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)