Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_010960817.1 MCA_RS07615 methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_000008325.1:WP_010960817.1 Length = 1237 Score = 1687 bits (4368), Expect = 0.0 Identities = 842/1224 (68%), Positives = 1002/1224 (81%), Gaps = 4/1224 (0%) Query: 8 LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67 L+ L ERIL LDG MGTMIQ Y+L EAD+RG+RFADWP DLKGNNDLL L++P+VI AI Sbjct: 14 LKRLLKERILFLDGAMGTMIQRYKLAEADYRGQRFADWPRDLKGNNDLLSLTRPDVIEAI 73 Query: 68 HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127 H AY EAGADI+ETN+FN+T I+MADY ME L EIN A+A+LAR AD + +TP++PR Sbjct: 74 HWAYLEAGADIVETNSFNATRISMADYGMEPLVYEINVASARLARQVADRMSRQTPDRPR 133 Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187 +VAGVLGPT+RTASISP VNDP FRNI FD LVA+Y E+ + LV+GGAD+ILIET+FDTL Sbjct: 134 FVAGVLGPTSRTASISPSVNDPGFRNIGFDELVASYDEAVRGLVDGGADIILIETIFDTL 193 Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247 NAKAAVFAV+ FE G LP+MISGTITDASGRTLSGQTTEAF+NSLRHA ++ GLNC Sbjct: 194 NAKAAVFAVERFFEQEGYTLPVMISGTITDASGRTLSGQTTEAFWNSLRHARPISIGLNC 253 Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307 ALG +LRQ+V+ELSRIA+ YV+AHPNAGLPN FGEYD + MA++I +WA+ GFLNI+ Sbjct: 254 ALGAKQLRQHVEELSRIADTYVSAHPNAGLPNEFGEYDESPEAMAREIADWAEQGFLNII 313 Query: 308 GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTG 367 GGCCGTTP HI A+ AV+ PR++PEIP ACRL+GLEP NI SLFVNVGERTNVTG Sbjct: 314 GGCCGTTPAHIEAIHDAVQHFPPRRIPEIPPACRLAGLEPCNITAGSLFVNVGERTNVTG 373 Query: 368 SAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIA 427 SA F+R+I+E KY EAL+VARQQVE+GAQIID+NMDEGMLD+ AAMV+FLNLIA EPDIA Sbjct: 374 SAAFRRMIREAKYDEALEVARQQVESGAQIIDVNMDEGMLDSRAAMVQFLNLIAAEPDIA 433 Query: 428 RVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDE 487 RVP+MIDSSKW+++E GLKC+QGKGIVNSIS+KEG AF+HHA+L+RRYGAAV+VMAFDE Sbjct: 434 RVPVMIDSSKWEILEAGLKCLQGKGIVNSISLKEGEAAFLHHARLVRRYGAAVIVMAFDE 493 Query: 488 QGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACE 547 QGQADTR RK+EIC RAY++LTE+ GFP EDIIFDPNIFAVATGIEEH+ Y DFI A Sbjct: 494 QGQADTRERKVEICERAYRLLTEKAGFPAEDIIFDPNIFAVATGIEEHDRYGLDFIEAVA 553 Query: 548 DIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDD 607 +IK LPHAL+SGGVSNVSFSFRGND VREAIHAVFLY+AIR GMDMGIVNAGQLAIY++ Sbjct: 554 EIKSRLPHALVSGGVSNVSFSFRGNDAVREAIHAVFLYHAIRAGMDMGIVNAGQLAIYEE 613 Query: 608 LPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSL 667 +P ELRDAVEDVIL RR+D TERLL +A++YRG + + WRS V+KRLE++L Sbjct: 614 VPEELRDAVEDVILARREDATERLLAIADRYRGEEGAGSERKADMAWRSLPVDKRLEHAL 673 Query: 668 VKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQ 727 VKGI EFIE DTEEAR+Q RP+ VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMK+ Sbjct: 674 VKGIDEFIEVDTEEARRQFERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKK 733 Query: 728 AVAYLEPFIEASK--EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVP 785 AVAYL P+++A K + TNGK+++ATVKGDVHDIGKNIVGVVLQCN +E++DLGVMVP Sbjct: 734 AVAYLMPYMDAEKAGTEVGTNGKILMATVKGDVHDIGKNIVGVVLQCNGFEVIDLGVMVP 793 Query: 786 AEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVK 845 +KIL+TA+E N D+IGLSGLITPSLDEMV+VA+EMER GF IPL+IGGATTS+AHTAVK Sbjct: 794 CDKILQTAREENVDIIGLSGLITPSLDEMVHVAREMERLGFEIPLMIGGATTSRAHTAVK 853 Query: 846 IEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVT 905 IE NY GPTVYV +ASR+VGV +LLS +D+F AR RKEYE VR H ++ + ++ Sbjct: 854 IEPNYHGPTVYVTDASRSVGVAGSLLSADLKDEFTARLRKEYEEVRRHHAGRRIQGTLLS 913 Query: 906 LEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPRIL 964 L+ AR F DW Y PP H LG++ +A +E + YIDW+PFF TW LAG YPRIL Sbjct: 914 LQQARARAFHTDWAHYVPPAPHLLGLEVFDAYPLEEIAGYIDWSPFFHTWELAGSYPRIL 973 Query: 965 EDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVIN 1024 +DEVVG A+ L +DA ML L+ ++ L RGV+G FPAN GDD+ ++ DE+RT + Sbjct: 974 DDEVVGEHARTLLQDARAMLALLTEQRWLTARGVIGFFPANSEGDDVVLWTDESRTERLA 1033 Query: 1025 VSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDY 1083 V