKLTLNAIKVLEARYLLKDEDGKIIETPRQMFRRV 145
Query: 175 AVGI 178
A I
Sbjct: 146 ARHI 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 = 228 bits (582), Expect = 1e-65
Identities = 164/625 (26%), Positives = 266/625 (42%), Gaps = 112/625 (17%)
Query: 151 LERSYLLK---VQGKVVERPQHMLMRVAVGIHKDDIDSAIKTYHMMSQRWFTHASPTLFN 207
R YLLK V+G+V E A + + + +++ ++ A+P N
Sbjct: 14 FRRGYLLKGETVEGRVREIAST-----AEKLDIRP-GFEERFFEYLARGKYSLATPVWAN 67
Query: 208 AGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNG 267
G R SC + DS+ I + E +++K+ GG + +IR G+ I TNG
Sbjct: 68 TGLDRGLPISCAGSYV-GDSVLDILEGQAEVGMMAKNGGGTSSYLGDIRPRGADIS-TNG 125
Query: 268 TSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARD 327
TSNG +F++ QG +R G +A Y++ H D E+L ++ + +H
Sbjct: 126 TSNGADGFAPLFDNFINVKTQGATRR-GEWAGYVDFEHPDFEEWLGIQLENPASQH---- 180
Query: 328 LFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKVVQAQ 387
+ + + V D + E++ G +K +
Sbjct: 181 VGWGVEVGDDWYEKM---------------------------------IAGDPEK----R 203
Query: 388 NLWFEILKSQIETGTPYMLFKDTCNKKSNQ--QNLG-TIKSSNLCTEVIQYTSPTETAVC 444
W +++ S+ TG PYM F+ N+ + Q +N G I++SNLCTE+ + E+ VC
Sbjct: 204 ARWAKLMYSRARTGIPYMWFRWNANELAPQVIKNSGIPIRASNLCTEIALPSDDMESFVC 263
Query: 445 NLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNY 504
L+S+ + Y K + + R+ D + +E + K ++Y
Sbjct: 264 CLSSLNVLHY----------DEWKDTDAVETLVRFLD--------SVCSEFIAKAKGLSY 305
Query: 505 YPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSE 564
+ A R R R IG+G G +PF+S EA LN +I++TI A S E
Sbjct: 306 --MHRAVRFAERARAIGLGTLGWHSYLQSNRIPFESGEAHILNAEIYKTIKERAEEASRE 363
Query: 565 IAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTA 624
+A R +G P + RN+ L+A PT
Sbjct: 364 LAER-------YGEP-------------------EVCEGTGR------RNATLIAIAPTK 391
Query: 625 STSQILGN-NECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDG 683
S++ ILG + EP SN + + G+ V N L L E G ++ + I Y +G
Sbjct: 392 SSAFILGQVSPSIEPLVSNYFIQDSNKGDVVRKNPVLAKVLKEKGTDQELVWDIITYHNG 451
Query: 684 SVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLN--IHMDQPNFGKLTS 741
SVQ + + +E K+++KT +EI Q ++ +A R +ID +QSLN I D+
Sbjct: 452 SVQHLDFLTDEEKSVFKTFYEISQMAIIRLAAARQKHIDQAQSLNLFISPDEKPSVDANV 511
Query: 742 LHFHAWLRGLKTGMYYLRSRAAADA 766
L AW GLK+ +YY RS A A
Sbjct: 512 LRAFAWDPGLKS-LYYQRSERGAQA 535
>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 = 192 bits (489), Expect = 1e-51
Identities = 179/680 (26%), Positives = 295/680 (43%), Gaps = 120/680 (17%)
Query: 134 EIIYDRDFDYDYF--GFKTLERSYLLKV--QGKVVERPQHMLMRVAVGIHKDDIDSAIK- 188
E Y F + F FK SY LK + +ER + + VA+ + D + A +
Sbjct: 76 EHAYASKFRFPSFMGAFK-FYTSYALKTNDGKRYLERYEDRVCMVALTLANGDEELAKQL 134
Query: 189 TYHMMSQRWFTHASPTLFNAGTP-RAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGG 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 IFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEF 367
I FLD +K + E+ R + L + +PD F E + N LF P + + +G F
Sbjct: 252 ILRFLDTKKENADEKIRIKTLSLGVVIPDKFFELAKENKDMYLFSPYD---VEREYGVPF 308
Query: 368 ER--LYTKYEK----EGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLG 421
+ + KY++ KK + A++ + + + Q E+G PY++F+DT N+ +G
Sbjct: 309 DDIDITEKYDEMVANPRIRKKKINARDFFQTLAEIQFESGYPYIMFEDTVNRA--NPIIG 366
Query: 422 TIKSSNLCTEVIQYTSPT------------ETAVCNLASIALPRYVREMGVPMESHPSKL 469
IK SNLC+E++Q + + CNL S+ + + P
Sbjct: 367 RIKMSNLCSEILQVSEASLYNDYLEYDEIGHDISCNLGSLNI--------ANVMDSP--- 415
Query: 470 VGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDV-NYYPVETARRSNLRHRPIGIGVQGLA 528
DF + E T I L + D+ + V + R+ N IG+G L
