Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_013821081.1 METME_RS22690 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000214665.1:WP_013821081.1
Length = 1223
Score = 1664 bits (4309), Expect = 0.0
Identities = 819/1224 (66%), Positives = 1005/1224 (82%), Gaps = 8/1224 (0%)
Query: 3 SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
+ +++L QL +RIL LDG MGTMIQSY+L E D+RG RFADW DLKGNNDLL L++P+
Sbjct: 2 NSIQRLNQQLKQRILYLDGAMGTMIQSYKLGEKDYRGTRFADWTSDLKGNNDLLSLTQPD 61
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I AIH AY EAG+DIIETNTFN+T IAMADY ME L+ EIN A+A+LA+ A+E +A T
Sbjct: 62 IIKAIHKAYLEAGSDIIETNTFNATKIAMADYHMEDLAYEINVASARLAKQAAEEISALT 121
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
P+KPR+VAGVLGPTNRT+S+SPDVNDP FRNITFD LV AY E+T+ L++GGAD+ILIET
Sbjct: 122 PDKPRFVAGVLGPTNRTSSMSPDVNDPGFRNITFDDLVDAYSEATQGLIDGGADIILIET 181
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
VFDTLNAKAA+FAV+ F+ LG +LP+MISGTITDASGRTLSGQT AF+ SL+H + ++
Sbjct: 182 VFDTLNAKAAIFAVENTFDKLGYKLPVMISGTITDASGRTLSGQTAAAFWTSLKHVKPIS 241
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAG 302
G NCALG ELRQY++ELS IA+ YV+AHPNAGLPN FGEYD + MA ++ +WA +G
Sbjct: 242 IGFNCALGAQELRQYIEELSNIADTYVSAHPNAGLPNEFGEYDETPEQMAAELADWAASG 301
Query: 303 FLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGER 362
+LNI+GGCCGT+P I A+ AV PR++PE+ C L+GLE ++IG ++LFVNVGER
Sbjct: 302 YLNIIGGCCGTSPDTIRAIVEAVGKYPPRQIPELEKRCHLAGLEAMSIGPETLFVNVGER 361
Query: 363 TNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAG 422
TNVTGSA FK++I EE+Y +AL+VA+QQVENGAQIIDINMDEGMLD++AAMVRFLNL+A
Sbjct: 362 TNVTGSAIFKKMIIEERYEDALEVAKQQVENGAQIIDINMDEGMLDSKAAMVRFLNLLAA 421
Query: 423 EPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVV 482
EPDIA+VPIM+DSSKW+++E GLKCIQGKG+VNSIS+KEG +AFI HAKL+RRYGAAV+V
Sbjct: 422 EPDIAKVPIMLDSSKWEILEAGLKCIQGKGVVNSISIKEGEEAFIKHAKLVRRYGAAVIV 481
Query: 483 MAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDF 542
MAFDEQGQADT RKIEIC RAYKILTE++GFPPEDIIFDPNIFAVATGIEEHNNY DF
Sbjct: 482 MAFDEQGQADTMQRKIEICTRAYKILTEQIGFPPEDIIFDPNIFAVATGIEEHNNYGVDF 541
Query: 543 IGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQL 602
I A IK+ LPHALISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAGQL
Sbjct: 542 IEATRIIKQTLPHALISGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQL 601
Query: 603 AIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKR 662
AIY D+P+ELRD VEDVILNR +GTE+LLE+AEKYRG T A + EWR W V+KR
Sbjct: 602 AIYADIPSELRDTVEDVILNRTPEGTEKLLEIAEKYRG--TGQVAKQETLEWREWPVSKR 659
Query: 663 LEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA 722
LE++LVKGI ++I++DTE+A Q+A +P+ VIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA
Sbjct: 660 LEHALVKGIADYIDEDTEQALQEAEKPLHVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA 719
Query: 723 RVMKQAVAYLEPFIEASKEQG--KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
RVMK+AVAYL PF++A + +TNGK+++ATVKGDVHDIGKNIV VVLQCNNYE++DL
Sbjct: 720 RVMKKAVAYLMPFMDAEVDGSVRQTNGKVLMATVKGDVHDIGKNIVAVVLQCNNYEVIDL 779
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPA+ IL+TA+E D+IGLSGLITPSLDEMV+VAKEM+RQGFTIPL+IGGATTS+A
Sbjct: 780 GVMVPADTILKTAREEKVDVIGLSGLITPSLDEMVHVAKEMQRQGFTIPLMIGGATTSRA 839
Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
HTAVKIE NY PT+YV +ASR+VGVV+ALLS+ Q+ +FV +TR EYE VR +H + +
Sbjct: 840 HTAVKIEPNYQHPTIYVTDASRSVGVVSALLSEDQKAEFVEKTRAEYEQVRERHKGRHAK 899
Query: 901 TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGK 959
P + L+ AR N FD+ Y P LG+Q ++ +++L +YIDWTPFF TW L+G+
Sbjct: 900 NPQLDLQKARHN--KFDFAGYRPVKPKFLGIQVIDHFPLDSLVSYIDWTPFFQTWELSGR 957
Query: 960 YPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETR 1019
YP IL D+VVG+EA +LF DA ML +L E+ L + V+G FPAN + DDI +Y D++R