HHLRQQ +K G YCLADFVAP SG ADY+G FAVT G +A + F HDDY Sbjct: 1034 VLHHLRQQQDKPGGQPAYCLADFVAPVGSGVADYLGGFAVTVGHGIEAPLERFARVHDDY 1093 Query: 1084 NKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACP 1143 + IM+KALADRLAEAFAE +H+RVR+ +WGYAP E+L NE LI E Y+GIRPAPGYPACP Sbjct: 1094 SGIMLKALADRLAEAFAERMHQRVRREFWGYAPEESLDNEALIAEAYRGIRPAPGYPACP 1153 Query: 1144 EHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDY 1203 +HTEKAT++ LL+ E ++G+ LTESFAM+P +SVSGWYFSH +KY+ V +I RDQVEDY Sbjct: 1154 DHTEKATLFRLLDAEANSGISLTESFAMYPASSVSGWYFSHASAKYFNVGKIGRDQVEDY 1213 Query: 1204 ARRKGMSVTEVERWLAPNLGYDAD 1227 ARRKGM+V EVERWLA +LGYDAD Sbjct: 1214 ARRKGMTVREVERWLASSLGYDAD 1237 Lambda K H 0.318 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 3795 Number of extensions: 162 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 1227 Length of database: 1237 Length adjustment: 47 Effective length of query: 1180 Effective length of database: 1190 Effective search space: 1404200 Effective search space used: 1404200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 59 (27.3 bits)
Align candidate WP_010960817.1 MCA_RS07615 (methionine synthase)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR02082.hmm # target sequence database: /tmp/gapView.22209.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02082 [M=1182] Accession: TIGR02082 Description: metH: methionine synthase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1805.2 0.0 0 1805.0 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010960817.1 MCA_RS07615 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010960817.1 MCA_RS07615 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1805.0 0.0 0 0 1 1182 [] 18 1202 .. 18 1202 .. 0.99 Alignments for each domain: == domain 1 score: 1805.0 bits; conditional E-value: 0 TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66 l++ril lDGamGt++q+++L ead+rg+ +ad++r+lkGnndlL+lt+P+vi+aih ay+eaGaDi lcl|NCBI__GCF_000008325.1:WP_010960817.1 18 LKERILFLDGAMGTMIQRYKLAEADYRGQrFADWPRDLKGNNDLLSLTRPDVIEAIHWAYLEAGADI 84 579**************************************************************** PP TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132 vetn Fn+t i++adY++e ++ye+n ++a+lar+vad ++ +tp+++RfvaG+lGPt+++a++sp+ lcl|NCBI__GCF_000008325.1:WP_010960817.1 85 VETNSFNATRISMADYGMEPLVYEINVASARLARQVADRMSrQTPDRPRFVAGVLGPTSRTASISPS 151 *****************************************899*********************** PP TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199 v++p+frn+ +delv++Y e+v+gl+dGG+D++Liet+fDtlnakaa+fave+ fe++g lP++is lcl|NCBI__GCF_000008325.1:WP_010960817.1 152 VNDPGFRNIGFDELVASYDEAVRGLVDGGADIILIETIFDTLNAKAAVFAVERFFEQEGYTLPVMIS 218 ******************************************************************* PP TIGR02082 200 gvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266 g+i+d+sGrtLsGqt+eaf +sl+ha +++GLnCalGa++lr++v+els++a+++vs++PnaGLPn lcl|NCBI__GCF_000008325.1:WP_010960817.1 219 GTITDASGRTLSGQTTEAFWNSLRHARPISIGLNCALGAKQLRQHVEELSRIADTYVSAHPNAGLPN 285 ******************************************************************* PP TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333 ++geYd+ pe +a++++++ae+g+lni+GGCCGttP+hi ai +av+ pr+ +e++++++l+gle lcl|NCBI__GCF_000008325.1:WP_010960817.1 286 EFGEYDESPEAMAREIADWAEQGFLNIIGGCCGTTPAHIEAIHDAVQHFPPRRIPEIPPACRLAGLE 352 ******************************************************************* PP TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400 + +i+ s fvn+GeRtnv+Gs+ fr++i++ +y+eal++a+qqve+Gaqi+D+n+De++lD++a+m lcl|NCBI__GCF_000008325.1:WP_010960817.1 353 PCNITAGSLFVNVGERTNVTGSAAFRRMIREAKYDEALEVARQQVESGAQIIDVNMDEGMLDSRAAM 419 ******************************************************************* PP TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467 +++l+l+a+epdia+vP+m+Dss++e+leaGLk++qGk+ivnsislk+Ge++Fl++a+l+++yGaav lcl|NCBI__GCF_000008325.1:WP_010960817.1 420 