Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_084544571.1 H566_RS21925 methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_000482785.1:WP_084544571.1 Length = 911 Score = 1012 bits (2617), Expect = 0.0 Identities = 554/894 (61%), Positives = 647/894 (72%), Gaps = 40/894 (4%) Query: 341 RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400 RLSGLE L+I +D+LFVNVGERTNVTGS F RLI +Y +AL VARQQVENGAQIID+ Sbjct: 22 RLSGLEALSIDDDTLFVNVGERTNVTGSKMFARLILNGEYDQALAVARQQVENGAQIIDV 81 Query: 401 NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460 NMDE MLD++AAM RFLNLIA EPDIARVPIMIDSSKW+VIE GLKC+QGK IVNSIS+K Sbjct: 82 NMDEAMLDSKAAMTRFLNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKSIVNSISLK 141 Query: 461 EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520 EG FIH AKL RRYGAAV+VMAFDE+GQADT ARK EIC RAYK+LTE+VGF PEDII Sbjct: 142 EGEANFIHQAKLCRRYGAAVIVMAFDEKGQADTFARKTEICARAYKVLTEKVGFAPEDII 201 Query: 521 FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580 FDPNIFA+ATGIEEH+NYA DFI AC I+ LPHA ISGGVSNVSFSFRGN+PVREAIH Sbjct: 202 FDPNIFAIATGIEEHDNYAVDFIEACRWIRANLPHARISGGVSNVSFSFRGNEPVREAIH 261 Query: 581 AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNR---------RDDGTERL 631 VFLY+AIR GM MGIVNAGQL +Y DL ELR+ VEDV+LNR TERL Sbjct: 262 TVFLYHAIRAGMTMGIVNAGQLGVYADLDPELRERVEDVVLNRVPKQAEGEEPKTATERL 321 Query: 632 LELAEKYRGSKTDDTANAQQAEWRSW-----EVNKRLEYSLVKGITEFIEQDTEEAR--- 683 LE+AE+++G+ N +WR V +RL ++LV GIT FI +DTEEAR Sbjct: 322 LEIAERFKGAGGKKEEN---LDWRGTPDNPVPVEQRLSHALVHGITNFITEDTEEARAAI 378 Query: 684 -QQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQ 742 + RPIEVIEGPLM GMNVVGDLFG+GKMFLPQVVKSARVMKQAVA+L PFIE K Q Sbjct: 379 AARGGRPIEVIEGPLMAGMNVVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPFIEEEKRQ 438 Query: 743 -------GKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKE 795 ++ GK+VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP +IL AK Sbjct: 439 IEAAGGDVRSKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCSEILAKAKV 498 Query: 796 VNADLIGLSGLITPSLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYS 851 AD+IGLSGLITPSL+EM VA EM+R F IPLLIGGATTS+ HTAVKI +Y Sbjct: 499 EGADIIGLSGLITPSLEEMAYVATEMQRDDFFRVKKIPLLIGGATTSRVHTAVKIAPHYD 558 Query: 852 GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARD 911 GP VYV +ASR+V V +LLSD +++ EY+ VR H KK TP + L AR Sbjct: 559 GPVVYVPDASRSVSVAQSLLSDEGAARYISELEAEYDRVRTAHANKK-ATPLLPLAEARA 617 Query: 912 NDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVG 970 + A DW+A P LG +E + L YIDW PFF TW L G +P +L+D VVG Sbjct: 618 HKPAIDWRAAAPVKPKFLGRREFRNYDLAELARYIDWGPFFQTWDLHGAFPALLDDPVVG 677 Query: 971 VEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDE---TRTHVINVS 1026 A+++F D ML KL + LN VVG +PAN G + I +Y D+ HV+ Sbjct: 678 ESARKVFADGQAMLKKLIDGRQLNASAVVGFWPANSDGAETITLYTDDDARDEAHVLFRW 737 Query: 1027 HHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNK 1085 +LRQQT K G N CLAD++AP SG DYIG FAVT GL D LA+ +EA HDDY+ Sbjct: 738 KNLRQQTAKREGVENKCLADYIAPLDSGVRDYIGVFAVTAGLGADKLAERYEAAHDDYSA 797 Query: 1086 IMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEH 1145 IMVKALADRLAEAFAE +HERVRK WGYAP+E L+NEELI+E Y GIRPAPGYPACP H Sbjct: 798 IMVKALADRLAEAFAEAMHERVRKDLWGYAPDEALTNEELIKEKYVGIRPAPGYPACPRH 857 Query: 1146 TEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199 K ++ L+ GM LTESFAM P +SVSG+Y SHP ++Y+ V +I +Q Sbjct: 858 EVKREMFAALDATA-IGMGLTESFAMTPASSVSGFYLSHPKAQYFNVGEIGDEQ 910 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: 2641 Number of extensions: 100 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: 911 Length adjustment: 45 Effective length of query: 1182 Effective length of database: 866 Effective search space: 1023612 Effective search space used: 1023612 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: 58 (26.9 bits)
Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_051377698.1 H566_RS21930 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_000482785.1:WP_051377698.1 Length = 353 Score = 397 bits (1021), Expect = e-115 Identities = 201/346 (58%), Positives = 259/346 (74%), Gaps = 13/346 (3%) Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADW-PCDL--------KGN 52 S +L ++ RIL+LDG MGTMIQ Y+L+EA +RG RFADW P DL KGN Sbjct: 5 SDLAARLADAMSRRILILDGAMGTMIQRYKLDEAAYRGARFADWQPADLAPGKQLFLKGN 64 Query: 53 NDLLVLSKPEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLAR 112 NDLLVL++PEVIA IH Y AGADIIETNTF +T++A ADY M L+ E+N AAA+LAR Sbjct: 65 NDLLVLTQPEVIAEIHGKYLAAGADIIETNTFGATSVAQADYHMADLAYEMNLAAARLAR 124 Query: 113 ACADEWTARTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVE 172 A D+++ T +KPR+VAG LGPT +TASISPDVNDP RN++FD LVAAY E + L + Sbjct: 125 AECDKYS--TADKPRFVAGALGPTPKTASISPDVNDPGARNVSFDELVAAYHEQARGLWD 182 Query: 173 GGADLILIETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFY 232 GGADL L+ET+FDTLNAKAA+FA+ FE G LPIMISGT+TDASGR LSGQT AF+ Sbjct: 183 GGADLFLVETIFDTLNAKAALFAIDQLFEERGATLPIMISGTVTDASGRILSGQTVAAFW 242 Query: 233 NSLRHAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADT 290 +S+RHA +T GLNCALG +R Y+ ELS+IA+ + +PNAGLPN + +D D Sbjct: 243 HSVRHARPITIGLNCALGAALMRPYIAELSKIADTRICVYPNAGLPNPMSDTGFDETPDV 302 Query: 291 MAKQIREWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEI 336 ++ ++E+A+AGF+NI GGCCGTTP+HIAA+++AV + PR++P++ Sbjct: 303 TSRLLKEFAEAGFVNIAGGCCGTTPEHIAAIAQAVATVTPRRVPDL 348 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: 1004 Number of extensions: 37 Number of successful extensions: 4 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: 353 Length adjustment: 38 Effective length of query: 1189 Effective length of database: 315 Effective search space: 374535 Effective search space used: 374535 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: 54 (25.4 bits)
Align candidate WP_084544571.1 H566_RS21925 (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.4807.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 1211.0 0.0 0 1210.8 0.0 1.0 1 lcl|NCBI__GCF_000482785.1:WP_084544571.1 H566_RS21925 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_084544571.1 H566_RS21925 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1210.8 0.0 0 0 320 1182 .] 14 903 .. 3 903 .. 0.95 Alignments for each domain: == domain 1 score: 1210.8 bits; conditional E-value: 0 TIGR02082 320 rqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilD 386 ++ +++lsgleal+i++++ fvn+GeRtnv+Gsk f++li +++y++al +a+qqve+Gaqi+D lcl|NCBI__GCF_000482785.1:WP_084544571.1 14 PPRRSRPLRLSGLEALSIDDDTLFVNVGERTNVTGSKMFARLILNGEYDQALAVARQQVENGAQIID 80 555678899********************************************************** PP TIGR02082 387 invDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerF 453 +n+De++lD++a+m+++l+l+asepdia+vP+m+Dss++ev+eaGLk++qGk+ivnsislk+Ge++F lcl|NCBI__GCF_000482785.1:WP_084544571.1 81 VNMDEAMLDSKAAMTRFLNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKSIVNSISLKEGEANF 147 ******************************************************************* PP TIGR02082 454 lekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGie 520 +++akl ++yGaav+vmafDe+Gqa+t ++k ei+ Rayk+ltekvgf pediifDpni++iatGie lcl|NCBI__GCF_000482785.1:WP_084544571.1 148 IHQAKLCRRYGAAVIVMAFDEKGQADTFARKTEICARAYKVLTEKVGFAPEDIIFDPNIFAIATGIE 214 ******************************************************************* PP TIGR02082 521 ehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnag 587 ehd+ya+dfiea+r+i+ +lP+a+isgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+ mgivnag lcl|NCBI__GCF_000482785.1:WP_084544571.1 215 EHDNYAVDFIEACRWIRANLPHARISGGVSNVSFSFRGNEPVREAIHTVFLYHAIRAGMTMGIVNAG 281 ******************************************************************* PP TIGR02082 588 klavyddidkelrevvedlildrr.........reatekLlelaelykgtkeksskea..qeaewrn 643 +l vy+d+d+elre ved++l+r + ate+Lle+ae++kg k++++ + + lcl|NCBI__GCF_000482785.1:WP_084544571.1 282 QLGVYADLDPELRERVEDVVLNRVpkqaegeepKTATERLLEIAERFKGAGGKKEENLdwRGTPDNP 348 ***********************999999999999**************998855443114444556 PP TIGR02082 644 lpveeRLeralvkGeregieedleear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvv 706 +pve+RL++alv+G++++i ed+eear + +p+e+iegpL++Gm+vvGdLFG+GkmfLPqvv lcl|NCBI__GCF_000482785.1:WP_084544571.1 349 VPVEQRLSHALVHGITNFITEDTEEARaaiaARGGRPIEVIEGPLMAGMNVVGDLFGQGKMFLPQVV 415 789***********************9666556789******************************* PP TIGR02082 707 ksarvmkkavayLePylekekeed.......kskGkivlatvkGDvhDiGknivdvvLscngyevvd 766 ksarvmk+ava+L+P++e+ek + +skGkiv+atvkGDvhDiGkniv+vvL+cn++evv+ lcl|NCBI__GCF_000482785.1:WP_084544571.1 416 KSARVMKQAVAHLIPFIEEEKRQIeaaggdvRSKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVN 482 *********************88789999999*********************************** PP TIGR02082 767 lGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvk....iPlllGGaalskahv 829 +Gv+vP+ +il +ak + aD+iglsGLi++sl+em++va em+r + iPll+GGa++s+ h+ lcl|NCBI__GCF_000482785.1:WP_084544571.1 483 MGVMVPCSEILAKAKVEGADIIGLSGLITPSLEEMAYVATEMQRDDFFrvkkIPLLIGGATTSRVHT 549 ********************************************98744556*************** PP TIGR02082 830 avkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaa 896 avkia++Y+g+vvyv das++v+v+++lls++ a +++++++ey+ +r+ + + k+ + l++++a lcl|NCBI__GCF_000482785.1:WP_084544571.1 550 AVKIAPHYDGPVVYVPDASRSVSVAQSLLSDEGAARYISELEAEYDRVRTAHAN-KKATPLLPLAEA 615 ***************************************************998.6788999***** PP TIGR02082 897 rkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglear 962 r ++ a+d++ ++ +++pkflG+++++++ ++el yiDw ++F +W+l+g +p l+d+++g+ ar lcl|NCBI__GCF_000482785.1:WP_084544571.1 616 RAHKPAIDWR-AAAPVKPKFLGRREFRNYdLAELARYIDWGPFFQTWDLHGAFPALLDDPVVGESAR 681 **********.9******************************************************* PP TIGR02082 963 klfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqs 1028 k+f+d +++l+kl+ ++l+a++vvG++Pa+s g ++i++ytd+ e++++ ++ ++q+ + + lcl|NCBI__GCF_000482785.1:WP_084544571.1 682 KVFADGQAMLKKLIDGRQLNASAVVGFWPANSDGaETITLYTDDDARDEAHVLFRWKNLRQQTAKRE 748 *******************************986379*****9988777777776665555444444 PP TIGR02082 1029 dr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaell 1094 + ++claD+ia+ +sG +Dy+g+++vtaglga++la+++ea +ddy++i+vkaladrlaea+ae + lcl|NCBI__GCF_000482785.1:WP_084544571.1 749 GVeNKCLADYIAPLDSGVRDYIGVFAVTAGLGADKLAERYEAAHDDYSAIMVKALADRLAEAFAEAM 815 436**************************************************************** PP TIGR02082 1095 hervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslal 1161 hervRk+lwgya +e+l +e+l+ke+Y Girpa+GYpacP h+ k+++++ l+a iG+ ltes+a+ lcl|NCBI__GCF_000482785.1:WP_084544571.1 816 HERVRKDLWGYAPDEALTNEELIKEKYVGIRPAPGYPACPRHEVKREMFAALDATAIGMGLTESFAM 882 ******************************************************************* PP TIGR02082 1162 aPeasvsglyfahpeakYfav 1182 +P++svsg+y++hp+a+Yf+v lcl|NCBI__GCF_000482785.1:WP_084544571.1 883 TPASSVSGFYLSHPKAQYFNV 903 *******************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (911 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: 00:00:00.11 # Mc/sec: 9.49 // [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