Sbjct: 958 YPAILSDQVVGIEASKLFADAQAMLKQLVDEQWLTAKAVIGFFPANSIDDDIVLYTDDSR 1017
Query: 1020 THVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEA 1078
T +V HHLRQQ K G NYCL+DF+AP SG ADY+G FAVT G+ + FE
Sbjct: 1018 TQQRDVLHHLRQQNVKAPGRPNYCLSDFIAPVGSGIADYMGGFAVTAGIGIETKLAEFEK 1077
Query: 1079 QHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPG 1138
HDDY+ IM+KALADRLAEAFAE +H++VRK YWGYA E N +LI E YQGIRPAPG
Sbjct: 1078 DHDDYSSIMLKALADRLAEAFAECMHQKVRKEYWGYAAEETHDNHDLIEEAYQGIRPAPG 1137
Query: 1139 YPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRD 1198
YPACP+HTEKA ++ELL V + T ++LTE+FAM+P A+VSGWYFSHP+S+Y+ V +I +D
Sbjct: 1138 YPACPDHTEKAKLFELLNVTESTTIELTENFAMYPTAAVSGWYFSHPESQYFNVGKIDQD 1197
Query: 1199 QVEDYARRKGMSVTEVERWLAPNL 1222
Q++DYA+RKG+++ ERWLA +L
Sbjct: 1198 QLQDYAKRKGINLEVAERWLAAHL 1221
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: 3615
Number of extensions: 128
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: 1223
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1176
Effective search space: 1387680
Effective search space used: 1387680
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_013821081.1 METME_RS22690 (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.11846.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 1835.6 0.7 0 1835.4 0.7 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013821081.1 METME_RS22690 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013821081.1 METME_RS22690 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1835.4 0.7 0 0 1 1182 [] 11 1191 .. 11 1191 .. 0.98
Alignments for each domain:
== domain 1 score: 1835.4 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++ril lDGamGt++qs++L e+d+rg +ad++++lkGnndlL+lt+P++i+aih+ay+eaG+Di
lcl|NCBI__GCF_000214665.1:WP_013821081.1 11 LKQRILYLDGAMGTMIQSYKLGEKDYRGTrFADWTSDLKGNNDLLSLTQPDIIKAIHKAYLEAGSDI 77
589**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
+etntFn+t+ia+adY++ed+aye+n ++a+la+++a+e++ ltp+k+RfvaG+lGPtn+++++spd
lcl|NCBI__GCF_000214665.1:WP_013821081.1 78 IETNTFNATKIAMADYHMEDLAYEINVASARLAKQAAEEISaLTPDKPRFVAGVLGPTNRTSSMSPD 144
******************************************************************* PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p+frn+t+d+lvdaY+e+++gl+dGG+D++LietvfDtlnakaa+fave+ f++ g +lP++is
lcl|NCBI__GCF_000214665.1:WP_013821081.1 145 VNDPGFRNITFDDLVDAYSEATQGLIDGGADIILIETVFDTLNAKAAIFAVENTFDKLGYKLPVMIS 211
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266
g+i+d+sGrtLsGqt +af +sl+h + +++G nCalGa+elr++++els++a+++vs++PnaGLPn
lcl|NCBI__GCF_000214665.1:WP_013821081.1 212 GTITDASGRTLSGQTAAAFWTSLKHVKPISIGFNCALGAQELRQYIEELSNIADTYVSAHPNAGLPN 278
******************************************************************* PP
TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
++geYd+tpe++a++l+++a+ g+lni+GGCCGt P+ irai eav + pr+ +ele+++ l+gle
lcl|NCBI__GCF_000214665.1:WP_013821081.1 279 EFGEYDETPEQMAAELADWAASGYLNIIGGCCGTSPDTIRAIVEAVGKYPPRQIPELEKRCHLAGLE 345
******************************************************************* PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
a++i++e+ fvn+GeRtnv+Gs+ f+k+i++e ye+al++akqqve+Gaqi+Din+De++lD++a+m
lcl|NCBI__GCF_000214665.1:WP_013821081.1 346 AMSIGPETLFVNVGERTNVTGSAIFKKMIIEERYEDALEVAKQQVENGAQIIDINMDEGMLDSKAAM 412
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
+++l+lla+epdiakvP+mlDss++e+leaGLk+iqGk++vnsis+k+Gee+F+++akl+++yGaav
lcl|NCBI__GCF_000214665.1:WP_013821081.1 413 VRFLNLLAAEPDIAKVPIMLDSSKWEILEAGLKCIQGKGVVNSISIKEGEEAFIKHAKLVRRYGAAV 479
******************************************************************* PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
+vmafDe+Gqa+t+++kiei++Rayk+lte++gfppediifDpni+++atGieeh++y++dfiea+r
lcl|NCBI__GCF_000214665.1:WP_013821081.1 480 IVMAFDEQGQADTMQRKIEICTRAYKILTEQIGFPPEDIIFDPNIFAVATGIEEHNNYGVDFIEATR 546
******************************************************************* PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
ik++lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+la+y+di+ elr+
lcl|NCBI__GCF_000214665.1:WP_013821081.1 547 IIKQTLPHALISGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQLAIYADIPSELRD 613
******************************************************************* PP
TIGR02082 602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668
+ved+il+r +e tekLle+ae+y+gt + +++++ ewr++pv++RLe+alvkG++++i+ed+e+
lcl|NCBI__GCF_000214665.1:WP_013821081.1 614 TVEDVILNRTPEGTEKLLEIAEKYRGTGQV--AKQETLEWREWPVSKRLEHALVKGIADYIDEDTEQ 678
***************************999..667999***************************** PP
TIGR02082 669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed..ksk 733
a++++++pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkavayL+P++++e + + +++
lcl|NCBI__GCF_000214665.1:WP_013821081.1 679 ALQEAEKPLHVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKKAVAYLMPFMDAEVDGSvrQTN 745
********************************************************998666669** PP
TIGR02082 734 GkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800
Gk+++atvkGDvhDiGkniv vvL+cn+yev+dlGv+vP+++il++a+++k DviglsGLi++slde
lcl|NCBI__GCF_000214665.1:WP_013821081.1 746 GKVLMATVKGDVHDIGKNIVAVVLQCNNYEVIDLGVMVPADTILKTAREEKVDVIGLSGLITPSLDE 812
******************************************************************* PP
TIGR02082 801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeel 867
mv+va+em+r+g++iPl++GGa++s+ah+avki+++Y+ +++yv+das++v vv++llse++kae++
lcl|NCBI__GCF_000214665.1:WP_013821081.1 813 MVHVAKEMQRQGFTIPLMIGGATTSRAHTAVKIEPNYQHPTIYVTDASRSVGVVSALLSEDQKAEFV 879
******************************************************************* PP
TIGR02082 868 ekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyi 933
ek+++eye++re+++ ++ k +l +++ar+++f++ +++++pkflG++v+++ ++ l++yi
lcl|NCBI__GCF_000214665.1:WP_013821081.1 880 EKTRAEYEQVRERHKGRHAKNPQLDLQKARHNKFDFAG---YRPVKPKFLGIQVIDHFpLDSLVSYI 943
******************************99998865...59************************ PP
TIGR02082 934 DwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddie 1000
Dw+++F +Wel g+yp il+d+++g+ea klf+da+++l++l+ e+ l+a++v+G+fPa+s++ddi+
lcl|NCBI__GCF_000214665.1:WP_013821081.1 944 DWTPFFQTWELSGRYPAILSDQVVGIEASKLFADAQAMLKQLVDEQWLTAKAVIGFFPANSIDDDIV 1010
******************************************************************* PP
TIGR02082 1001 iytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakk 1066
+ytd++++q+ +++ +r +q + +r ++cl+Dfia+ sGi+Dy+g ++vtag+g+e +
lcl|NCBI__GCF_000214665.1:WP_013821081.1 1011 LYTDDSRTQQRDVLHHLR---QQNVKAPGRpNYCLSDFIAPVGSGIADYMGGFAVTAGIGIETKLAE 1074
*****9977766666654...5555666667********************************99** PP
TIGR02082 1067 leakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpac 1133
+e+++ddy+si++kaladrlaea+ae +h++vRke+wgya+ee +d++dl+ e Y+Girpa+GYpac
lcl|NCBI__GCF_000214665.1:WP_013821081.1 1075 FEKDHDDYSSIMLKALADRLAEAFAECMHQKVRKEYWGYAAEETHDNHDLIEEAYQGIRPAPGYPAC 1141
******************************************************************* PP
TIGR02082 1134 PdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
Pdhteka+l+eLl++ + + ++lte++a++P+a+vsg+yf+hpe++Yf+v
lcl|NCBI__GCF_000214665.1:WP_013821081.1 1142 PDHTEKAKLFELLNVTEsTTIELTENFAMYPTAAVSGWYFSHPESQYFNV 1191
*************98766******************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1223 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: 13.03
//
[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