Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012592503.1 MSIL_RS18005 methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_000021745.1:WP_012592503.1 Length = 1245 Score = 1483 bits (3838), Expect = 0.0 Identities = 763/1221 (62%), Positives = 922/1221 (75%), Gaps = 15/1221 (1%) Query: 14 ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73 +RILVLDG MGTMIQ ++ E FRGERFADWP DL+GNNDLL L++P+ I IH AY + Sbjct: 20 KRILVLDGAMGTMIQQHKFTEEQFRGERFADWPSDLRGNNDLLSLTQPKAIEQIHRAYID 79 Query: 74 AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133 AGADII TNTFNST+I+ ADY M+ L E+N +A+L R AD + K R+VAG L Sbjct: 80 AGADIIATNTFNSTSISQADYGMQELVFELNRESARLCRVAADA-AEKHDGKRRFVAGAL 138 Query: 134 GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193 GPT+RTASISPDVN+P FR ++FD L AY E+ +AL+EGGADL++IET+FDTLNAKAA+ Sbjct: 139 GPTSRTASISPDVNNPGFRAVSFDELRDAYDEAARALIEGGADLLIIETIFDTLNAKAAL 198 Query: 194 FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253 V+ F LGVE P+MISGTITD SGRTLSGQT AF++SLRHA+ LT GLNCALG E Sbjct: 199 AGVRDAFAKLGVEAPVMISGTITDLSGRTLSGQTPTAFWHSLRHADPLTIGLNCALGARE 258 Query: 254 LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313 +R ++ ELSRIA+ V A+PNAGLPN FG YD + MA + E+A +G +N+VGGCCGT Sbjct: 259 MRAHLAELSRIADTLVCAYPNAGLPNEFGLYDESPEYMASLVGEFADSGLVNVVGGCCGT 318 Query: 314 TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373 TP HI A+++ +EG+APR++PEI RLSGLEP + + FVNVGERTNVTGSAKF++ Sbjct: 319 TPAHIHAIAKRIEGVAPREIPEIAPLLRLSGLEPFVLAPEIPFVNVGERTNVTGSAKFRK 378 Query: 374 LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433 LIK+ ++ ALDVAR QV GAQIID+NMDEG+LD+E AMV FLNLIA EPDIARVP+MI Sbjct: 379 LIKQGDFAAALDVARDQVAAGAQIIDVNMDEGLLDSEKAMVEFLNLIAAEPDIARVPVMI 438 Query: 434 DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493 DSSK+ VIE GLKC+QGK +VNSISMKEGV+ FI A+ +R YGAAVVVMAFDE+GQADT Sbjct: 439 DSSKFSVIEAGLKCVQGKSVVNSISMKEGVEKFIADARTVRAYGAAVVVMAFDEKGQADT 498 Query: 494 RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553 RK+EIC +AY+ILT+E GFPPEDIIFDPNIFA+ATGIEEHNNY DFI A +I++ Sbjct: 499 FERKVEICAKAYQILTQEAGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATREIRKRF 558 Query: 554 PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613 P ISGGVSN+SFSFRGN+PVREA+HAVFLY+AI+ GMDMGIVNAGQLA+Y ++ LR Sbjct: 559 PLVHISGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYAEIEPGLR 618 Query: 614 DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673 +A EDV+LNRR D TERLL +AE +RG + + WR V KRLE++LV GITE Sbjct: 619 EACEDVVLNRRPDATERLLAIAEGFRGHGVEKA--ERDLVWREQPVIKRLEHALVNGITE 676 Query: 674 FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733 F+E D EEAR + RP++VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMKQAVAYL Sbjct: 677 FVELDVEEARAASKRPLDVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAYLL 736 Query: 734 PFIEASKEQG-----KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEK 788 P+++ K + T GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGVMVPA K Sbjct: 737 PYMDEEKRKNGGSERSTAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAK 796 Query: 789 ILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQ 848 IL A+ D IGLSGLITPSLDEM VA EMER+GF +PLLIGGATTS+ HTAVKI Sbjct: 797 ILSVARAEKVDAIGLSGLITPSLDEMCYVAAEMEREGFDLPLLIGGATTSRVHTAVKIHP 856 Query: 849 NYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVART-RKEYETVRIQHGRKKPRTPPVTL 906 NY+ G TVYV +ASR VGVV +LL ++ RD A T R EYE V H R + + + Sbjct: 857 NYTRGQTVYVNDASRAVGVVQSLLGESARD--AAETFRAEYEKVAAAHRRGEAEKLRLPI 914 Query: 907 EAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPRILE 965 AR N DW Y PP G + + + L YIDWTPFF TW L G+YP IL+ Sbjct: 915 GKARANALKIDWDDYAPPRPTFTGSRVFRSYDVAELIPYIDWTPFFQTWELRGRYPAILD 974 Query: 966 DEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINV 1025 D G A+ LF DA ML ++ E L+P+ V+G +PAN VGDDI +Y E+R+ + Sbjct: 975 DPKQGEAARSLFDDAQAMLKRMVEEHWLDPKAVIGFWPANSVGDDIALYTGESRSEKLAA 