Sbjct: 416 -----------DFGRTVE-TAI--RALTAVSDMSHIRNVPSIRKGNAASHAIGLGQMNLH 461
Query: 529 DTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSK------ 582
G+ + S EA F T+ Y++LR S EIA G ET+ G S
Sbjct: 462 GYLAREGIAYGSPEALDFTNIYFMTVNYYSLRRSMEIARERG--ETFAGFEQSDYASGEY 519
Query: 583 ------GILQPD-------MWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTSQI 629
P G++ R DW L+D + + G+ + +A PT S S I
Sbjct: 520 FDKYVSQEFAPKTEKVRELFEGIHIPTREDWAELKDDVMEYGLYHQNRLAVAPTGSISYI 579
Query: 630 LGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQKI- 688
N+ TS+I+ PI+ I +G + ++
Sbjct: 580 --NHS-----TSSIH---------------------------PIVSKIEIRKEGKIGRVY 605
Query: 689 ---PQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHM-DQPNFGKLTSLHF 744
P + E Y+ ++I + ++D ++D SL + D L
Sbjct: 606 YPAPFLTNENLEYYQDAYDIDMEKIIDTYATATQHVDQGLSLTLFFKDTATTRDLNRAQI 665
Query: 745 HAWLRGLKTGMYYLRSRAAA 764
+AW +G+KT +YY+R R A
Sbjct: 666 YAWHKGIKT-LYYIRLRQLA 684
>gnl|CDD|236069 PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 699
Score = 174 bits (442), Expect = 2e-45
Identities = 175/732 (23%), Positives = 302/732 (41%), Gaps = 125/732 (17%)
Query: 85 NLHKNTK--KSFSETIKDMYNHYNERSGLKAPLIADDVYDIIMKNAARLD----SEIIYD 138
L K+ + + E IKD ++ L+ +D Y + + D ++ Y
Sbjct: 26 QLEKDQEALVVYLEEIKDNTIFFDTEIERLRYLVDNDFYFNVFDIYSEEDLIEVTDYAYS 85
Query: 139 RDFDY-DYFGFKTLERSYLLKVQGK--VVERPQHMLMRVAVGIHKDDIDSAIKTYHMMSQ 195
F++ Y + Y LK K +E + + VA+ + D A + M +
Sbjct: 86 IKFNFASYMSASKFYKDYALKTNDKKQYLEDYEDHVAIVALYLANGDKAKAKQFISAMVE 145
Query: 196 RWFTHASPTLFNAGTPR-AQLSSCFLVCMKD--DSIEGIYDTLKECAIISKSAGGIGVSV 252
+ + A+PT NAG R +L SCFL+ + D +SI I T K+ +SK GG+ +++
Sbjct: 146 QRYQPATPTFLNAGRARRGELVSCFLLEVDDSLNSINFIDSTAKQ---LSKIGGGVAINL 202
Query: 253 HNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFL 312
+RA G I+G G + G++P+ ++ Y DQ G +R GA AVYL +H D+ EFL
Sbjct: 203 SKLRARGEAIKGIKGAAKGVLPVAKLLEGGFSYADQLG-QRPGAGAVYLNIFHYDVEEFL 261
Query: 313 DLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPN---EAPG--LADCWGTEF 367
D +K + E+ R + L VP F E + + +F P+ + G L D +
Sbjct: 262 DTKKVNADEDLRLSTISTGLIVPSKFFELAKEGKDFYMFAPHTVYKEYGVTLDD---IDL 318
Query: 368 ERLYTKYEKEGKA-KKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSS 426
E +Y KK A+ + +I ++Q+++G PY++FKD NK N+G IK S
Sbjct: 319 EEMYDDLVANPNVKKKKKNAREMLNKIAQTQLQSGYPYLMFKDNANKVHPNSNIGQIKMS 378
Query: 427 NLCTEVIQYTSPTETAV---------------CNLASIALPRYVREMGVPMESHPSKLVG 471
NLCTE+ Q ET++ CNL S+ + + V MES
Sbjct: 379 NLCTEIFQL---QETSIINDYGIEDEIKRDISCNLGSLNI------VNV-MES------- 421
Query: 472 SRGSKNRYFDFEKLAEVTGIVTENLNKIIDV-NYYPVETARRSNLRHRPIGIGVQGLADT 530
+K + + L + DV N R++N +G+GV L
Sbjct: 422 -----------KKFRDSVHSGMDALTVVSDVANIQNAPGVRKANSELHSVGLGVMNLHGY 470
Query: 531 FILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHG------------- 577
+ ++S EA+ F + ++++ S EIA G ETY
Sbjct: 471 LAKNKIGYESEEAKDFANTFFMMMNFYSIERSMEIAKERG--ETYQDFEKSDYANGKYFE 528
Query: 578 -------SPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTSQIL 630
P + + + G++ + DW L+ + + G+ ++ +A PT S S +
Sbjct: 529 KYTTQDFEPKFEKVREL-FEGMHIPTKEDWKKLQQDVEQYGLYHAYRLAIAPTQSISYVQ 587
Query: 631 GNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQKIPQ 690
P I R + E + +P
Sbjct: 588 NATSSVMPIVDQIERRTYGNAE-------------------------------TFYPMPF 616
Query: 691 IPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHM-DQPNFGKLTSLHFHAWLR 749
+ + YK+ + Q L+D+ +ID S +++ + + +L L+ +A +
Sbjct: 617 LSPQTMWYYKSAFNTDQMKLIDLIATIQTHIDQGISTILYVNSEISTRELARLYVYAHHK 676
Query: 750 GLKTGMYYLRSR 761
GLK+ +YY R++
