Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_011767448.1 AZO_RS18695 methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_000061505.1:WP_011767448.1 Length = 1233 Score = 1503 bits (3892), Expect = 0.0 Identities = 773/1235 (62%), Positives = 938/1235 (75%), Gaps = 18/1235 (1%) Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61 + + E+LR QL +RIL+LDG MGTMIQ Y+L EAD+RG RF + P DLKGNNDLLVL++P Sbjct: 3 ADRSEELRQQLAQRILILDGAMGTMIQQYKLGEADYRGTRFLEHPKDLKGNNDLLVLTRP 62 Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121 +V+ IH AY +AGADIIET +FN+T ++ A+Y M ++ E+N A+A+L R DE+TAR Sbjct: 63 DVVGEIHRAYLDAGADIIETCSFNATRVSQAEYGMADIAYELNVASARLVRELCDEFTAR 122 Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181 P KPRY AGVLGPT+RT SISPDVNDP +RNI FD LV Y ES K L+EGGADL+LIE Sbjct: 123 NPAKPRYCAGVLGPTSRTLSISPDVNDPGYRNIEFDALVEDYYESAKGLMEGGADLLLIE 182 Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241 T+FDTLNAKAAVFAV+ F+ L LP+MISGTITDASGRTLSGQT EAF+NSL HA + Sbjct: 183 TIFDTLNAKAAVFAVEKLFDDLDRRLPVMISGTITDASGRTLSGQTAEAFWNSLAHARPI 242 Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADTMAKQIREWA 299 +FGLNCALG ELR YV ELS + + +V+AHPNAGLPN YD + +A+ + EWA Sbjct: 243 SFGLNCALGAKELRAYVDELSNVCDTFVSAHPNAGLPNPLAPTGYDETPEQLAEAVVEWA 302 Query: 300 QAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNV 359 Q+G +NI+GGCCGTTP HIAA+++AV + PR++P+I RLSGLEP N+G DSLFVNV Sbjct: 303 QSGLVNILGGCCGTTPAHIAAIAQAVAQVPPRRVPDIEKKLRLSGLEPFNVGADSLFVNV 362 Query: 360 GERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNL 419 GERTNVTGS F R+I E ++ +AL VARQQVENGAQ+IDINMDE MLD+ AAM RFL L Sbjct: 363 GERTNVTGSKAFARMILEGRFDDALAVARQQVENGAQVIDINMDEAMLDSVAAMERFLKL 422 Query: 420 IAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAA 479 IA EPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEG ++F+ A+L RRYGAA Sbjct: 423 IASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGEESFLRQARLARRYGAA 482 Query: 480 VVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYA 539 V+VMAFDE+GQADT ARKIEIC RAY++L +GFPPEDIIFDPNIFA+ATGIEEH+NYA Sbjct: 483 VIVMAFDEKGQADTYARKIEICARAYELLV-GIGFPPEDIIFDPNIFAIATGIEEHDNYA 541 Query: 540 QDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNA 599 DFI + IK LPHA SGGVSNVSFSFRGN+PVREAIH VFLY+AI+ G+ MGIVNA Sbjct: 542 VDFIQSVAWIKANLPHAKTSGGVSNVSFSFRGNEPVREAIHTVFLYHAIKAGLTMGIVNA 601 Query: 600 GQLAIYDDLPAELRDAVEDVILNRR----DDGTERLLELAEKYRGSKTDDTANAQQAEWR 655 G L +YDDL LR+ VEDV+LNR+ + E L+ELA+ + K DT WR Sbjct: 602 GMLGVYDDLDPVLREKVEDVVLNRKPASGQNPGEALVELAQTVKEGKAKDT--GPDLAWR 659 Query: 656 SWEVNKRLEYSLVKGITEFIEQDTEEAR----QQATRPIEVIEGPLMDGMNVVGDLFGEG 711 W V +RL+++LVKGITEF+ DTEE R + P+ VIEGPLM GM+VVGDLFG G Sbjct: 660 EWSVEERLKHALVKGITEFVVADTEEVRARLESEGKPPLAVIEGPLMAGMDVVGDLFGAG 719 Query: 712 KMFLPQVVKSARVMKQAVAYLEPFIEASKEQ--GKTNGKMVIATVKGDVHDIGKNIVGVV 769 KMFLPQVVKSARVMKQAVA+L P+IEA K + + G++VIATVKGDVHDIGKNIVGVV Sbjct: 720 KMFLPQVVKSARVMKQAVAHLIPYIEAEKARTGATSKGRIVIATVKGDVHDIGKNIVGVV 779 Query: 770 LQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIP 829 L CN YE++DLGVMVP +KIL A+E A IGLSGLITPSL+EM +VA EM+RQGF +P Sbjct: 780 LGCNGYEVIDLGVMVPTDKILNAAREHGAQAIGLSGLITPSLEEMSHVAAEMQRQGFDVP 839 Query: 830 LLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYET 889 LLIGGATTS+AHTA+KI +Y P VYV +ASR VGVV ALLS+ DF A+ +Y+ Sbjct: 840 LLIGGATTSRAHTAIKIAPHYQQPVVYVPDASRAVGVVTALLSEGGAGDFKAQLAADYDK 899 Query: 890 VRIQHGRKKPRTPPVTLEAARDNDF-AFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWT 948 +R QH KK V+LEAAR N + + Y P + LGV ++ ++ LR+YIDW Sbjct: 900 IRAQHANKK-GVQLVSLEAARANAYNPLSVEGYEPVEPNTLGVMALDVDLDELRDYIDWG 958 Query: 949 PFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG 1008 PFF TW LAG +P+IL+DEVVG A+ +F DA ML+ L A + + + V GLFPAN VG Sbjct: 959 PFFQTWDLAGSFPKILDDEVVGETARNVFNDAQAMLEDLIAGEWVQAKAVFGLFPANSVG 1018 Query: 1009 DDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGL 1067 DDI Y DE+R + H LRQQ E+ G ++CLADFVAPK SG D+ GAFAVT GL Sbjct: 1019 DDIAFYADESRDEPMMTWHGLRQQHERPAGKPHWCLADFVAPKASGVRDWCGAFAVTAGL 1078 Query: 1068 EEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIR 1127 + FEA HDDY IM+K+LADRLAEA AE+LHERVRK YWGYA +E L N LI+ Sbjct: 1079 GIEHKLAEFEAAHDDYRAIMLKSLADRLAEATAEWLHERVRKEYWGYAADEQLDNAALIK 1138 Query: 1128 ENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDS 1187 E Y+GIRPAPGYPACP+HT KA +++LL+ + GM LTES AM P ASVSG+YF+HP+S Sbjct: 1139 EQYKGIRPAPGYPACPDHTVKAALFQLLDAPTNAGMGLTESMAMTPAASVSGFYFAHPES 1198 Query: 1188 KYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222 Y+A+++I RDQV D+A+R G++ RWLAP L Sbjct: 1199 HYFAISKIGRDQVTDWAQRTGLTEEAAARWLAPLL 1233 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: 3703 Number of extensions: 145 Number of successful extensions: 10 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: 1233 Length adjustment: 47 Effective length of query: 1180 Effective length of database: 1186 Effective search space: 1399480 Effective search space used: 1399480 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_011767448.1 AZO_RS18695 (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.1372.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 1704.5 0.0 0 1704.3 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011767448.1 AZO_RS18695 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011767448.1 AZO_RS18695 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1704.3 0.0 0 0 2 1182 .] 14 1203 .. 13 1203 .. 0.98 Alignments for each domain: == domain 1 score: 1704.3 bits; conditional E-value: 0 TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67 +ril+lDGamGt++q+++L ead+rg + +++++lkGnndlL+lt+P+v+ +ihray++aGaDi+ lcl|NCBI__GCF_000061505.1:WP_011767448.1 14 AQRILILDGAMGTMIQQYKLGEADYRGTrFLEHPKDLKGNNDLLVLTRPDVVGEIHRAYLDAGADII 80 79**************************9************************************** PP TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdv 133 et Fn+t +++a+Y+++d ayeln ++a+l re +deft ++p k+R+ aG+lGPt+++ ++spdv lcl|NCBI__GCF_000061505.1:WP_011767448.1 81 ETCSFNATRVSQAEYGMADIAYELNVASARLVRELCDEFTaRNPAKPRYCAGVLGPTSRTLSISPDV 147 ******************************************************************* PP TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200 ++p++rn+++d lv+ Y e++kgl++GG+DllLiet+fDtlnakaa+fave++f++ r+lP++isg lcl|NCBI__GCF_000061505.1:WP_011767448.1 148 NDPGYRNIEFDALVEDYYESAKGLMEGGADLLLIETIFDTLNAKAAVFAVEKLFDDLDRRLPVMISG 214 ******************************************************************* PP TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267 +i+d+sGrtLsGqt eaf +sl ha +++GLnCalGa+elr +v els+ +++vs++PnaGLPn lcl|NCBI__GCF_000061505.1:WP_011767448.1 215 TITDASGRTLSGQTAEAFWNSLAHARPISFGLNCALGAKELRAYVDELSNVCDTFVSAHPNAGLPNP 281 ******************************************************************* PP TIGR02082 268 lg..eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgl 332 l+ Yd+tpe+la+a+ e+a+ gl+ni+GGCCGttP+hi+aia+av+++ pr+++++e+k++lsgl lcl|NCBI__GCF_000061505.1:WP_011767448.1 282 LAptGYDETPEQLAEAVVEWAQSGLVNILGGCCGTTPAHIAAIAQAVAQVPPRRVPDIEKKLRLSGL 348 *9999************************************************************** PP TIGR02082 333 ealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgead 399 e+++++ +s fvn+GeRtnv+Gsk f+++i ++ +++al +a+qqve+Gaq++Din+De++lD++a+ lcl|NCBI__GCF_000061505.1:WP_011767448.1 349 EPFNVGADSLFVNVGERTNVTGSKAFARMILEGRFDDALAVARQQVENGAQVIDINMDEAMLDSVAA 415 ******************************************************************* PP TIGR02082 400 mkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaa 466 m+++l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk+ivnsis+k+Gee Fl++a+l+++yGaa lcl|NCBI__GCF_000061505.1:WP_011767448.1 416 MERFLKLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGEESFLRQARLARRYGAA 482 ******************************************************************* PP TIGR02082 467 vvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieai 533 v+vmafDe+Gqa+t+++kiei+ Ray+ll+ +gfppediifDpni++iatGieehd+ya+dfi+++ lcl|NCBI__GCF_000061505.1:WP_011767448.1 483 VIVMAFDEKGQADTYARKIEICARAYELLVG-IGFPPEDIIFDPNIFAIATGIEEHDNYAVDFIQSV 548 *******************************.