Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_011913349.1 PST_RS11205 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000013785.1:WP_011913349.1
Length = 1230
Score = 1605 bits (4156), Expect = 0.0
Identities = 817/1229 (66%), Positives = 974/1229 (79%), Gaps = 9/1229 (0%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
+++++ L+ L++RIL+LDGGMGTMIQSY+L E+D+RGERF DWP D+KGNNDLL+LS+P
Sbjct: 5 NARLQALQHALSQRILILDGGMGTMIQSYKLEESDYRGERFTDWPSDVKGNNDLLLLSRP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+VI AI AY +AGADI+ETNTFN+T ++ ADY ME L E+N A+LAR AD TA
Sbjct: 65 DVIQAIEKAYLDAGADILETNTFNATRVSQADYGMEELVYELNVEGARLAREVADAKTAE 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
TP++PR+VAGVLGPT+RT SISPDVN+P +RN+TFD LV Y E+T+ L+EGGADLILIE
Sbjct: 125 TPDRPRFVAGVLGPTSRTCSISPDVNNPGYRNVTFDLLVENYTEATRGLIEGGADLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FAV+ FE GVELPIMISGTITDASGRTLSGQTTEAF+NS+RHA+ +
Sbjct: 185 TIFDTLNAKAAIFAVQQVFEEDGVELPIMISGTITDASGRTLSGQTTEAFWNSVRHAKPI 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALG +LR Y++EL+ A+ +V+AHPNAGLPNAFGEYD MA + E+A +
Sbjct: 245 SVGLNCALGAKDLRPYLEELANKADTHVSAHPNAGLPNAFGEYDETPAEMAAVVEEFAAS 304
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
GFLNI+GGCCGTTP HI A++ AV PR +P+IP ACRLSGLEP I SLFVNVGE
Sbjct: 305 GFLNIIGGCCGTTPAHIQAIAEAVAKYPPRVIPDIPKACRLSGLEPFTIDRSSLFVNVGE 364
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTN+TGSAKF RLI+EE Y+EAL+VA QQVE GAQ+IDINMDEGMLD++AAMV FLNLIA
Sbjct: 365 RTNITGSAKFARLIREENYTEALEVALQQVEAGAQVIDINMDEGMLDSKAAMVTFLNLIA 424
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ F HHA L +RYGAAVV
Sbjct: 425 GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFKHHAHLCKRYGAAVV 484
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDE GQADT ARK EIC+R+Y IL EVGFPPEDIIFDPNIFA+ATGIEEHNNYA D
Sbjct: 485 VMAFDEAGQADTAARKREICQRSYDILVNEVGFPPEDIIFDPNIFAIATGIEEHNNYAVD 544
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI AC I+ LP+AL SGGVSNVSFSFRGN+PVREAIH+VFL++AI+ G+ MGIVNAGQ
Sbjct: 545 FIEACAFIRDNLPYALTSGGVSNVSFSFRGNNPVREAIHSVFLFHAIKAGLTMGIVNAGQ 604
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
L IYD++P ELRDAVEDV+LNR GTE LLE+A+KY+G A+ EWR+ V+K
Sbjct: 605 LEIYDEIPKELRDAVEDVVLNRCAGGTEALLEIADKYKGD--GSVKEAETEEWRNLPVDK 662
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LVKGIT FI +DTEE RQQ RPIEVIEGPLM GMNVVGDLFG GKMFLPQVVKS
Sbjct: 663 RLEHALVKGITAFIVEDTEECRQQCARPIEVIEGPLMSGMNVVGDLFGAGKMFLPQVVKS 722
Query: 722 ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
ARVMKQAVA+L PFIEA K + + GK+++ATVKGDVHDIGKNIVGVVL CN Y++VD+
Sbjct: 723 ARVMKQAVAHLIPFIEAEKGGKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDVVDM 782
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPAEKIL+TA D+IGLSGLITPSLDEMV+VAKEM+RQGF++PL+IGGATTSKA
Sbjct: 783 GVMVPAEKILQTAIAEKCDIIGLSGLITPSLDEMVHVAKEMQRQGFSLPLMIGGATTSKA 842
Query: 841 HTAVKIEQNYSG-PTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
HTAVKI+ YS VYV +ASR VGV LLS + FV +TR+EY +R + +
Sbjct: 843 HTAVKIDPQYSNDAVVYVTDASRAVGVATTLLSKELKPAFVDKTREEYAMIRERTANRSA 902
Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
RT ++ A N FDW Y P G Q +E + TL +YIDWTPFF+ W LAG
Sbjct: 903 RTERLSYLDAIANKPPFDWSGYAPVKPSFTGRQVLEDIDLRTLVDYIDWTPFFIAWDLAG 962
Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
KYPRILEDEVVG A LF DA ML KL EK + R V G +PAN+V DD+E+Y D
Sbjct: 963 KYPRILEDEVVGEAATSLFNDAQAMLKKLVDEKLIRARAVFGFWPANQVQDDDLEVYGDN 1022
Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
+ HHLRQQT K N LADFVAPK +G DY+G F T G+ + LA A+
Sbjct: 1023 GEK--LATLHHLRQQTIKADAKPNLSLADFVAPKSTGITDYVGGFICTAGIGAEELAKAY 1080
Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
+ + DDYN IMVKALADRLAEA AE+LHE+VRK YWGYAP+E LSNEELIRE Y+GIRPA
Sbjct: 1081 QDKGDDYNSIMVKALADRLAEACAEWLHEQVRKHYWGYAPDERLSNEELIREQYKGIRPA 1140
Query: 1137 PGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQ 1196
PGYPACP+HTEK T+++LL+ + + + LTE +AM P A+VSGWYF+HP+++Y+AV +I
Sbjct: 1141 PGYPACPDHTEKGTLFQLLDADGISQVTLTEHYAMLPTAAVSGWYFAHPEAQYFAVGKID 1200
Query: 1197 RDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
+DQVE Y++RKG + ERWL PNLGYD
Sbjct: 1201 KDQVESYSQRKGQELAISERWLMPNLGYD 1229
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: 3716
Number of extensions: 165
Number of successful extensions: 7
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: 1230
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1183
Effective search space: 1395940
Effective search space used: 1395940
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_011913349.1 PST_RS11205 (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.3728.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 1773.3 0.0 0 1773.1 0.0 1.0 1 lcl|NCBI__GCF_000013785.1:WP_011913349.1 PST_RS11205 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011913349.1 PST_RS11205 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1773.1 0.0 0 0 1 1182 [] 15 1196 .. 15 1196 .. 0.98
Alignments for each domain:
== domain 1 score: 1773.1 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++ril+lDG+mGt++qs++L+e d+rge ++d+++++kGnndlL l++P+vi+ai +ay++aGaDi
lcl|NCBI__GCF_000013785.1:WP_011913349.1 15 LSQRILILDGGMGTMIQSYKLEESDYRGErFTDWPSDVKGNNDLLLLSRPDVIQAIEKAYLDAGADI 81
589**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
+etntFn+t +++adY++e+++yeln ++a+larevad t tp+++RfvaG+lGPt+++ ++spd
lcl|NCBI__GCF_000013785.1:WP_011913349.1 82 LETNTFNATRVSQADYGMEELVYELNVEGARLAREVADAKTaETPDRPRFVAGVLGPTSRTCSISPD 148
**************************************99999************************ PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p++rnvt+d lv+ Y+e+++gl++GG+Dl+Liet+fDtlnakaa+fav++vfee g+elPi+is
lcl|NCBI__GCF_000013785.1:WP_011913349.1 149 VNNPGYRNVTFDLLVENYTEATRGLIEGGADLILIETIFDTLNAKAAIFAVQQVFEEDGVELPIMIS 215
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266
g+i+d+sGrtLsGqt+eaf +s++ha+ +++GLnCalGa++lr++++el+++a++ vs++PnaGLPn
lcl|NCBI__GCF_000013785.1:WP_011913349.1 216 GTITDASGRTLSGQTTEAFWNSVRHAKPISVGLNCALGAKDLRPYLEELANKADTHVSAHPNAGLPN 282
******************************************************************* PP
TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
a+geYd+tp e+a++++efa+ g+lni+GGCCGttP+hi+aiaeav++ pr ++++++++lsgle
lcl|NCBI__GCF_000013785.1:WP_011913349.1 283 AFGEYDETPAEMAAVVEEFAASGFLNIIGGCCGTTPAHIQAIAEAVAKYPPRVIPDIPKACRLSGLE 349
******************************************************************* PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
+++i++ s fvn+GeRtn++Gs+kf++li++e+y eal++a qqve Gaq++Din+De++lD++a+m
lcl|NCBI__GCF_000013785.1:WP_011913349.1 350 PFTIDRSSLFVNVGERTNITGSAKFARLIREENYTEALEVALQQVEAGAQVIDINMDEGMLDSKAAM 416
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
+++l+l+a+epdi++vP+m+Dss++ev+eaGLk+iqGk+ivnsis+k+G+e+F ++a+l k+yGaav
lcl|NCBI__GCF_000013785.1:WP_011913349.1 417 VTFLNLIAGEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFKHHAHLCKRYGAAV 483
******************************************************************* PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
vvmafDe Gqa+ta++k ei++R y++l+++vgfppediifDpni++iatGieeh++ya+dfiea+
lcl|NCBI__GCF_000013785.1:WP_011913349.1 484 VVMAFDEAGQADTAARKREICQRSYDILVNEVGFPPEDIIFDPNIFAIATGIEEHNNYAVDFIEACA 550
******************************************************************* PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
i+ +lP+a +sgGvsnvsFs+rgn++vRea+hsvFL++aikaGl mgivnag+l++yd+i+kelr+
lcl|NCBI__GCF_000013785.1:WP_011913349.1 551 FIRDNLPYALTSGGVSNVSFSFRGNNPVREAIHSVFLFHAIKAGLTMGIVNAGQLEIYDEIPKELRD 617
******************************************************************* PP
TIGR02082 602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668
+ved++l+r te Lle+a++ykg + kea+++ewrnlpv++RLe+alvkG++ +i ed+ee
lcl|NCBI__GCF_000013785.1:WP_011913349.1 618 AVEDVVLNRCAGGTEALLEIADKYKGDGSV--KEAETEEWRNLPVDKRLEHALVKGITAFIVEDTEE 682
**************************9998..999******************************** PP
TIGR02082 669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskG 734
r++ +p+e+iegpL+ Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+ek + ++kG
lcl|NCBI__GCF_000013785.1:WP_011913349.1 683 CRQQCARPIEVIEGPLMSGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIEAEKGGKpEAKG 749
***********************************************************766599** PP
TIGR02082 735 kivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldem 801
ki++atvkGDvhDiGkniv+vvL+cngy+vvd+Gv+vP+ekil++a +k D+iglsGLi++sldem
lcl|NCBI__GCF_000013785.1:WP_011913349.1 750 KILMATVKGDVHDIGKNIVGVVLGCNGYDVVDMGVMVPAEKILQTAIAEKCDIIGLSGLITPSLDEM 816
******************************************************************* PP
TIGR02082 802 vevaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkkaeel 867
v+va+em+r+g+++Pl++GGa++skah+avki+++Y+ vvyv+das+av v+ +lls++ k +++
lcl|NCBI__GCF_000013785.1:WP_011913349.1 817 VHVAKEMQRQGFSLPLMIGGATTSKAHTAVKIDPQYSNdAVVYVTDASRAVGVATTLLSKELKPAFV 883
************************************872699************************* PP
TIGR02082 868 ekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyi 933
+k++eey ire+ ++ +++ ls +a ++ +d+s + +++p f G++vle++ + +l++yi
lcl|NCBI__GCF_000013785.1:WP_011913349.1 884 DKTREEYAMIRERTANRSARTERLSYLDAIANKPPFDWS-GYAPVKPSFTGRQVLEDIdLRTLVDYI 949
***************************************.9************************** PP
TIGR02082 934 DwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddi 999
Dw+++F++W+l+gkyp+il+de++g+ a+ lf+da+++l+kl+ ekl+rar+v+G++Pa++v+ dd+
lcl|NCBI__GCF_000013785.1:WP_011913349.1 950 DWTPFFIAWDLAGKYPRILEDEVVGEAATSLFNDAQAMLKKLVDEKLIRARAVFGFWPANQVQdDDL 1016
***********************************************************9765268* PP
TIGR02082 1000 eiytdetvsqetkpiatvrek.leqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelak 1065
e+y d++ ++at+++ +++++ + + +l+laDf+a+k++Gi+Dy+g ++ tag+gaeelak
lcl|NCBI__GCF_000013785.1:WP_011913349.1 1017 EVYGDNGE-----KLATLHHLrQQTIKADAKPNLSLADFVAPKSTGITDYVGGFICTAGIGAEELAK 1078
****8877.....5666655415566666666*********************************** PP
TIGR02082 1066 kleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpa 1132
++++k ddy+si+vkaladrlaea ae+lhe+vRk++wgya +e l++e+l++e+Y+Girpa+GYpa
lcl|NCBI__GCF_000013785.1:WP_011913349.1 1079 AYQDKGDDYNSIMVKALADRLAEACAEWLHEQVRKHYWGYAPDERLSNEELIREQYKGIRPAPGYPA 1145
******************************************************************* PP
TIGR02082 1133 cPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
cPdhtek tl++Ll+a+ ++lte +a+ P+a+vsg+yfahpea+Yfav
lcl|NCBI__GCF_000013785.1:WP_011913349.1 1146 CPDHTEKGTLFQLLDADGiSQVTLTEHYAMLPTAAVSGWYFAHPEAQYFAV 1196
******************567****************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1230 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: 0.09u 0.03s 00:00:00.12 Elapsed: 00:00:00.11
# Mc/sec: 12.26
//
[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