RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780502|ref|YP_003064915.1| ribonucleotide-diphosphate
reductase subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
(954 letters)
>gnl|CDD|145819 pfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel
domain.
Length = 516
Score = 695 bits (1797), Expect = 0.0
Identities = 251/538 (46%), Positives = 340/538 (63%), Gaps = 24/538 (4%)
Query: 368 LSSCFLTTVPDDLYGIFGALQENAMLAKYSGGLGNDWTPVRGLGAHIHGTNGKSQGVIPF 427
LSSCFL +V D L I+ L+E A+L+K GG+G + + +R G+ I GT G S GV+PF
Sbjct: 1 LSSCFLLSVDDSLDSIYDTLKEAALLSKSGGGIGINLSKIRAKGSPIRGTGGVSSGVVPF 60
Query: 428 LKVANDTAVAVNQGGKRKGAVCAYLETWHIDVEEFLDLRKNTGDDRRRTHDMNTANWIPD 487
LKV +DTA VNQGGKR+GAV YLE WH D+EEFLDL+KN GD+ R ++N W+PD
Sbjct: 61 LKVFDDTARYVNQGGKRRGAVAVYLEVWHPDIEEFLDLKKNNGDEEVRARNLNLGVWVPD 120
Query: 488 LFMKRVTQNAGWTLFSPDEVSDLHDLYGKEFEIAYENYERQADRGEIKVFRKISAVALWR 547
LFMKRV + WTLFSP E L DLYG+EFE YE V + + A LW
Sbjct: 121 LFMKRVENDGDWTLFSPREAPGLEDLYGEEFEEEYEK----------IVKKTVKARELWF 170
Query: 548 KMLTMLFETGHPWITFKDPCNIRSPQQHVGVVHSSNLCTEITLNSSSEETAVCNLGSINL 607
K++ +ETG P+I FKD N +P +H+G + SSNLCTEI +S E AVCNLGSINL
Sbjct: 171 KIVESAWETGEPYILFKDAVNRHNPNKHLGTIKSSNLCTEIVQPTSPGEDAVCNLGSINL 230
Query: 608 LAHFANNQFDYDKLASTIRTAVRVLDNVIDINCHTIEKAKKSNHTHRAIGLGLMGFQSAL 667
+ FD+++L +R AVR LDNVID+N + + +A+KSN HR+IGLG+MG AL
Sbjct: 231 AKFVKDGTFDFEELREVVRLAVRALDNVIDLNDYPVPEARKSNKRHRSIGLGVMGLADAL 290
Query: 668 HLLHIPYASPEAVEIADESMEFISFHAISASVELAQERGAYSSFKGSLWDQGVFPIDSIG 727
L IPY S EA E+ADE E I ++A+ AS ELA+E+G + F+GS + +G+ P D
Sbjct: 291 AKLGIPYDSEEARELADEIFETIYYYALKASNELAKEKGPFPGFEGSKYAKGILPFD--- 347
Query: 728 LLAEVRDELAMNRTSRLPWDELKKRVKTIGMRNSNCMAIAPTATIANICGVSQSIDPSYQ 787
LA+ D+L T + W+EL++ +K G+RNS AIAPT +I+ I G ++ I+P +
Sbjct: 348 -LAKTVDDLGPKTT-KEDWEELREDIKKHGLRNSQLTAIAPTGSISQIAGTTEGIEPIFS 405
Query: 788 NLYVKSNMSGDFTVVNSFLVNELKQRDLWDEAMISDLKYHDGSIGNIERIPDDLKKIHAT 847
N+Y + SG+F VVN +L +L++ LW M GS+ I IP +LK + T
Sbjct: 406 NVYSRRVKSGEFLVVNPYLSRDLRELGLWTLEMK-------GSVQGIPEIPAELKAYYKT 458
Query: 848 AFEIDPMWLIESASRRQKWIDQAQSLNLYLDEP-SGKKLDFIYRQAWLMGLKT-TYYL 903
AF+ID I+ A+ RQ ++DQ+ S L+L EP + L +Y AW +GLKT TYY