VQFLNLIAAEPDIARVPVMIDSSKWEILEAGLKCLQGKGIVNSISLKEGEAAFLHHARLVRRYGAAV 486 ******************************************************************* PP TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534 +vmafDe+Gqa+t+++k+ei++Ray+lltek+gfp+ediifDpni+++atGieehdry++dfiea+ lcl|NCBI__GCF_000008325.1:WP_010960817.1 487 IVMAFDEQGQADTRERKVEICERAYRLLTEKAGFPAEDIIFDPNIFAVATGIEEHDRYGLDFIEAVA 553 ******************************************************************* PP TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601 eik +lP+a +sgGvsnvsFs+rgndavRea+h+vFLy+ai+aG+Dmgivnag+la+y+++++elr+ lcl|NCBI__GCF_000008325.1:WP_010960817.1 554 EIKSRLPHALVSGGVSNVSFSFRGNDAVREAIHAVFLYHAIRAGMDMGIVNAGQLAIYEEVPEELRD 620 ******************************************************************* PP TIGR02082 602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668 +ved+il+rr++ate+Ll +a++y+g + + s+ ++ +wr+lpv++RLe+alvkG+ e+ie d+ee lcl|NCBI__GCF_000008325.1:WP_010960817.1 621 AVEDVILARREDATERLLAIADRYRGEEGAGSERKADMAWRSLPVDKRLEHALVKGIDEFIEVDTEE 687 ******************************9**9********************************* PP TIGR02082 669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed..ksk 733 ar++ ++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmkkavayL+Py+++ek+ + ++ lcl|NCBI__GCF_000008325.1:WP_010960817.1 688 ARRQFERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLMPYMDAEKAGTevGTN 754 ***********************************************************8775579* PP TIGR02082 734 GkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800 Gki++atvkGDvhDiGkniv+vvL+cng+ev+dlGv+vP++kil++a++++ D+iglsGLi++slde lcl|NCBI__GCF_000008325.1:WP_010960817.1 755 GKILMATVKGDVHDIGKNIVGVVLQCNGFEVIDLGVMVPCDKILQTAREENVDIIGLSGLITPSLDE 821 ******************************************************************* PP TIGR02082 801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeel 867 mv+va+emer g++iPl++GGa++s+ah+avki+++Y+g++vyv+das++v v+ +lls++ k+e++ lcl|NCBI__GCF_000008325.1:WP_010960817.1 822 MVHVAREMERLGFEIPLMIGGATTSRAHTAVKIEPNYHGPTVYVTDASRSVGVAGSLLSADLKDEFT 888 ******************************************************************* PP TIGR02082 868 ekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyi 933 +++++eyee+r+++ ++ + + ls+++ar f++d+ ++ +pap+ lG +v++a+ +ee+ yi lcl|NCBI__GCF_000008325.1:WP_010960817.1 889 ARLRKEYEEVRRHHAGRRIQGTLLSLQQARARAFHTDWA-HYVPPAPHLLGLEVFDAYpLEEIAGYI 954 ***************************************.9************************** PP TIGR02082 934 DwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddie 1000 Dw ++F +Wel+g+yp+il+de++g+ ar l +da+++l l++++ l+argv+G+fPa+s+gdd++ lcl|NCBI__GCF_000008325.1:WP_010960817.1 955 DWSPFFHTWELAGSYPRILDDEVVGEHARTLLQDARAMLALLTEQRWLTARGVIGFFPANSEGDDVV 1021 ******************************************************************* PP TIGR02082 1001 iytdetvsqetkpiatvrekleqlrqqsdr.....ylclaDfiaskesGikDylgallvtaglgaee 1062 ++tde++ t+ +a+++ +lrqq+d+ +claDf+a+ sG +Dylg ++vt+g g+e+ lcl|NCBI__GCF_000008325.1:WP_010960817.1 1022 LWTDESR---TERLAVLH----HLRQQQDKpggqpAYCLADFVAPVGSGVADYLGGFAVTVGHGIEA 1081 ****999...88888885....55555555555599******************************* PP TIGR02082 1063 lakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafG 1129 +++ +ddy+ i++kaladrlaea+ae +h+rvR+e+wgya ee+ld+e l+ e YrGirpa+G lcl|NCBI__GCF_000008325.1:WP_010960817.1 1082 PLERFARVHDDYSGIMLKALADRLAEAFAERMHQRVRREFWGYAPEESLDNEALIAEAYRGIRPAPG 1148 ******************************************************************* PP TIGR02082 1130 YpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182 YpacPdhtekatl++Ll+ae G+ ltes+a++P++svsg+yf+h +akYf+v lcl|NCBI__GCF_000008325.1:WP_010960817.1 1149 YPACPDHTEKATLFRLLDAEAnSGISLTESFAMYPASSVSGWYFSHASAKYFNV 1202 ********************99******************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1237 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10 # Mc/sec: 13.29 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory