Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_077243567.1 B1A74_RS01430 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_001995255.1:WP_077243567.1
Length = 1263
Score = 1655 bits (4287), Expect = 0.0
Identities = 820/1247 (65%), Positives = 988/1247 (79%), Gaps = 24/1247 (1%)
Query: 1 MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60
M++ + + L ERIL+LDGGMGT IQ Y L EAD+RGERF DW DLKGNNDLL L++
Sbjct: 1 MTATRQDIENALKERILILDGGMGTTIQLYELGEADYRGERFKDWESDLKGNNDLLSLTR 60
Query: 61 PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120
P++I IHN Y EAGADIIE NTFN T IAMADY ME L E+N +AKLAR AD WTA
Sbjct: 61 PDIIEQIHNDYLEAGADIIEANTFNGTRIAMADYHMEDLVPELNRESAKLARKAADAWTA 120
Query: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180
+TP+KPR+VAG+LGPTNRTASISPDVNDP RN+ FD LVAAY+E+ +AL+EGG DL+LI
Sbjct: 121 KTPDKPRFVAGILGPTNRTASISPDVNDPGARNVDFDTLVAAYKEAAEALIEGGVDLLLI 180
Query: 181 ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240
ETVFDTLNAKAA+FAVKT + LG +LPIMISGTITDASGRTLSGQTTEAF+NS+RHA
Sbjct: 181 ETVFDTLNAKAAIFAVKTLEDELGKDLPIMISGTITDASGRTLSGQTTEAFWNSVRHANP 240
Query: 241 LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300
++ GLNCALG E+RQYV+ELSRIA+ +V+AHPNAGLPN FG+YD + MA + WA+
Sbjct: 241 VSIGLNCALGAKEMRQYVEELSRIADTHVSAHPNAGLPNEFGDYDESPEQMAADVGPWAE 300
Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
G LNI+GGCCGT P+HI AM AVE PRK+PE+ ACRLSGLEP NI +DSLFVNVG
Sbjct: 301 QGMLNIIGGCCGTLPEHIRAMREAVEKFPPRKVPEVSPACRLSGLEPCNITDDSLFVNVG 360
Query: 361 ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
ERTNVTGS KF RLI+ E+Y AL+VA QVE GAQIID+NMDEGML+++ AMVRFLNL+
Sbjct: 361 ERTNVTGSRKFLRLIQNEEYDVALEVALNQVEGGAQIIDVNMDEGMLESQDAMVRFLNLL 420
Query: 421 AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
AGEPDIARVP+MIDSSK+++IE GLKC+QGK +VNSISMKEG + FI A+L RRYGAA+
Sbjct: 421 AGEPDIARVPVMIDSSKFEIIEAGLKCVQGKPVVNSISMKEGEENFIKQAELCRRYGAAI 480
Query: 481 VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
VVMAFDE GQAD R++EIC RAYK+LTE+VGFP EDIIFDPNIFAVATGIEEHNNY
Sbjct: 481 VVMAFDEDGQADNEQRRVEICTRAYKLLTEKVGFPAEDIIFDPNIFAVATGIEEHNNYGV 540
Query: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
DFI A IK +LPHALISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAG
Sbjct: 541 DFIEATRRIKNDLPHALISGGVSNVSFSFRGNEPVREAIHAVFLYHAIKAGMDMGIVNAG 600
Query: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
QLA+YDD+ +L++AVEDV+LNRRDD T+RLLEL+E+Y+G + EWR WEV+
Sbjct: 601 QLAVYDDIDEKLKEAVEDVVLNRRDDATDRLLELSEEYKGQ--GGGKKEENLEWREWEVS 658
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
KRLE+SLVKGI ++ DTEEARQ RPI+VIEGPLMDGMNVVGDLFGEGKMFLPQVVK
Sbjct: 659 KRLEHSLVKGIDTYVVDDTEEARQAYDRPIQVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 718
Query: 721 SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
SARVMK+AVA+L P+IEA K + NGK+++ATVKGDVHDIGKNIVGVVLQCNN+E++D+
Sbjct: 719 SARVMKKAVAHLIPYIEAEKTGTENNGKILMATVKGDVHDIGKNIVGVVLQCNNFEVIDI 778
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVM P +IL+ AKE + D+IGLSGLITPSL+EM N A ++ER+G T PL+IGGATTS+A
Sbjct: 779 GVMQPGAEILKAAKEHDVDVIGLSGLITPSLEEMANFAADLEREGMTTPLMIGGATTSRA 838
Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
HTAVKIE NYSGP V+V++ASR VGV +L+S R+++ A R+EYE +R+Q+ +K +
Sbjct: 839 HTAVKIEPNYSGPVVWVKDASRAVGVAQSLISPELRENYAAEIREEYEKLRVQNAGRKKK 898
Query: 901 TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV--------------------EASIET 940
++LE AR N DW AY P L +++ + +
Sbjct: 899 VQWLSLEKARANKPEIDWSAYAPAKPKALETEDLPGEPTVLHPHGDGSVLLRFDDFDLNK 958
Query: 941 LRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVG 1000
++ YIDWTPFF +W L YPRILEDE VG EA++LFKD +ML ++ EK + RGVVG
Sbjct: 959 VKEYIDWTPFFHSWQLHAAYPRILEDEKVGEEARKLFKDGQEMLQRMIDEKWVTCRGVVG 1018
Query: 1001 LFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYI 1058
FPAN V DDIE+Y DE R+ V+ HHLRQQTEK G ++ LADFV PK +G DYI
Sbjct: 1019 FFPANSVDHDDIEVYTDENRSQVLKKLHHLRQQTEKRRGQPSHSLADFVMPKEAGGPDYI 1078
Query: 1059 GAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNE 1118
GAFAV+ G + DA A+ +E +DDY+ I+VK+LADRLAEAFAE +HE VRK YWGY +E
Sbjct: 1079 GAFAVSAGGDVDAKAEEYEKANDDYHAILVKSLADRLAEAFAECMHEYVRKYYWGYVADE 1138
Query: 1119 NLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVS 1178
L NE+LI E YQGIRPAPGYPACPEHTEKAT+WELL+ E++ M LTES+AM P ++VS
Sbjct: 1139 QLENEDLIEEKYQGIRPAPGYPACPEHTEKATLWELLQAEENADMTLTESYAMLPVSAVS 1198
Query: 1179 GWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
GWYF+HP+S+Y+ + ++ RDQVEDYA+RKGMS E ERWLAPN+GYD
Sbjct: 1199 GWYFAHPESRYFGLGKVNRDQVEDYAKRKGMSFEEAERWLAPNIGYD 1245
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: 3925
Number of extensions: 158
Number of successful extensions: 5
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: 1263
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1215
Effective search space: 1432485
Effective search space used: 1432485
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_077243567.1 B1A74_RS01430 (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.12659.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 1765.7 0.0 0 1765.4 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077243567.1 B1A74_RS01430 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001995255.1:WP_077243567.1 B1A74_RS01430 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1765.4 0.0 0 0 1 1181 [. 12 1211 .. 12 1212 .. 0.98
Alignments for each domain:
== domain 1 score: 1765.4 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++ril+lDG+mGt++q ++L ead+rge ++d++++lkGnndlL+lt+P++i++ih++y+eaGaDi
lcl|NCBI__GCF_001995255.1:WP_077243567.1 12 LKERILILDGGMGTTIQLYELGEADYRGErFKDWESDLKGNNDLLSLTRPDIIEQIHNDYLEAGADI 78
579**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
+e ntFn+t ia+adY++ed++ eln+++aklar++ad +t +tp+k+RfvaG lGPtn++a++spd
lcl|NCBI__GCF_001995255.1:WP_077243567.1 79 IEANTFNGTRIAMADYHMEDLVPELNRESAKLARKAADAWTaKTPDKPRFVAGILGPTNRTASISPD 145
******************************************************************* PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p+ rnv++d+lv+aYke++++l++GGvDllLietvfDtlnakaa+fav+++ +e g++lPi+is
lcl|NCBI__GCF_001995255.1:WP_077243567.1 146 VNDPGARNVDFDTLVAAYKEAAEALIEGGVDLLLIETVFDTLNAKAAIFAVKTLEDELGKDLPIMIS 212
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266
g+i+d+sGrtLsGqt+eaf +s++ha+ +++GLnCalGa+e+r++v+els++a++ vs++PnaGLPn
lcl|NCBI__GCF_001995255.1:WP_077243567.1 213 GTITDASGRTLSGQTTEAFWNSVRHANPVSIGLNCALGAKEMRQYVEELSRIADTHVSAHPNAGLPN 279
******************************************************************* PP
TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
++g+Yd+ pe++a+ + +ae+g+lni+GGCCGt Pehira+ eav++ prk++e+ ++++lsgle
lcl|NCBI__GCF_001995255.1:WP_077243567.1 280 EFGDYDESPEQMAADVGPWAEQGMLNIIGGCCGTLPEHIRAMREAVEKFPPRKVPEVSPACRLSGLE 346
******************************************************************* PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
+ +i+++s fvn+GeRtnv+Gs+kf +li++e+y+ al++a +qve Gaqi+D+n+De++l+++ +m
lcl|NCBI__GCF_001995255.1:WP_077243567.1 347 PCNITDDSLFVNVGERTNVTGSRKFLRLIQNEEYDVALEVALNQVEGGAQIIDVNMDEGMLESQDAM 413
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
+++l+lla+epdia+vP+m+Dss+fe++eaGLk++qGk +vnsis+k+Gee+F+++a+l ++yGaa+
lcl|NCBI__GCF_001995255.1:WP_077243567.1 414 VRFLNLLAGEPDIARVPVMIDSSKFEIIEAGLKCVQGKPVVNSISMKEGEENFIKQAELCRRYGAAI 480
******************************************************************* PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
vvmafDe+Gqa++ ++++ei++Rayklltekvgfp+ediifDpni+++atGieeh++y++dfiea+r
lcl|NCBI__GCF_001995255.1:WP_077243567.1 481 VVMAFDEDGQADNEQRRVEICTRAYKLLTEKVGFPAEDIIFDPNIFAVATGIEEHNNYGVDFIEATR 547
******************************************************************* PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
+ik++lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+aikaG+Dmgivnag+lavyddid+ l+e
lcl|NCBI__GCF_001995255.1:WP_077243567.1 548 RIKNDLPHALISGGVSNVSFSFRGNEPVREAIHAVFLYHAIKAGMDMGIVNAGQLAVYDDIDEKLKE 614
******************************************************************* PP
TIGR02082 602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668
+ved++l+rr++at++Llel e ykg+ k++++ ewr+++v++RLe++lvkG+ ++ +d+ee
lcl|NCBI__GCF_001995255.1:WP_077243567.1 615 AVEDVVLNRRDDATDRLLELSEEYKGQGGG--KKEENLEWREWEVSKRLEHSLVKGIDTYVVDDTEE 679
***************************999..778999***************************** PP
TIGR02082 669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGk 735
ar+ + +p+++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkava+L+Py+e+ek+ ++++Gk
lcl|NCBI__GCF_001995255.1:WP_077243567.1 680 ARQAYDRPIQVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKKAVAHLIPYIEAEKTGTENNGK 746
******************************************************************* PP
TIGR02082 736 ivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemv 802
i++atvkGDvhDiGkniv+vvL+cn++ev+d+Gv++P ++il+aak+++ DviglsGLi++sl+em+
lcl|NCBI__GCF_001995255.1:WP_077243567.1 747 ILMATVKGDVHDIGKNIVGVVLQCNNFEVIDIGVMQPGAEILKAAKEHDVDVIGLSGLITPSLEEMA 813
******************************************************************* PP
TIGR02082 803 evaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelek 869
+ a ++er+g+++Pl++GGa++s+ah+avki+++Y+g+vv+vkdas+av v+++l+s + +++++++
lcl|NCBI__GCF_001995255.1:WP_077243567.1 814 NFAADLEREGMTTPLMIGGATTSRAHTAVKIEPNYSGPVVWVKDASRAVGVAQSLISPELRENYAAE 880
******************************************************************* PP
TIGR02082 870 ikeeyeeirekfgekkeklialsekaarkevfaldrse................dlevpapkflGtk 920
i+eeye++r + +k+k++ ls+++ar ++ ++d+s + +v +p+ G+
lcl|NCBI__GCF_001995255.1:WP_077243567.1 881 IREEYEKLRVQNAGRKKKVQWLSLEKARANKPEIDWSAyapakpkaletedlpgEPTVLHPHGDGSV 947
*************************************999999999999988888888889999988 PP
TIGR02082 921 vleas...ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrar 984
l+ ++++ +yiDw+++F +W+l+ yp+il+de++g+earklfkd +e+l++++ ek +++r
lcl|NCBI__GCF_001995255.1:WP_077243567.1 948 LLRFDdfdLNKVKEYIDWTPFFHSWQLHAAYPRILEDEKVGEEARKLFKDGQEMLQRMIDEKWVTCR 1014
77644459*********************************************************** PP
TIGR02082 985 gvvGlfPaqsv.gddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDyl 1049
gvvG+fPa+sv +ddie+ytde +sq k++ +r +q+++ +++ +laDf+ +ke+G Dy+
lcl|NCBI__GCF_001995255.1:WP_077243567.1 1015 GVVGFFPANSVdHDDIEVYTDENRSQVLKKLHHLR---QQTEKRRGQpSHSLADFVMPKEAGGPDYI 1078
*********873699*********88777777765...666666666689***************** PP
TIGR02082 1050 gallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedl 1116
ga++v+ag +++ a+++e+ +ddy++ilvk+ladrlaea+ae +he vRk +wgy ++e+l++edl
lcl|NCBI__GCF_001995255.1:WP_077243567.1 1079 GAFAVSAGGDVDAKAEEYEKANDDYHAILVKSLADRLAEAFAECMHEYVRKYYWGYVADEQLENEDL 1145
******************************************************************* PP
TIGR02082 1117 lkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfa 1181
+ e+Y+Girpa+GYpacP+htekatl+eLl+ae+ ++ltes+a+ P ++vsg+yfahpe++Yf
lcl|NCBI__GCF_001995255.1:WP_077243567.1 1146 IEEKYQGIRPAPGYPACPEHTEKATLWELLQAEEnADMTLTESYAMLPVSAVSGWYFAHPESRYFG 1211
********************************999******************************5 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1263 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: 00:00:00.10
# Mc/sec: 13.71
//
[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