Sbjct: 459 AFDIDQKGHIDMAAARQPFVDQSISKTLFLPEPATASDLKSLYLYAWKLGLKTGTYYR 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 = 663 bits (1712), Expect = 0.0
Identities = 250/595 (42%), Positives = 321/595 (53%), Gaps = 141/595 (23%)
Query: 317 PQAFFMRVAMGLALKETEKEKRAVEFYNLLSSFHFMCSTPTLFNSGTRHPQLSSCFLTTV 376
PQ MRVA+GLA + E A EFY+LLS F +TPTLFN+GT QLSSCFL TV
Sbjct: 1 PQDRLMRVALGLASGDLEW---AKEFYDLLSKQRFTPATPTLFNAGTPRGQLSSCFLLTV 57
Query: 377 PDDLYGIFGALQENAMLAKYSGGLGNDWTPVRGLGAHIHGTNGKSQGVIPFLKVANDTAV 436
D L I+ ++E A L+K GG+G + + +R G+ I GTNG S GVIPFLK+ NDTA
Sbjct: 58 DDSLESIYDTIKECAQLSKIGGGIGLNLSNIRATGSPIRGTNGASNGVIPFLKLLNDTAR 117
Query: 437 AVNQGGKRKGAVCAYLETWHIDVEEFLDLRKNTGDDRRRTHDMNTANWIPDLFMKRVTQN 496
V+QGG+RKGA YLE WH D+EEFLDL+KN GD+RRR D+ WIPDLFM+RV
Sbjct: 118 YVDQGGQRKGAGAVYLEIWHPDIEEFLDLKKNNGDERRRARDLFYGVWIPDLFMERV--- 174
Query: 497 AGWTLFSPDEVSDLHDLYGKEFEIAYENYERQADRGEIKVFRKISAVALWRKMLTMLFET 556
ER LWRK+L FET
Sbjct: 175 -----------------------------ERD----------------LWRKILESQFET 189
Query: 557 GHPWITFKDPCNIRSPQQHVGVVHSSNLCTEITLNSS-----SEETAVCNLGSINLLAHF 611
G+P+I FKD CN ++PQ+H+G + SSNLCTEI +S E AVCNL SINL
Sbjct: 190 GYPYILFKDTCNRKNPQKHLGTIKSSNLCTEILQPTSPSEDEPGEDAVCNLASINLGNF- 248
Query: 612 ANNQFDYDKLASTIRTAVRVLDNVIDINCHTIEKAKKSNHTHRAIGLGLMGFQSALHLLH 671
++KL ++ AVR LDNVID+N + + +AK+SN HRAIGLG+MG L LL
Sbjct: 249 ----VTFEKLEEVVKLAVRALDNVIDLNYYPVPEAKRSNMRHRAIGLGVMGLHDYLALLR 304
Query: 672 IPYASPEAVEIADESMEFISFHAISASVELAQERGAYSSFKGSLWDQGVFPIDSIGLLAE 731
IPY S EA+++ D E I+++A+ AS ELA+ERG
Sbjct: 305 IPYESEEALDLNDRIFETINYYALKASCELAKERG------------------------- 339
Query: 732 VRDELAMNRTSRLPWDELKKRVKTIGMRNSNCMAIAPTATIANICGVSQSIDPSYQNLYV 791
G+RNS +AIAPTA+I+ I G + SI+P N+YV
Sbjct: 340 -------------------------GLRNSLLLAIAPTASISQILGATPSIEPITSNIYV 374
Query: 792 KSNMSGDFTVVNSFLVNELKQRDLWDEAMISDLKYHDGSIGNIERIPDDLKKIHATAFEI 851
+ +SG+F VVN L +L + L+ TA+EI
Sbjct: 375 RRVLSGEFPVVNPHLEKDLWEYGLY-----------------------------KTAYEI 405
Query: 852 DPMWLIESASRRQKWIDQAQSLNLYLDEP-SGKKLDFIYRQAWLMGLKTTYYLRS 905
D WLI+ A+ RQK IDQ QSLNL+L P + + L+ +Y AW GLKT YYLR+
Sbjct: 406 DQRWLIDLAADRQKHIDQGQSLNLFLTPPATTRDLNSLYFYAWKKGLKTLYYLRT 460
>gnl|CDD|36328 KOG1112, KOG1112, KOG1112, Ribonucleotide reductase, alpha subunit
[Nucleotide transport and metabolism].