Sbjct: 677 GLKS-LYYTRNK 687
>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 721
Score = 161 bits (409), Expect = 3e-41
Identities = 130/480 (27%), Positives = 217/480 (45%), Gaps = 77/480 (16%)
Query: 192 MMSQRWFTHASPTLFNAGTP-RAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGV 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 FLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEF--- 367
FLD ++ + E+ R + L L +PD+ E + N +LF P + + +G
Sbjct: 261 FLDTKRENADEKIRIKSLSLGLVIPDITFELAKENKDMALFSPYD---IKREYGKPMSDI 317
Query: 368 ---ERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIK 424
E Y K + A+ L+ I + E+G PY+LF DT NK++ G I
Sbjct: 318 SITEEYYNLLANPAIKKTYISARKLFQTIAELHFESGYPYLLFDDTVNKRNPHAKKGRIV 377
Query: 425 SSNLCTEVIQYTSPT------------ETAVCNLASIALPRYVREMGVPMESHPSKLVGS 472
SNLC+E+ Q ++P+ E CNL S+ + + MES P
Sbjct: 378 MSNLCSEIAQVSTPSTFNEDLSFKKIGEDICCNLGSLNIAK-------AMESGP------ 424
Query: 473 RGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGL----A 528
+FE+L + + ++++ D++ P + + N + +G+G L A
Sbjct: 425 --------EFEQLIYTSIRALDRVSRVSDLSCAP--SIEKGNAANHAVGLGAMNLHGFLA 474
Query: 529 DTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKG----- 583
I +DS EA F T+ Y+A + S+++A +G + + S + G
Sbjct: 475 TNHIY----YDSKEAVDFTDLFFYTMAYYAFKASNQLAKEKGAFAGFELSKYADGSYFDK 530
Query: 584 --ILQPDMW--------------GVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTS 627
W GV + DW L + I K G+ NS L+A PT S S
Sbjct: 531 YTKEDAKKWTPKTAKVKELLQKYGVTIPTQADWQELVEDIKKTGLANSHLLAVAPTGSIS 590
>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 720
Score = 161 bits (408), Expect = 5e-41
Identities = 146/508 (28%), Positives = 223/508 (43%), Gaps = 102/508 (20%)
Query: 192 MMSQRWFTHASPTLFNAG-TPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGV 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 FLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERL 370
FL +K + E+ R + L + VPD F E + N LF P E+
Sbjct: 263 FLSTKKENADEKVRVKTLSLGVTVPDKFYELARKNEDMYLFSP-----------YSVEKE 311
Query: 371 Y---------TKYEKEGKA-----KKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSN 416
Y TK E A K ++A++L EI K Q E+G PY++ DT N ++N
Sbjct: 312 YGVPFNYVDITKEYDELVANPNIRKTKIKARDLETEISKLQQESGYPYIINIDTAN-RAN 370
Query: 417 QQNLGTIKSSNLCTEVIQYTSPTE-----------TAV-CNLASIALPRYVREMGVPMES 464
+ G I SNLC+E++Q +P+ T + CNL S + V M +
Sbjct: 371 PID-GKIIMSNLCSEILQVQTPSLINDAQEYVKMGTDISCNLGSTNI--------VNMMT 421
Query: 465 HPSKLVGSRGSKNRYFDFEKLAEVT----GIVTENLNKIIDVNYYPVETARRSNLRHRPI 520
P DF + E VT++ N ID V + + N + I
Sbjct: 422 SP--------------DFGRSIETMVRALTFVTDSSN--IDA----VPSIKHGNSQAHTI 461
Query: 521 GIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPV 580
G+G GL + + S E+ + F + Y L S+ IA G ET+H
Sbjct: 462 GLGAMGLHSYLAQNHIEYGSPESLEFTSIYFMLLNYWTLVASNNIARERG--ETFHNFEK 519
Query: 581 SK------------GILQPD-------MWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPM 621
SK G P G+ DW LRD + K+G+ + +A
Sbjct: 520 SKYADGSYFDKYVTGDFVPKSDKVKELFKGIFIPTAADWAALRDAVMKDGLYHQNRLAVA 579
Query: 622 PTASTSQILGNNEC---FEPYTSNIYSR 646
P S S I N+ P T I R
Sbjct: 580 PNGSISYI---NDTSASIHPITQRIEER 604
>gnl|CDD|236179 PRK08188, PRK08188, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 714
Score = 155 bits (394), Expect = 3e-39
Identities = 183/691 (26%), Positives = 295/691 (42%), Gaps = 133/691 (19%)
Query: 137 YDRDF-----DYDY---FGFKTL------ERSYLLKV-QGK-VVERPQHMLMRVAVGIHK 180
Y R+F D+ Y F F+T SY LK GK +ER + + VA+ + +
Sbjct: 80 YSRNFVKTLFDHAYAKKFRFQTFLGAFKYYTSYTLKTFDGKRYLERFEDRVCMVALTLAQ 139