1034 Query: 1026 SHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYN 1084 H LRQQ T + G N L+DF+AP GK DYIGAF VT G +E +AD F +DDY Sbjct: 1035 FHTLRQQLTRRDGKPNIALSDFIAP-AGGKPDYIGAFVVTAGAQEGKIADRFAKANDDYG 1093 Query: 1085 KIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPE 1144 I+VKALADR+AEA AE +HERVR+ +W YAP+E +S ++ +RE Y+GIRPAPGYPA P+ Sbjct: 1094 SILVKALADRIAEALAERMHERVRREFWAYAPDEAISEDDRLREEYRGIRPAPGYPAQPD 1153 Query: 1145 HTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYA 1204 HTEKAT++ELL EK G+ LTESFAMWPGASVSG YF+HP + Y+ VA+I+RDQVEDYA Sbjct: 1154 HTEKATLFELLAAEKRIGVSLTESFAMWPGASVSGLYFAHPQAHYFGVAKIERDQVEDYA 1213 Query: 1205 RRKGMSVTEVERWLAPNLGYD 1225 RKGMSV E+ERWLAP L YD Sbjct: 1214 LRKGMSVAEMERWLAPILNYD 1234 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: 3661 Number of extensions: 133 Number of successful extensions: 8 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: 1245 Length adjustment: 48 Effective length of query: 1179 Effective length of database: 1197 Effective search space: 1411263 Effective search space used: 1411263 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_012592503.1 MSIL_RS18005 (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.3061049.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 1727.5 0.0 0 1727.3 0.0 1.0 1 NCBI__GCF_000021745.1:WP_012592503.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021745.1:WP_012592503.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1727.3 0.0 0 0 2 1182 .] 19 1201 .. 18 1201 .. 0.98 Alignments for each domain: == domain 1 score: 1727.3 bits; conditional E-value: 0 TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetnt 71 +krilvlDGamGt++q+++ te++Frge +ad++++l+GnndlL+lt+P +i++ihray +aGaDi+ tnt NCBI__GCF_000021745.1:WP_012592503.1 19 RKRILVLDGAMGTMIQQHKFTEEQFRGErFADWPSDLRGNNDLLSLTQPKAIEQIHRAYIDAGADIIATNT 89 79********************************************************************* PP TIGR02082 72 FnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvt 142 Fnst+i++adY++++++ eln+++a+l r +ad +++ k+RfvaG+lGPt+++a++spdv++p+fr v NCBI__GCF_000021745.1:WP_012592503.1 90 FNSTSISQADYGMQELVFELNRESARLCRVAADAAEKHDGKRRFVAGALGPTSRTASISPDVNNPGFRAVS 160 ************************************999******************************** PP TIGR02082 143 ydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGq 213 +del+daY e++++l++GG+Dll+iet+fDtlnakaal +v+++f++ g+e P++isg+i+d sGrtLsGq NCBI__GCF_000021745.1:WP_012592503.1 161 FDELRDAYDEAARALIEGGADLLIIETIFDTLNAKAALAGVRDAFAKLGVEAPVMISGTITDLSGRTLSGQ 231 *********************************************************************** PP TIGR02082 214 tleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalke 284 t af +sl+ha+ l++GLnCalGa e+r ++ els++a++lv ++PnaGLPn++g Yd+ pe +a+ + e NCBI__GCF_000021745.1:WP_012592503.1 232 TPTAFWHSLRHADPLTIGLNCALGAREMRAHLAELSRIADTLVCAYPNAGLPNEFGLYDESPEYMASLVGE 302 *********************************************************************** PP TIGR02082 285 faeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGs 355 fa gl+n+vGGCCGttP+hi+aia+ +++++pr+ +e+ + ++lsgle++ +a+e fvn+GeRtnv+Gs NCBI__GCF_000021745.1:WP_012592503.1 303 FADSGLVNVVGGCCGTTPAHIHAIAKRIEGVAPREIPEIAPLLRLSGLEPFVLAPEIPFVNVGERTNVTGS 373 *********************************************************************** PP TIGR02082 356 kkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefe 426 +kfrklik++d+ +al++a++qv Gaqi+D+n+De+llD+e++m+++l+l+a+epdia+vP+m+Dss+f NCBI__GCF_000021745.1:WP_012592503.1 374 AKFRKLIKQGDFAAALDVARDQVAAGAQIIDVNMDEGLLDSEKAMVEFLNLIAAEPDIARVPVMIDSSKFS 444 *********************************************************************** PP TIGR02082 427 vleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykllte 497 v+eaGLk++qGk++vnsis+k+G+e+F+ a+ ++ yGaavvvmafDe+Gqa+t ++k+ei+ +ay++lt+ NCBI__GCF_000021745.1:WP_012592503.1 445 