Length = 796
Score = 593 bits (1529), Expect = e-170
Identities = 286/779 (36%), Positives = 444/779 (56%), Gaps = 45/779 (5%)
Query: 189 MYDGLSESDLETALIFSSRTLIEKEPNYAKVTARFLLEKLRREVLTTVYKKPQKATHHEM 248
+Y+G++ +L+ ++ ++ K P+YA + AR + L +K+ +K +
Sbjct: 47 VYEGVTTVELDNLAAETAASMTTKHPDYAILAARIAVSNL--------HKQTKKVFSEVI 98
Query: 249 QCLYPEYFCRYI--EEGVKARLLHESMMDFDLVY---LANDLKYERDFAFEYLGLQILYD 303
+ L+ ++ G A ++ + + + + L + + Y+RDF++ Y G + L
Sbjct: 99 EDLH-----NHVNPHTGKHAPMISDEVYNIVMENKDRLNSAIIYDRDFSYNYFGFKTLER 153
Query: 304 RYFLHINGSRIEMPQAFFMRVAMGLALKETEKEKRAVEFYNLLSSFHFMCSTPTLFNSGT 363
Y L ING E PQ MRVA+G+ ++ E A+E YNL+S +F ++PTLFN+GT
Sbjct: 154 SYLLKINGEVAERPQHMLMRVALGIHGEDIEA---AIETYNLMSERYFTHASPTLFNAGT 210
Query: 364 RHPQLSSCFLTTVPDD-LYGIFGALQENAMLAKYSGGLGNDWTPVRGLGAHIHGTNGKSQ 422
PQLSSCFL T+ DD + GI+ L++ AM++K +GG+G + +R G++I GTNG S
Sbjct: 211 PRPQLSSCFLLTMKDDSIEGIYDTLKQCAMISKSAGGIGLNVHNIRATGSYIAGTNGTSN 270
Query: 423 GVIPFLKVANDTAVAVNQGG-KRKGAVCAYLETWHIDVEEFLDLRKNTGDDRRRTHDMNT 481
G+IP ++V N+TA V+QGG KR GA YLE WH D+ +FL+LRKNTG + R D+
Sbjct: 271 GLIPMIRVFNNTARYVDQGGNKRPGAFAIYLEPWHADIFDFLELRKNTGKEEFRARDLFY 330
Query: 482 ANWIPDLFMKRVTQNAGWTLFSPDEVSDLHDLYGKEFEIAYENYERQADRGEIKVFRKIS 541
A WIPDLFMKRV N W+LF P+E L D++G EFE Y YE+ E + + +
Sbjct: 331 ALWIPDLFMKRVENNGEWSLFCPNEAPGLDDVWGDEFEALYTKYEK-----EGRGKKTVK 385
Query: 542 AVALWRKMLTMLFETGHPWITFKDPCNIRSPQQHVGVVHSSNLCTEITLNSSSEETAVCN 601
A LW +L ETG P++ +KD CN +S QQ++G + SSNLCTEI SS +ETAVCN
Sbjct: 386 AQKLWYAILEAQVETGTPYMLYKDACNRKSNQQNLGTIKSSNLCTEIVEYSSPDETAVCN 445
Query: 602 LGSINLLAHFANNQ-FDYDKLASTIRTAVRVLDNVIDINCHTIEKAKKSNHTHRAIGLGL 660
L SI L + +D++KLA + R L+ +ID+N + +E+A++SN HR IG+G+
Sbjct: 446 LASIALPMFVTPEKTYDFEKLAEVTKVVTRNLNKIIDVNYYPVEEARRSNMRHRPIGIGV 505
Query: 661 MGFQSALHLLHIPYASPEAVEIADESMEFISFHAISASVELAQERGAYSSFKGSLWDQGV 720
G A LL +P+ S EA + + E I + A+ AS ELAQ+ G Y +++GS +G+
Sbjct: 506 QGLADAFILLRLPFESAEARLLNKQIFETIYYAALEASCELAQKEGPYETYEGSPVSKGI 565
Query: 721 FPIDSIGLLAEVRDELAMNRTSRLPWDELKKRVKTIGMRNSNCMAIAPTATIANICGVSQ 780
D + T W L++++ G+RNS +A PTA+ + I G ++
Sbjct: 566 LQFDMWNVKP----------TDLWDWATLREKIAKHGVRNSLLVAPMPTASTSQILGNNE 615
Query: 781 SIDPSYQNLYVKSNMSGDFTVVNSFLVNELKQRDLWDEAMISDLKYHDGSIGNIERIPDD 840
+P N+Y + +SG+F +VN L+ +L + LWD+ M + L ++GSI NI IP D
Sbjct: 616 CFEPYTSNIYSRRVLSGEFQIVNPHLLKDLVELGLWDDEMKNKLIANNGSIQNIPEIPQD 675
Query: 841 LKKIHATAFEIDPMWLIESASRRQKWIDQAQSLNLYLDEPSGKKLDFIYRQAWLMGLKT- 899
LK+++ T +EI +I+ A+ R +IDQ+QSLN++L +P+ KL ++ W GLKT
Sbjct: 676 LKELYKTVWEISQKTVIDMAADRGAFIDQSQSLNIHLAKPNYGKLTSMHFYGWKKGLKTG 735
Query: 900 TYYLRSRSATS-----VEKSTLKGVDGKLNAVPVTDPNSSTHSLGIPSSCTSDTECEVC 953
YYLR+R A + V+K L + ++ + S + C +C
Sbjct: 736 MYYLRTRPAANAIQFTVDKKVLNEKAEVAEGDSKEEEEDEYNTAVMVCSLDNPEACLMC 794
>gnl|CDD|73173 COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide
transport and metabolism].