Query: 181 DDIDSAIK-TYHMMSQRWFTHASPTLFNAGTP-RAQLSSCFLVCMKDDSIEGIYDTLKEC 238
D A + ++S R F A+PT N G R +L SCFL+ + +D++E I ++
Sbjct: 140 GDETLARQLVDEIISGR-FQPATPTFLNCGKKQRGELVSCFLLRI-EDNMESIGRSINSA 197
Query: 239 AIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFA 298
+SK GG+ + + N+R G+ I+ S+G++P++++ D Y +Q G R+GA A
Sbjct: 198 LQLSKRGGGVALLLSNLREAGAPIKRIENQSSGVIPVMKLLEDAFSYANQLGA-RQGAGA 256
Query: 299 VYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPG 358
VYL H DI FLD ++ + E+ R + L + +PD+ E + N LF P +
Sbjct: 257 VYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFELAKENEDMYLFSPYD--- 313
Query: 359 LADCWGTEF------ERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCN 412
+ +G F E+ E KK + A+ + + + Q E+G PY++F+DT N
Sbjct: 314 VERVYGKPFADISVTEKYDEMVADERIRKKKINAREFFQTLAEIQFESGYPYIMFEDTVN 373
Query: 413 KKSNQQNLGTIKSSNLCTEVIQYTSPTETA------------VCNLASIALPRYVREMGV 460
+ + G I SNLC+E++Q S +E CNL S+ +
Sbjct: 374 RANPIA--GRINMSNLCSEILQVNSASEYNEDLSYAHIGKDISCNLGSLNIAH------- 424
Query: 461 PMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNY-YPVETARRSNLRHRP 519
M+S DF + E T I L + D+++ V + + N
Sbjct: 425 TMDSP---------------DFGRTVE-TAI--RALTAVSDMSHIRSVPSIEKGNAASHA 466
Query: 520 IGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSP 579
IG+G L G+ + S EA F T+ YHALR S+ +A G ET+ G
Sbjct: 467 IGLGQMNLHGYLAREGIFYGSEEALDFTNIYFYTVTYHALRASNLLARERG--ETFAGFE 524
Query: 580 VSK------------GILQP---------DMWGVNPSDRWDWGGLRDMISKNGVRNSLLV 618
SK QP G+ + DW LRD + ++G+ N L
Sbjct: 525 QSKYASGEYFDKYTQQDWQPKTAKVRELFARAGITIPTQEDWAQLRDDVMRHGIYNQNLQ 584
Query: 619 APMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKI 678
A PT S S I N+ TS+I+ PI+
Sbjct: 585 AVPPTGSISYI--NHS-----TSSIH---------------------------PIVSKIE 610
Query: 679 IYDDGSVQKI----PQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHM-DQ 733
I +G + ++ P + + Y+ +EI + ++D ++D SL + D
Sbjct: 611 IRKEGKIGRVYYPAPYMTNDNLEYYQDAYEIGPEKIIDTYAAATQHVDQGLSLTLFFPDT 670
Query: 734 PNFGKLTSLHFHAWLRGLKTGMYYLRSRAAA 764
+ +AW +G+KT +YY+R R A
Sbjct: 671 ATTRDINKAQIYAWRKGIKT-LYYIRLRQMA 700
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 148 bits (375), Expect = 1e-36
Identities = 106/408 (25%), Positives = 176/408 (43%), Gaps = 73/408 (17%)
Query: 191 HMMSQRWFTHASPTLFNAGTP-RAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIG 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 EFLDLRKNHGKEEHRARDL-----------------FY-----ALWVPDLFMERVQSNGL 347
EF++ + KEE + R L Y ++ V D FM V+++G
Sbjct: 242 EFIETK---AKEEDKIRALRDAGYDMDLGGEAYSSVQYQNANNSVRVSDEFMRAVENDGE 298
Query: 348 WSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLF 407
+ L + +G+ + V A+ L+ +I ++ E P + +
Sbjct: 299 FGL----------------------RARTDGEVIETVDAKELFRKIAEAAWECADPGIQY 336
Query: 408 KDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPS 467
DT N G I +SN C+E Y ++ CNLAS+ L +++R+ G
Sbjct: 337 DDTINDWHTCPESGRINASNPCSE---YMFLDNSS-CNLASLNLMKFLRDDGT------- 385
Query: 468 KLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGL 527
FD E +V + I +P E R+ R +G+G L
Sbjct: 386 ------------FDVESFRHAVELVITAMEISICFADFPTEKIARNTRAFRQLGLGYANL 433
Query: 528 ADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETY 575
+ G+P+DS + L I + A R S+E+A GP+E Y
Sbjct: 434 GALLMATGLPYDSDGGRALAAAITSLMTGEAYRRSAELAGVVGPFEGY 481
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 136 bits (343), Expect = 1e-32
Identities = 85/274 (31%), Positives = 136/274 (49%), Gaps = 31/274 (11%)
Query: 440 ETAVCNLASIALPRYVR--EMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLN 497
E CNLASI L ++V+ E G P YFD+++ A V V + L+
Sbjct: 1304 EYESCNLASINLAKFVKYDENGKP-----------------YFDWDEYAYVIQKVAKYLD 1346
Query: 498 KIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYH 557
IDVN +P+ + R IG+G+ GLAD LG+P++S E + + + E + ++
Sbjct: 1347 NAIDVNKFPLPEIDYNTKLTRRIGVGMMGLADALFKLGIPYNSEEGFKFMRKVTEYLTFY 1406
Query: 558 ALRTSSEIAAREGPYETYHGSPVSKGIL------QPDMWGVNPSDRWDWGGLRDMISKNG 611
A + S E A + G + Y + KG L P++W + W L + I K G
Sbjct: 1407 AYKYSVEAAKKRGTFPLYEKTEYPKGELPVEGFYHPEIWNL------PWDKLVEEIKKYG 1460
Query: 612 VRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWS 671
VRN+++ PT S S I + EP + +Y + V GEF V+ +L + GL+S
Sbjct: 1461 VRNAMVTTCPPTGSVSMIADTSSGIEPIFALVYKKSVTVGEFYYVDPVFEAELKKRGLYS 1520
Query: 672 PIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEI 705
+ KI + GSVQ + +IPE+++ ++ T +I
Sbjct: 1521 EELLKKISDNYGSVQGLEEIPEDMQRVFVTALDI 1554
Score = 48.6 bits (115), Expect = 1e-05
Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 170 MLMRVAVGIHKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIE 229
ML R ++ +I+ + + +M+ + F +P L N+G P LS+CF+V ++DD +E
Sbjct: 228 MLERGEFDKYEKEIE---EYFRLMTNQIFMPNTPALINSGRPLGMLSACFVVPIEDD-ME 283
Query: 230 GIYDTLKECAIISKSAGG 247
I + A+I K+ GG
Sbjct: 284 SIMKAAHDVAMIQKAGGG 301
Score = 40.5 bits (94), Expect = 0.004
Identities = 40/184 (21%), Positives = 78/184 (42%), 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 FEFLDLR-KNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEF 367
+F+ + KN G ++ +W + F E ++ + L P
Sbjct: 816 EKFIHAKEKNIGTNVLSNFNISVGIW--EDFWEALKEGKKYPLINP-------------- 859
Query: 368 ERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKS--NQQNLGTIKS 425
+ G+ K + ++L+ E+ P ++F D N+++ + G I++
Sbjct: 860 --------RTGEVVKEIDPKSLFEELAYMAWAKADPGVIFFDVINRRNVLKEAKGGPIRA 911
Query: 426 SNLC 429
+N C
Sbjct: 912 TNPC 915
>gnl|CDD|180772 PRK06948, PRK06948, ribonucleotide reductase-like protein;
Provisional.
Length = 595
Score = 129 bits (327), Expect = 2e-31
Identities = 110/416 (26%), Positives = 172/416 (41%), Gaps = 57/416 (13%)
Query: 246 GGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWH 305
GGIG I + + S G+ L F+ + G+R AV L H
Sbjct: 121 GGIGYDFSAIPPADARPDADHPDSPGVCAALDRFDRICAALPFRDGRRGAQMAV-LRCDH 179
Query: 306 ADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLF---CPNEAPGLADC 362
D+ F+ ++ R ++ V D FM+ V + W+L P A G A
Sbjct: 180 PDLLAFVAAKRGRA----RWTTFNLSVAVTDAFMQAVAQDLPWALRHRAPPRRAAGGALR 235
Query: 363 WGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGT 422
G + Y V A++LW EI+ + ++ P +LF DT + + +
Sbjct: 236 -GADGAWTYA----------TVPARHLWREIVSAARDSAEPGLLFVDTIDAANPLREHER 284
Query: 423 IKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDF 482
I ++N C E Q P + V L I L R+VR HP + G + R FDF
Sbjct: 285 IDATNPCGE--QPLPPYGSCV--LGPIDLSRFVR--------HPFGV----GGEPR-FDF 327
Query: 483 EKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTE 542
LA I L+ +D+ +P+ R + R IG+GV GLAD ++ + +DS
Sbjct: 328 AALATAVRIQVRMLDNALDLTRWPLAAHAREARQKRRIGVGVTGLADALTMMRLRYDSPA 387
Query: 543 AQQLNKDIFETIYYHALRTSSEIAAREGPYETY----HGSPVSKGILQPDMWGVNPSDRW 598
A+++ + I + +HA S+ +AA G Y H + G P
Sbjct: 388 AREMARYIASDLRHHAYAASAALAAERGAYPLCDPAAHLDALRAGPPLP----------- 436
Query: 599 DWGGLRDMISKNGVRNSLLVAPMPTASTSQILGNNEC---FEPYTSNIYSRRVLSG 651
+ I+++G+RNS L++ P S S G+N C EP + I R V +G
Sbjct: 437 --HAVCHAIARHGLRNSHLLSFAPVGSVSLAFGDN-CSPGIEPARAWIEHRPVRAG 489
>gnl|CDD|215855 pfam00317, Ribonuc_red_lgN, Ribonucleotide reductase, all-alpha
domain.
Length = 79
Score = 98.5 bits (246), Expect = 6e-25
Identities = 32/79 (40%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 141 FDYDYFGFKTLERSYLLKV-QGKVVERPQHMLMRVAVGIH-----KDDIDSAIKTYHMMS 194
Y K LE YLLK G+V+E PQ M MRVA+ + +D ++ A + Y ++S
Sbjct: 1 RFLTYLAAKVLEDRYLLKDEDGEVLETPQDMFMRVALALAGAEPPEDRLELAEEFYDLLS 60
Query: 195 QRWFTHASPTLFNAGTPRA 213
F A+PTL NAGTP
Sbjct: 61 SLKFLPATPTLMNAGTPLG 79
>gnl|CDD|236152 PRK08115, PRK08115, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 858
Score = 104 bits (261), Expect = 6e-23
Identities = 91/346 (26%), Positives = 148/346 (42%), Gaps = 53/346 (15%)
Query: 338 FMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTK----------YEKEG---KAKKVV 384
FME V+++ + L P+ + + E +Y + +EK G + + +
Sbjct: 379 FMEAVENDEEYELRFPD-----VENYTEEEMEIYNEEWHEVGDVREWEKMGYPVRTYRKI 433
Query: 385 QAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLG-TIKSSNLCTEVIQYTSPTETAV 443
+A+ LW I + P + F D N+ +N + G + ++N C E Q +P +V
Sbjct: 434 KAKELWNLINICATYSAEPGIFFIDNANEMTNAKAYGQKVVATNPCGE--QPLAPY--SV 489
Query: 444 CNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVN 503
CNLA+I L + + + D+EKL + + +ID
Sbjct: 490 CNLAAINLANMADK------------------ETKTVDYEKLKRTVEVGVRMQDNVIDAT 531
Query: 504 YYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSS 563
Y +E ++ L R +G+GV GL D I + S E QL IFETI A RTS
Sbjct: 532 PYFLEENKKQALGERRVGLGVMGLHDLLIYCETVYGSEEGNQLVDQIFETIATTAYRTSI 591
Query: 564 EIAAREGPYETYHGSP------VSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLL 617
E+A +G + G + + + P D +R+ I K G+RNS L
Sbjct: 592 ELAKEKGSFPFLVGQTEEETAKLREAFINTGYMKKMPED------IREDILKYGIRNSHL 645
Query: 618 VAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHD 663
+ PT ST ++G + EPY S Y R G+F+ V ++ +
Sbjct: 646 LTVAPTGSTGTMVGVSTGLEPYFSFSYYRSGRLGKFIEVKADIVQE 691
Score = 62.9 bits (153), Expect = 5e-10
Identities = 41/128 (32%), Positives = 63/128 (49%), Gaps = 6/128 (4%)
Query: 188 KTYHMMSQRWFTHASPTLFNAGTPR-AQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAG 246
K Y + F A L+ AG+ +C+++ DS EGI + 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 = 66.1 bits (162), Expect = 2e-13
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 7/91 (7%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGL-SIEHCDPVLVSQKVCTGVYKG--VTTSQLD 57
M V+KRDG++E +KI ++K + L ++ ++++V + G ++T ++
Sbjct: 1 MKVIKRDGRREPFDREKIRRAIEKAARALRPVDPEQAEEIAEEVEEELRDGGEISTEEIQ 60
Query: 58 ELAAETAAAMTTNHPDYASLAARIVVSNLHK 88
+L +T HPDYA A I+ NL K
Sbjct: 61 DLVEKTLME----HPDYAVARAYILYRNLRK 87
>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 = 59.1 bits (143), Expect = 4e-09
Identities = 84/452 (18%), Positives = 134/452 (29%), Gaps = 118/452 (26%)
Query: 205 LFNAGTPRAQLSSCFLVCMKD--------------DSIEGIYDTLKECAIISKSAGGIGV 250
+ G P + C LV D E I T + A+ + + G GV
Sbjct: 12 VITVGRPDLPFTGCVLVDYGDSLDPGIKGVNETAKSINEAIQKTYQIIALAASNQNGGGV 71
Query: 251 SVHN----IRATGSYIRG-TNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVY----L 301
S + GS +GT V FN + V QG G+ A
Sbjct: 72 SFARASSILSPYGSRDYAKGSGTETDAVEAADAFNLALKEVGQGNGRTGAATGFIGGVHK 131
Query: 302 EPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLAD 361
EFL+L +G E L P+L S+ ++ PG
Sbjct: 132 GKGDKISQEFLNLALANGGEGIP-------LNFPNL-----------SVRVSSDKPG--- 170
Query: 362 CWGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLG 421
L E + I + +TG+P +
Sbjct: 171 -------ILVKAVELKQL-------------IAEEARKTGSPGIFN-------------- 196
Query: 422 TIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFD 481
+CNL S+ L R + GS + +
Sbjct: 197 -------------------DELCNLVSLNLARIM-------------EKAINGSMDVVLE 224
Query: 482 FEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDST 541
L E+ + L+ +ID + + T R +G+G+ G+AD I LG+
Sbjct: 225 E--LEELAFLAVRALDCVIDSHDERIPTIELGGDERRTVGLGIAGVADLLIKLGLEKVGD 282
Query: 542 -EAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDW 600
EA L ++ + + H ++ ++E + S S GV+PS
Sbjct: 283 PEADDLAAELVDQLKKHLVKATNERGFNFLLGLSPSESNSSGAPATN---GVSPSRGXIA 339
Query: 601 GGLRDMISKNGVRNSLLVAPMPTASTSQILGN 632
L I S VA + + + I
Sbjct: 340 IVLNGDIGPEESLAS--VAILQFYADNGISDT 369
>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1220
Score = 57.3 bits (139), Expect = 3e-08
Identities = 62/253 (24%), Positives = 101/253 (39%), Gaps = 66/253 (26%)
Query: 334 VPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEI 393
V D F+ V+++G W+L +GK K ++A++LW +I
Sbjct: 403 VTDEFLRAVENDGDWNL----------------------TARTDGKVAKTLKARDLWEKI 440
Query: 394 LKSQIETGTPYMLFKDTCN-----KKSNQQNLGTIKSSNLCTEVIQYTSPTETAVCNLAS 448
+ + P + F T N S G I++SN C+E Y +TA CNLAS
Sbjct: 441 GYAAWASADPGLQFNTTINDWHTCPAS-----GPIRASNPCSE---YMFLDDTA-CNLAS 491
Query: 449 IALPRYVREMGVPMESHPSKLVGSRGSKNRYFD---FEKLAEVTGIVTENLNKIIDV--N 503
+ L + E + FD +E + +V E I V
Sbjct: 492 LNLLTFRDE------------------DTKRFDVEAYEHACRLWTVVLE-----ISVLMA 528
Query: 504 YYPV-ETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTS 562
+P E A S R +G+G + + +G+P+DS E + + + + A TS
Sbjct: 529 QFPSKEIAELS-YEFRTLGLGYANIGGLLMTMGIPYDSDEGRAICGALSAIMTGVAYATS 587
Query: 563 SEIAAREGPYETY 575
+E+A GP+ Y
Sbjct: 588 AEMAKELGPFPGY 600
Score = 32.2 bits (74), Expect = 1.3
Identities = 32/104 (30%), Positives = 52/104 (50%), Gaps = 3/104 (2%)
Query: 212 RAQLSSCFLVCMKDDSIE--GIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTS 269
Q +CF+ ++DD + GI D A + K G G + N+R G + G G S
Sbjct: 193 HPQPHACFIQSVEDDLVNEGGIMDLWVREARLFKYGSGTGSNFSNLRGEGEKLSG-GGKS 251
Query: 270 NGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLD 313
+G++ L++ + A + GG R+ A V ++ H DI EF+D
Sbjct: 252 SGLMSFLKIGDRAAGAIKSGGTTRRAAKMVIVDIDHPDIEEFID 295
>gnl|CDD|234064 TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific. Members of
this family are homodimeric ferredoxins from nitrogen
fixation regions of many nitrogen-fixing bacteria. As
characterized in Rhodobacter capsulatus, these proteins
are homodimeric, with two 4Fe-4S clusters bound per
monomer. Although nif-specific, this protein family is
not usiveral, as other nitrogenase systems may
substitute flavodoxins, or different types of ferredoxin
[Central intermediary metabolism, Nitrogen fixation].
Length = 91
Score = 31.6 bits (72), Expect = 0.32
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 784 DDDDAKMAQMVCSLTNREECMACGS 808
DDDD ++ + V + N C+ CG+
Sbjct: 53 DDDDDEIERKVMVVANPGNCIGCGA 77
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 30.9 bits (69), Expect = 2.7
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 414 KSNQQNLGTIKSSNL-CTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHP 466
K ++ +GT +N +E + P +AV + A+ A P + M +PM S P
Sbjct: 341 KKQRKKVGTSDDNNTPMSEKRKREDPNSSAVFSKAT-AEPAFKSAMAIPMPSMP 393
>gnl|CDD|237339 PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
Length = 394
Score = 31.0 bits (71), Expect = 2.8
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 54 SQLD-ELAAETAAAMTTNHPDYASLAA-RIVV 83
SQL +L ET AM T P ++ RI V
Sbjct: 167 SQLGFDLETETFEAMKTQAPLLEKISVERIFV 198
>gnl|CDD|180977 PRK07432, PRK07432, 5'-methylthioadenosine phosphorylase;
Provisional.
Length = 290
Score = 30.5 bits (69), Expect = 2.9
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 58 ELAAETAAAMTTN---HPDYASLAARIVVSNLHK---NTKKSFSETIK 99
E+A T A +T HPD+ S+ +V+ NLHK N +K ET++
Sbjct: 201 EIAYATLALVTDYDCWHPDHDSVTVEMVIGNLHKNAVNAQKVIQETVR 248
>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 = 2.9
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 12/64 (18%)
Query: 147 GFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHKDD------IDSAIK------TYHMMS 194
GF K G V ++ +G+ K D + A+ TY +S
Sbjct: 187 GFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADGTYQKIS 246
Query: 195 QRWF 198
++WF
Sbjct: 247 KKWF 250
>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 = 2.9
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 15/71 (21%)
Query: 45 TGVYKGVTTSQLDELAAETAAAMTTNHPDYASLAARI-----------VVSN----LHKN 89
TG GVT SQL ++A + T +L A V+ + +
Sbjct: 108 TGNAAGVTASQLADMARAISDVGGTQGAAAEALTALAAAGKFAGEQLEAVAQAAAKMSEA 167
Query: 90 TKKSFSETIKD 100
T +S ET+KD
Sbjct: 168 TGQSVDETVKD 178
>gnl|CDD|227289 COG4953, PbpC, Membrane carboxypeptidase/penicillin-binding protein
PbpC [Cell envelope biogenesis, outer membrane].
Length = 733
Score = 30.8 bits (70), Expect = 3.1
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 335 PDLFMERVQSNGLWSLFCPNEAPGLADCWGT------EFERLYTKYEKEGKAKKV 383
P F R++ G+ APGL+ G + +LY +GKA +
Sbjct: 405 PPRFAARLRQAGVHLYLPEGAAPGLSLILGGAGITLEDLAQLYAALANQGKAGPL 459
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 29.8 bits (68), Expect = 5.7
Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 1/91 (1%)
Query: 475 SKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILL 534
+K FE+L + + ++I P L + + IG+ GL + L
Sbjct: 294 AKGDEEFFEELDRYDLAKRKLIEELIAAGLLPFYKQYLWRLDNHFLTIGINGLNEALANL 353
Query: 535 G-MPFDSTEAQQLNKDIFETIYYHALRTSSE 564
G + E ++ + + I A E
Sbjct: 354 GGTDIEDEEGKKFGLRVLDFIREKAREAQEE 384
>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 = 29.9 bits (67), Expect = 6.7
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 252 VHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKR 293
+ +IR G+ ++G GT++G VP+ ++ D A + G R
Sbjct: 214 LSDIRPAGAELKGFGGTASGPVPLAKMLTDVAEILSNKAGGR 255
>gnl|CDD|129772 TIGR00689, rpiB_lacA_lacB, sugar-phosphate isomerase,
RpiB/LacA/LacB family. Proteins of known function in
this family act as sugar (pentose and/or
hexose)-phosphate isomerases, including the LacA and
LacB subunits of galactose-6-phosphate isomerases from
Gram-positive bacteria and RpiB. RpiB is the second
ribose phosphate isomerase of E. coli. It lacks
homology to RpiA, its inducer is unknown (but is not
ribose), and it can be replaced by the homologous
galactose-6-phosphate isomerase of Streptococcus
mutans, all of which suggests that the ribose phosphate
isomerase activity of RpiB is a secondary function. On
the other hand, there appear to be a significant number
of species which contain rpiB, lack rpiA and seem to
require rpi activity in order to complete the pentose
phosphate pathway.
Length = 144
Score = 28.5 bits (64), Expect = 7.5
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 63 TAAAMTTNHPDYASLAARIVVSN 85
T ++PDYA L A VV+
Sbjct: 32 TLYDERVDYPDYAKLVADKVVAG 54
>gnl|CDD|153085 cd01676, RNR_II_monomer, Class II ribonucleotide reductase,
monomeric form. Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class, are found to be
homodimers. This particular subfamily is found to be
active as a monomer. Adenosylcobalamin interacts
directly with an active site cysteine to form the
reactive cysteine radical.
Length = 658
Score = 29.8 bits (67), Expect = 7.6
Identities = 10/39 (25%), Positives = 19/39 (48%)
Query: 255 IRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKR 293
IR G ++G G ++G P+ ++ A ++ GK
Sbjct: 200 IRPAGERLKGFGGIASGPEPLKKLHKAIAAILNDRSGKP 238
>gnl|CDD|177979 PLN02345, PLN02345, endoglucanase.
Length = 469
Score = 29.3 bits (66), Expect = 9.9
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 13/66 (19%)
Query: 52 TTSQLDELAAETAAAMT-------TNHPDYASL----AARIVVSNLHKNTKKSFSETIKD 100
T+S E+AAETAAAM ++ Y+ A ++ N + S+SE+I +
Sbjct: 136 TSSPGSEVAAETAAAMAAASLVFKSSDSTYSDTLLKHAKQLF--NFADKYRGSYSESIPE 193
Query: 101 MYNHYN 106
+ ++YN
Sbjct: 194 VQDYYN 199
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 0.404
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: 41,062,244
Number of extensions: 4050754
Number of successful extensions: 3520
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3308
Number of HSP's successfully gapped: 76
Length of query: 808
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 703
Effective length of database: 6,280,432
Effective search space: 4415143696
Effective search space used: 4415143696
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)