*********************************** PP TIGR02082 534 reikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelr 600 +ik +lP+ak+sgGvsnvsFs+rgn++vRea+h+vFLy+aikaGl mgivnag+l vydd+d+ lr lcl|NCBI__GCF_000061505.1:WP_011767448.1 549 AWIKANLPHAKTSGGVSNVSFSFRGNEPVREAIHTVFLYHAIKAGLTMGIVNAGMLGVYDDLDPVLR 615 ******************************************************************* PP TIGR02082 601 evvedlildrr....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregie 663 e+ved++l+r+ ++ e L+ela++ k+ k+k++ +wr+++veeRL++alvkG++e++ lcl|NCBI__GCF_000061505.1:WP_011767448.1 616 EKVEDVVLNRKpasgQNPGEALVELAQTVKEGKAKDT--GPDLAWREWSVEERLKHALVKGITEFVV 680 ***********777778889********999999954..47789*********************** PP TIGR02082 664 edleear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePyleke 726 +d+ee r + k+pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+Py+e+e lcl|NCBI__GCF_000061505.1:WP_011767448.1 681 ADTEEVRarleSEGKPPLAVIEGPLMAGMDVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPYIEAE 747 *****98666667789*************************************************** PP TIGR02082 727 keed..kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDvigls 791 k+ + +skG+iv+atvkGDvhDiGkniv+vvL+cngyev+dlGv+vP++kil+aa+++ a igls lcl|NCBI__GCF_000061505.1:WP_011767448.1 748 KARTgaTSKGRIVIATVKGDVHDIGKNIVGVVLGCNGYEVIDLGVMVPTDKILNAAREHGAQAIGLS 814 *9988899*********************************************************** PP TIGR02082 792 GLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkll 858 GLi++sl+em +va em+r+g+++Pll+GGa++s+ah+a kia++Y+++vvyv das+av vv +ll lcl|NCBI__GCF_000061505.1:WP_011767448.1 815 GLITPSLEEMSHVAAEMQRQGFDVPLLIGGATTSRAHTAIKIAPHYQQPVVYVPDASRAVGVVTALL 881 ******************************************************************* PP TIGR02082 859 sekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas 925 se ++ +++ ++y++ir ++ + k+ ++ +s++aar + +++ e +e+++p+ lG+ l+ lcl|NCBI__GCF_000061505.1:WP_011767448.1 882 SEGGAGDFKAQLAADYDKIRAQHAN-KKGVQLVSLEAARANAYNPLSVEGYEPVEPNTLGVMALDVD 947 ***********************98.778999*********************************** PP TIGR02082 926 ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPa 992 ++el++yiDw ++F +W+l+g++pkil+de++g+ ar++f+da+++l+ l+a + ++a++v+GlfPa lcl|NCBI__GCF_000061505.1:WP_011767448.1 948 LDELRDYIDWGPFFQTWDLAGSFPKILDDEVVGETARNVFNDAQAMLEDLIAGEWVQAKAVFGLFPA 1014 ******************************************************************* PP TIGR02082 993 qsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtagl 1058 +svgddi+ y+de++ +p+ t + ++q ++ ++ + claDf+a+k+sG +D+ ga++vtagl lcl|NCBI__GCF_000061505.1:WP_011767448.1 1015 NSVGDDIAFYADESR---DEPMMTWHGLRQQHERPAGKpHWCLADFVAPKASGVRDWCGAFAVTAGL 1078 *************99...5666666666677777777679*************************** PP TIGR02082 1059 gaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGir 1125 g+e+ ++ea +ddy +i++k+ladrlaea ae+lhervRke+wgya++e+ld++ l+ke+Y+Gir lcl|NCBI__GCF_000061505.1:WP_011767448.1 1079 GIEHKLAEFEAAHDDYRAIMLKSLADRLAEATAEWLHERVRKEYWGYAADEQLDNAALIKEQYKGIR 1145 ******************************************************************* PP TIGR02082 1126 pafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182 pa+GYpacPdht ka l++Ll+a + G+ ltes+a++P+asvsg+yfahpe++Yfa+ lcl|NCBI__GCF_000061505.1:WP_011767448.1 1146 PAPGYPACPDHTVKAALFQLLDAPTnAGMGLTESMAMTPAASVSGFYFAHPESHYFAI 1203 **********************9999******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1233 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: 0.12u 0.05s 00:00:00.17 Elapsed: 00:00:00.16 # Mc/sec: 9.02 // [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