VIEAGLKCVQGKSVVNSISMKEGVEKFIADARTVRAYGAAVVVMAFDEKGQADTFERKVEICAKAYQILTQ 515 *********************************************************************** PP TIGR02082 498 kvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhs 568 ++gfppediifDpni++iatGieeh++y++dfiea+rei++++P ++isgGvsn+sFs+rgn++vRea+h+ NCBI__GCF_000021745.1:WP_012592503.1 516 EAGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATREIRKRFPLVHISGGVSNLSFSFRGNEPVREAMHA 586 *********************************************************************** PP TIGR02082 569 vFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqea 639 vFLy+ai+aG+Dmgivnag+lavy++i++ lre++ed++l+rr++ate+Ll +ae ++g + k ++ NCBI__GCF_000021745.1:WP_012592503.1 587 VFLYHAIQAGMDMGIVNAGQLAVYAEIEPGLREACEDVVLNRRPDATERLLAIAEGFRGHGVE--KAERDL 655 *************************************************************99..888999 PP TIGR02082 640 ewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksar 710 wr++pv +RLe+alv+G++e++e d+eear k+pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksar NCBI__GCF_000021745.1:WP_012592503.1 656 VWREQPVIKRLEHALVNGITEFVELDVEEARAASKRPLDVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSAR 726 *********************************************************************** PP TIGR02082 711 vmkkavayLePylekekeed.....kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPveki 776 vmk+avayL Py+++ek ++ +++Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP++ki NCBI__GCF_000021745.1:WP_012592503.1 727 VMKQAVAYLLPYMDEEKRKNggserSTAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAKI 797 *****************999999999********************************************* PP TIGR02082 777 leaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkd 846 l +a+ +k D iglsGLi++sldem +va emer+g+++Pll+GGa++s+ h+avki+++Y g++vyv+d NCBI__GCF_000021745.1:WP_012592503.1 798 LSVARAEKVDAIGLSGLITPSLDEMCYVAAEMEREGFDLPLLIGGATTSRVHTAVKIHPNYTrGQTVYVND 868 *************************************************************548******* PP TIGR02082 847 aseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkfl 917 as+av vv++ll e ++++ +e ++eye++ +++ + ++ l++ +ar + +++d+ d+ +p p+f NCBI__GCF_000021745.1:WP_012592503.1 869 ASRAVGVVQSLLGESARDA-AETFRAEYEKVAAAHRRGEAEKLRLPIGKARANALKIDWD-DYAPPRPTFT 937 ***************8665.59*************************************9.********** PP TIGR02082 918 Gtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvv 987 G++v++++ ++el++yiDw+++F +Welrg+yp il+d+++g+ ar lf+da+++l+++++e+ l +++v+ NCBI__GCF_000021745.1:WP_012592503.1 938 GSRVFRSYdVAELIPYIDWTPFFQTWELRGRYPAILDDPKQGEAARSLFDDAQAMLKRMVEEHWLDPKAVI 1008 *********************************************************************** PP TIGR02082 988 GlfPaqsvgddieiytdetvsqetkpiatvrekleq.lrqqsdrylclaDfiaskesGikDylgallvtag 1057 G++Pa+svgddi++yt+e++s +++a++++ ++q +r++ + +++l+Dfia+ + G+ Dy+ga++vtag NCBI__GCF_000021745.1:WP_012592503.1 1009 GFWPANSVGDDIALYTGESRS---EKLAAFHTLRQQlTRRDGKPNIALSDFIAP-AGGKPDYIGAFVVTAG 1075 ****************99995...45555555445505555555**********.88************** PP TIGR02082 1058 lgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpaf 1128 ++ ++a+++ + +ddy+silvkaladr+aealae +hervR+e+w+ya +e+ + +d l+e+YrGirpa+ NCBI__GCF_000021745.1:WP_012592503.1 1076 AQEGKIADRFAKANDDYGSILVKALADRIAEALAERMHERVRREFWAYAPDEAISEDDRLREEYRGIRPAP 1146 *********************************************************************** PP TIGR02082 1129 GYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182 GYpa+Pdhtekatl+eLl ae+ iG+ ltes+a++P asvsglyfahp+a+Yf v NCBI__GCF_000021745.1:WP_012592503.1 1147 GYPAQPDHTEKATLFELLAAEKrIGVSLTESFAMWPGASVSGLYFAHPQAHYFGV 1201 *********************99******************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1245 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 30.60 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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