Length = 651
Score = 567 bits (1462), Expect = e-162
Identities = 256/752 (34%), Positives = 357/752 (47%), Gaps = 117/752 (15%)
Query: 181 VLSETYKNMYDGLSESDLETALIFSSRTLIEKEPNYAKVTARFLLEKLRREVLTTVYKKP 240
T YDG + E ++ + + E +P+ ++ AR LR+E + +
Sbjct: 1 RELRTVIGFYDG--ITIAENLILAALTVIEEDDPDVQRLAARLAGSDLRKEAV-----RQ 53
Query: 241 QKATHHEMQCLYPEYFCRYIEEGVKARLLHESMMDFDLVYLANDLKYERDFAFEYLGLQI 300
+ ++ Y ++ L DL L + ERD F Y ++
Sbjct: 54 FGRFDVLDEKVFALVANGYYDQ-----RLLRLYSREDLDDLNKKILLERDRQFSYAAAKV 108
Query: 301 LYDRYFLHINGSR--IEMPQAFFMRVAMGLALKETE--KEKRAVEFYNLLSSFHFMCSTP 356
LY RY L +E+PQ FMRVA+ LA E + + A EFY+L+SS FM +TP
Sbjct: 109 LYSRYLLKDEDGSEILELPQDLFMRVALLLAQNEAPERRLEWAKEFYDLMSSLRFMPATP 168
Query: 357 TLFNSGTRHPQLSSCFLTTVPDDLYGIFGALQENAMLAKYSGGLGNDWTPVRGLGAHIHG 416
TL N GT QLSSCF+ V DD
Sbjct: 169 TLLNGGTPRGQLSSCFVLPVEDD------------------------------------- 191
Query: 417 TNGKSQGVIPFLKVANDTAVAVNQGGKRKGAVCAYLETWHIDVEEFLDLRKNTGDDRRRT 476
S GV+PF+K+ +D A+NQGG R+GA YL+ WH D+EEFLD ++N GD+ R
Sbjct: 192 ----SSGVVPFMKLLDDAFDAINQGGVRRGAQAVYLDIWHPDIEEFLDAKRNNGDEILRA 247
Query: 477 HDMNTANWIPDLFMKRVTQNAGWTLFSPDEVSDLHDLYGKEFEIAYENYERQADRGEIKV 536
D++ WIPDLFMKR + WTLFSP + + D+YG EFE Y YE
Sbjct: 248 FDISVGVWIPDLFMKRAKEGEDWTLFSPRDGYEAPDVYGAEFE-EYAEYEAD----PGIR 302
Query: 537 FRKISAVALWRKMLTMLFETGHPWITFKDPCNIRSPQ-QHVGVVHSSNLCTEITLNSSS- 594
++I A L+ K+ FETG P++ F D N R+P + G + +SNLC+EI +
Sbjct: 303 KKRIKARELFDKLAEAAFETGDPYLIFVDTLNRRNPNAEGGGAIRASNLCSEILQRTKPL 362
Query: 595 ------EETAVCNLGSINLLAHFANNQFDYDKLASTIRTAVRVLDNVIDINCHTIEKAKK 648
E A CNLGSINL D LA + AVR LDNVID+N + + +A++
Sbjct: 363 SLEQPLGEDASCNLGSINLAKFVKYG----DGLAELVAVAVRALDNVIDLNPYPVPEAER 418
Query: 649 SNHTHRAIGLGLMGFQSALHLLHIPYASPEAVEIADESMEFISFHAISASVELAQERGAY 708
+N RAIGLG+MG L L IPY S EA++ D E+I+++A+ AS ELA+ERG Y
Sbjct: 419 ANAESRAIGLGVMGLADLLAQLGIPYGSEEALKFNDRLFEYIAYYALKASAELAKERGPY 478
Query: 709 SSFKGSLWDQGVFPIDSIGLLAEVRDELAMNRTSRLPWDELKKRVKTIGMRNSNCMAIAP 768
F+GS W +G+ PID L D W++L++ +K G+RNS AIAP
Sbjct: 479 PYFEGSRWARGILPIDYPRLFGITED-----------WEKLREDIKKHGLRNSYLTAIAP 527
Query: 769 TATIANICGVSQSIDPSYQNLYVKSNMSGDFTVVNSFLVNELKQRDLWDEAMISDLKYHD 828
T +I+ I G + I+P + +Y + G F V L +L
Sbjct: 528 TGSISYIAGTTSGIEPIFALVYFRETKGGRFYYVVPPLFEDLLAYYGL------------ 575
Query: 829 GSIGNIERIPDDLKKIHATAFEIDPMWLIESASRRQKWIDQAQSLNLYLD-EPSGKKLDF 887
A+EIDP+W I+ + Q+WIDQ S L L + K L+
Sbjct: 576 -------------------AYEIDPLWHIDMQAAAQRWIDQGISKTLNLPNTATTKDLNK 616
Query: 888 IYRQAWLMGLKTTYYLRSRSATSVEKSTLKGV 919
Y AW +GLKTTYY R+ A V L
Sbjct: 617 AYLYAWKLGLKTTYYRRTSQAAQVLTVVLDCE 648
>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 = 320 bits (822), Expect = 1e-87
Identities = 149/459 (32%), Positives = 226/459 (49%), Gaps = 60/459 (13%)
Query: 339 AVEFYNLLSSFHFMCSTPTLFNSGT-RHPQLSSCFLTTVPDD-LYGIFGALQENAMLAKY 396
A EF+ LL S F+ ++PTL N+GT QLS+CF+ V DD + GIF AL+E A++ K
Sbjct: 1 ADEFFYLLLSQGFIPNSPTLMNAGTGELGQLSACFVLPVEDDSIEGIFDALKEAALIFKR 60
Query: 397 SGGLGNDWTPVRGLGAHIHGTNGKSQGVIPFLKVANDTAVAVNQGGKRKGAVCAYLETWH 456
GG+G +++ +R G + T G + G + F++V + + QGG R+GA L+ H
Sbjct: 61 GGGVGYNFSRLRPKGDIVKSTGGVASGPVSFMRVFDAATGVIKQGGTRRGANMGVLDVDH 120
Query: 457 IDVEEFLDLRKNTGDDRRRTHDMNTANW---IPDLFMKRVTQNAGWTLFSPDEVSDLHDL 513
D+EEF+D + +T + N + D FM+ V + W L +P E
Sbjct: 121 PDIEEFIDAK----MKEEKTVVLQNFNISVAVTDAFMEAVENDEPWELRNPREPDTG--- 173
Query: 514 YGKEFEIAYENYERQADRGEIKVFRKISAVALWRKMLTMLFETGHPWITFKDPCNIRSPQ 573
KV+R + A LW K++ +++ P + F D N +P
Sbjct: 174 ---------------------KVYRTVPARELWDKIVEAAWDSADPGVLFIDTINRWNPL 212
Query: 574 QHVGVVHSSNLCTEITLNSSSEETAVCNLGSINLLAHFANNQ-----FDYDKLASTIRTA 628
+G ++++N C E L CNLGSINL + F N FD+++L +R A
Sbjct: 213 PGLGRINATNPCGEQPLLPYE----SCNLGSINL-SKFVKNPFGGASFDFERLREAVRLA 267
Query: 629 VRVLDNVIDINCHTIEKAKKSNHTHRAIGLGLMGFQSALHLLHIPYASPEAVEIADESME 688
VR LDNVID+N + + + + R IGLG+MG L L IPY S EA E+A+ M
Sbjct: 268 VRFLDNVIDVNRYPLPEIAEETKATRRIGLGVMGLADMLIKLGIPYDSEEARELAERIMS 327
Query: 689 FISFHAISASVELAQERGAYSSFKGSLWDQGVFPIDSIGLLAEVRDELAMNRTSRLPWDE 748
FI A AS ELA+ERG + F S + ++ D+
Sbjct: 328 FIRDAAYRASAELAKERGPFPLFDASRYLMLKVI-----------------VNAKELPDD 370
Query: 749 LKKRVKTIGMRNSNCMAIAPTATIANICGVSQSIDPSYQ 787
+ + ++ G+RN++ IAPT TI+ I G S I+P +
Sbjct: 371 VLEEIEKYGIRNAHLTTIAPTGTISLIAGTSSGIEPIFS 409
Score = 28.4 bits (64), Expect = 9.5
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 852 DPMWLIESASRRQKWIDQAQS--LNLYLDEPSGKKL-DF--IYRQAWLMGLK--TTY 901
P + + Q W+D A S +NL P+ + D +Y AW +GLK T Y
Sbjct: 409 SPEDHVRMQAALQPWVDGAISKTINL----PNDATVEDVEAVYLLAWKLGLKGITVY 461
>gnl|CDD|144053 pfam00317, Ribonuc_red_lgN, Ribonucleotide reductase, all-alpha
domain.
Length = 79
Score = 94.6 bits (236), Expect = 1e-19
Identities = 35/77 (45%), Positives = 47/77 (61%), Gaps = 3/77 (3%)
Query: 293 FEYLGLQILYDRYFLHI-NGSRIEMPQAFFMRVAMGLALKETEKE--KRAVEFYNLLSSF 349
YL ++L DRY L +G +E PQ FMRVA+ LA E ++ + A EFY+LLSS
Sbjct: 3 LTYLAAKVLEDRYLLKDEDGEILETPQDMFMRVALALAGAELPEDRLELAEEFYDLLSSL 62
Query: 350 HFMCSTPTLFNSGTRHP 366
F+ +TPTL N+GT
Sbjct: 63 KFLPATPTLMNAGTPLG 79
>gnl|CDD|146230 pfam03477, ATP-cone, ATP cone domain.
Length = 89
Score = 74.2 bits (183), Expect = 2e-13
Identities = 31/98 (31%), Positives = 44/98 (44%), Gaps = 10/98 (10%)
Query: 30 QVIKRNGGVTSFDPSKISRAIMKAFMAVEGKGASRSIRVQDIIKNLTEQTVTRLLQHNKS 89
+VIKR+G FD KI RAI KA E D + + E+ L
Sbjct: 2 KVIKRDGRREPFDREKIRRAIEKACEKRE--------VDPDDAEEIAEEVEKELEDGGDR 53
Query: 90 ALIVHIEDIQDQVECSLMQSGHHKITREYVLYREERSD 127
+ E+IQD VE +L + + + R Y+LYR R +
Sbjct: 54 --EISTEEIQDLVEKTLAEHPDYAVARAYILYRNLRKE 89
Score = 31.5 bits (72), Expect = 1.3
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 151 DGTLISFNSKRLEMIVEEACSGLQ--DVSSKIVLSETYKNMYDGLSESDLETALIFSSRT 208
DG F+ +++ +E+AC + ++ + E K + DG + ++ T I +
Sbjct: 7 DGRREPFDREKIRRAIEKACEKREVDPDDAEEIAEEVEKELEDGG-DREISTEEI---QD 62
Query: 209 LIEK----EPNYAKVTARFLLEKLRRE 231
L+EK P+YA A L LR+E
Sbjct: 63 LVEKTLAEHPDYAVARAYILYRNLRKE 89
>gnl|CDD|31519 COG1328, NrdD, Oxygen-sensitive ribonucleoside-triphosphate
reductase [Nucleotide transport and metabolism].
Length = 700
Score = 61.8 bits (150), Expect = 8e-10
Identities = 31/104 (29%), Positives = 42/104 (40%), Gaps = 10/104 (9%)
Query: 30 QVIKRNGGVTSFDPSKISRAIMKAFMAVEGKGASRSIRVQDIIKNLTEQTVTRLLQHNKS 89
VIKR+G V FD +KI A+ KA +E + + +
Sbjct: 4 VVIKRDGRVAEFDRNKIINAVRKAAKEIE-------SFDIAKALIRATGVDEEVARIARE 56
Query: 90 ALIVHIEDIQDQVECSLMQSGHHKITREYVLYREERSDVRAAQS 133
V IE+IQ VE LM + + R Y+ YR ER VR
Sbjct: 57 ---VEIEEIQLLVEYLLMPMINKILARAYIEYRFERDRVRETLG 97
>gnl|CDD|153083 cd00576, RNR_PFL, Ribonucleotide reductase and Pyruvate formate
lyase. Ribonucleotide reductase (RNR) and pyruvate
formate lyase (PFL) are believed to have diverged from a
common ancestor. They have a structurally similar
ten-stranded alpha-beta barrel domain that hosts the
active site, and are radical enzymes. RNRs are found in
all organisms and provide the only mechanism by which
nucleotides are converted to deoxynucleotides. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs use a diiron-tyrosyl
radical while Class II RNRs use coenzyme B12
(adenosylcobalamin, AdoCbl). Class III RNRs use an FeS
cluster and S-adenosylmethionine to generate a glycyl
radical. PFL, an essential enzyme in anaerobic bacteria,
catalyzes the conversion of pyruvate and CoA to
acteylCoA and formate in a mechanism that uses a glycyl
radical.
Length = 401
Score = 54.5 bits (131), Expect = 1e-07
Identities = 71/387 (18%), Positives = 107/387 (27%), Gaps = 108/387 (27%)
Query: 341 EFYNLLSSFHFMCSTPTLFNSGTRHPQLSSCFLTTVPDDLYG---------------IFG 385
Y + S + G + C L D L I
Sbjct: 3 RIYEAVKSG--------VITVGRPDLPFTGCVLVDYGDSLDPGIKGVNETAKSINEAIQK 54
Query: 386 ALQENAMLAKYSGGLGNDWTPVRGLGAHI-----HGTNGKSQGVIPFLKVANDTAVAVNQ 440
Q A+ A G G + + + +G + N V Q
Sbjct: 55 TYQIIALAASNQNGGGVSFARASSILSPYGSRDYAKGSGTETDAVEAADAFNLALKEVGQ 114
Query: 441 GGKRKGAVCAYLETWHI-----DVEEFLDLRKNTGDDRRRTHDMNTANWIPDLFMKRVTQ 495
G R GA ++ H +EFL+L G + P+L + RV
Sbjct: 115 GNGRTGAATGFIGGVHKGKGDKISQEFLNLALANGGEGIPL-------NFPNLSV-RV-- 164
Query: 496 NAGWTLFSPDEVSDLHDLYGKEFEIAYENYERQADRGEIKVFRKISAVALWRKMLTMLFE 555
K + AV L + + +
Sbjct: 165 ------------------------------------SSDKPGILVKAVELKQLIAEEARK 188
Query: 556 TGHPWITFKDPCNIRSPQQHVGVVHSSNLCTEITLNSSSEETAVCNLGSINLLAHFANNQ 615
TG P I + CN V + NL I A +
Sbjct: 189 TGSPGIFNDELCN------LVSL----------------------NLARIMEKAINGSMD 220
Query: 616 FDYDKLASTIRTAVRVLDNVIDINCHTIEKAKKSNHTHRAIGLGLMGFQSAL-HLLHIPY 674
++L AVR LD VID + I + R +GLG+ G L L
Sbjct: 221 VVLEELEELAFLAVRALDCVIDSHDERIPTIELGGDERRTVGLGIAGVADLLIKLGLEKV 280
Query: 675 ASPEAVEIADESMEFISFHAISASVEL 701
PEA ++A E ++ + H + A+ E
Sbjct: 281 GDPEADDLAAELVDQLKKHLVKATNER 307
>gnl|CDD|33774 COG4015, COG4015, Predicted dinucleotide-utilizing enzyme of the
ThiF/HesA family [General function prediction only].
Length = 217
Score = 31.9 bits (72), Expect = 0.90
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 635 VIDINCHTIEKAKKSNHTHRAIGLGLMGFQSALHLLHIPYASPEAVEIAD 684
I +N +E+ KK IG G +G + AL LL + PE + + D
Sbjct: 3 GIFMNIEELERKKKPRGEVSLIGCGRLGVRVALDLLEVHRGGPERIYVFD 52
>gnl|CDD|144567 pfam01026, TatD_DNase, TatD related DNase. This family of proteins
are related to a large superfamily of metalloenzymes.
TatD, a member of this family has been shown
experimentally to be a DNase enzyme.
Length = 255
Score = 31.5 bits (72), Expect = 1.2
Identities = 23/107 (21%), Positives = 38/107 (35%), Gaps = 35/107 (32%)
Query: 640 CHTIEKAKKSNHTHRAIGLGLMG-----------------FQSALHL---------LHIP 673
+EK K + H + + +G +G F+ L L +H
Sbjct: 74 LEALEKLKLAEHP-KVVAIGEIGLDYYYVDESPKEAQEEVFRRQLELAKELDLPVVIHTR 132
Query: 674 YASPEAVEIADESME----FISFHAISASVELAQE---RGAYSSFKG 713
A + +EI E+ + H + S+E A+E G Y S G
Sbjct: 133 DAEEDLLEILKEAGAPGLRVV-LHCFTGSLETAKEILDLGFYISISG 178
>gnl|CDD|34255 COG4636, Uma2, Uncharacterized protein conserved in cyanobacteria
[Function unknown].
Length = 200
Score = 29.9 bits (66), Expect = 3.3
Identities = 24/106 (22%), Positives = 36/106 (33%), Gaps = 15/106 (14%)
Query: 789 LYVKSNMSGDFTVVNSFLVNELK-----QRDLWDEAMISDLK--------YHDGSIGNIE 835
L + G+ +N+FL N+L + L + D D S+ E
Sbjct: 37 LLIMPPPGGEHERINTFLGNDLGLYLEPLQGLGEAFGSPDCFVVPGSAYREPDVSVVCDE 96
Query: 836 RIPDDLKKIHATAFEIDPMWLIESASRRQKWIDQAQSLNLYLDEPS 881
R+ F+I P +IE S D + L LY P
Sbjct: 97 RLSYL--PQIDEEFDIAPDLVIEVLSPSDSDRDLQKKLRLYATIPG 140
>gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 29.3 bits (65), Expect = 5.3
Identities = 17/107 (15%), Positives = 34/107 (31%), Gaps = 6/107 (5%)
Query: 94 HIEDIQDQVECSLMQSGHHKITREYVLYREERSDVRAAQSHSKSDAPIAPKLKIMMDDGT 153
E I++ E L + E++ R A + LK M+
Sbjct: 469 LDERIEEITEDILEKIKKKTKNLEFLAMLAVRLIRAAKDIYDHFKKEEVFDLKAMV---- 524
Query: 154 LISFNSKRLEMIVEEACSGLQDVSSKIVLSETYKNMYDGLSESDLET 200
+S+++ + + EA + E Y+ E+D +
Sbjct: 525 --VASSRKVAVELYEAEIAARLDWHSKESLEGAIKDYNTEFETDFDK 569
>gnl|CDD|37691 KOG2480, KOG2480, KOG2480, 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA)
reductase [Lipid transport and metabolism].
Length = 602
Score = 28.8 bits (64), Expect = 7.2
Identities = 17/56 (30%), Positives = 22/56 (39%)
Query: 337 KRAVEFYNLLSSFHFMCSTPTLFNSGTRHPQLSSCFLTTVPDDLYGIFGALQENAM 392
+RA E L S FNS +R +L S T +LY F +AM
Sbjct: 311 RRAAEAKIWLESPENQEVLKKAFNSTSRFARLQSIHTTIAGRNLYIRFCTSTGDAM 366
>gnl|CDD|30371 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 28.6 bits (64), Expect = 8.3
Identities = 36/179 (20%), Positives = 63/179 (35%), Gaps = 26/179 (14%)
Query: 617 DYDKLASTIRTAVRVLDNVIDINCHTI-----EKAKKSNHTHRAIGLGLMGFQSALHLLH 671
D + + I A D I TI + ++ H A LG +A L
Sbjct: 222 DLEAIDKAIEEAKASTDKPTLIIVKTIIGKGSPNKEGTHKVHGAP-LGEEEVAAAKKALG 280
Query: 672 IPYASPEAVEIADESMEFISFHAISASVELAQERG--AYSSFKGSL--WDQGVFPIDSIG 727
PE E+ +E +ERG A +++ + + +P +
Sbjct: 281 WE---PEPFEVPEEVYAA---------FRAVEERGAKAEAAWNELFAAYKKK-YPELAAE 327
Query: 728 LLAEVRDELAMNRTSRLPWDELKKRVKTIGMRNSNCMAI-APTATIANICGVSQSIDPS 785
+ EL N + LP + + K+I R ++ A+ A + + G S + PS
Sbjct: 328 FERRLNGELPANWAAFLP--KFEANGKSIATRKASGKALNALAKKLPELIGGSADLAPS 384
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.133 0.393
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 11,419,301
Number of extensions: 608971
Number of successful extensions: 1299
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1264
Number of HSP's successfully gapped: 28
Length of query: 954
Length of database: 6,263,737
Length adjustment: 103
Effective length of query: 851
Effective length of database: 4,038,010
Effective search space: 3436346510
Effective search space used: 3436346510
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: 62 (27.6 bits)