Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate BWI76_RS01685 BWI76_RS01685 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__Koxy:BWI76_RS01685
Length = 1227
Score = 2321 bits (6015), Expect = 0.0
Identities = 1158/1227 (94%), Positives = 1192/1227 (97%)
Query: 1 MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60
MSSKVEQLR QL RILVLDGGMGTMIQSYRL+E DFRGERFADWPCDLKGNNDLLVLSK
Sbjct: 1 MSSKVEQLRQQLKARILVLDGGMGTMIQSYRLSEQDFRGERFADWPCDLKGNNDLLVLSK 60
Query: 61 PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120
PEVI AIH+AYFEAGADIIETNTFNSTTIAMADYQMESLSAEINF AAKLARA AD WTA
Sbjct: 61 PEVITAIHDAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFTAAKLARASADAWTA 120
Query: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180
RTPEKPRYVAGVLGPTNRTASISPDVNDPA+RNITFDGLV AYRESTKALVEGGADLILI
Sbjct: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAYRNITFDGLVEAYRESTKALVEGGADLILI 180
Query: 181 ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240
ETVFDTLNAKAA+FAVK EFEALGV+LPIMISGTITDASGRTLSGQTTEAFYNSLRHA+A
Sbjct: 181 ETVFDTLNAKAAIFAVKEEFEALGVDLPIMISGTITDASGRTLSGQTTEAFYNSLRHADA 240
Query: 241 LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300
LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMA QIREWA+
Sbjct: 241 LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAAQIREWAE 300
Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
AGFLNIVGGCCGTTP+HIAAMS AV GL PR+LPEIPVACRLSGLEPLNIG+DSLFVNVG
Sbjct: 301 AGFLNIVGGCCGTTPEHIAAMSHAVAGLPPRQLPEIPVACRLSGLEPLNIGDDSLFVNVG 360
Query: 361 ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
ERTNVTGSAKFKRLIKEEKY+EALDVARQQVE+GAQIIDINMDEGMLDAEAAM RFLNLI
Sbjct: 361 ERTNVTGSAKFKRLIKEEKYNEALDVARQQVESGAQIIDINMDEGMLDAEAAMTRFLNLI 420
Query: 421 AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
AGEPDIARVPIMIDSSKW+VIEKGLKCIQGKGIVNSISMKEGV+ FI HAK +RRYGAAV
Sbjct: 421 AGEPDIARVPIMIDSSKWEVIEKGLKCIQGKGIVNSISMKEGVEPFIQHAKKVRRYGAAV 480
Query: 481 VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
VVMAFDE GQADTR RKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ
Sbjct: 481 VVMAFDEVGQADTRERKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
Query: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG
Sbjct: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
Query: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
QLAIYDDLPAELRDAVEDVILNRRDDGTERLL+LAEKYRGSKTDDTANAQQAEWRSW+V
Sbjct: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLDLAEKYRGSKTDDTANAQQAEWRSWDVK 660
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
KRLEYSLVKGITEFIE DTEEARQQA RPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK
Sbjct: 661 KRLEYSLVKGITEFIELDTEEARQQAARPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
Query: 721 SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
SARVMKQAVAYLEP++EASKE+G +NGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL
Sbjct: 721 SARVMKQAVAYLEPYLEASKEKGSSNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPA+KIL+TA+EVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA
Sbjct: 781 GVMVPADKILKTAREVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
HTAVKIEQNYSGPTVYVQNASRTVGVVAALLS TQRDDFVARTRKEYETVRIQHGRKKPR
Sbjct: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSATQRDDFVARTRKEYETVRIQHGRKKPR 900
Query: 901 TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY 960
TPPVTLEAARDND AFDW++YTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY
Sbjct: 901 TPPVTLEAARDNDLAFDWESYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY 960
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
PRILEDEVVG EA+RLF DAN++LDKLSAEKTLNPRGVVGLFPANRVGDD+EIYRDETRT
Sbjct: 961 PRILEDEVVGEEAKRLFSDANELLDKLSAEKTLNPRGVVGLFPANRVGDDVEIYRDETRT 1020
Query: 1021 HVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQH 1080
HV+ V HHLRQQTEK GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADA+EAQH
Sbjct: 1021 HVLTVGHHLRQQTEKVGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAYEAQH 1080
Query: 1081 DDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYP 1140
DDYNKIMVKA+ADRLAEAFAEYLHERVRKVYWGYA NENLSNEELIRENYQGIRPAPGYP
Sbjct: 1081 DDYNKIMVKAIADRLAEAFAEYLHERVRKVYWGYAANENLSNEELIRENYQGIRPAPGYP 1140
Query: 1141 ACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV 1200
ACPEHTEKATIW LLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKY+AVAQIQRDQV
Sbjct: 1141 ACPEHTEKATIWALLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYFAVAQIQRDQV 1200
Query: 1201 EDYARRKGMSVTEVERWLAPNLGYDAD 1227
EDYA RKGMSV EVERWLAPNLGYDAD
Sbjct: 1201 EDYALRKGMSVAEVERWLAPNLGYDAD 1227
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: 3977
Number of extensions: 134
Number of successful extensions: 1
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: 1227
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1180
Effective search space: 1392400
Effective search space used: 1392400
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 BWI76_RS01685 BWI76_RS01685 (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.28128.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 1955.1 0.0 0 1954.9 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS01685 BWI76_RS01685 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS01685 BWI76_RS01685 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1954.9 0.0 0 0 2 1182 .] 13 1192 .. 12 1192 .. 0.99
Alignments for each domain:
== domain 1 score: 1954.9 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivet 69
+ rilvlDG+mGt++qs++L e+dFrge +ad++++lkGnndlL+l+kPevi+aih ayfeaGaDi+et
lcl|FitnessBrowser__Koxy:BWI76_RS01685 13 KARILVLDGGMGTMIQSYRLSEQDFRGErFADWPCDLKGNNDLLVLSKPEVITAIHDAYFEAGADIIET 81
689****************************************************************** PP
TIGR02082 70 ntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpe 137
ntFnst+ia+adY++e++++e+n++aaklar+ ad +t +tpek+R+vaG+lGPtn++a++spdv++p+
lcl|FitnessBrowser__Koxy:BWI76_RS01685 82 NTFNSTTIAMADYQMESLSAEINFTAAKLARASADAWTaRTPEKPRYVAGVLGPTNRTASISPDVNDPA 150
********************************************************************* PP
TIGR02082 138 frnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdks 206
+rn+t+d lv+aY+e++k+l++GG+Dl+LietvfDtlnakaa+fav+e+fe+ g++lPi+isg+i+d+s
lcl|FitnessBrowser__Koxy:BWI76_RS01685 151 YRNITFDGLVEAYRESTKALVEGGADLILIETVFDTLNAKAAIFAVKEEFEALGVDLPIMISGTITDAS 219
********************************************************************* PP
TIGR02082 207 GrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltp 275
GrtLsGqt+eaf++sl+ha++l++GLnCalG+delr++v+els++ae++v+++PnaGLPna+geYdl++
lcl|FitnessBrowser__Koxy:BWI76_RS01685 220 GRTLSGQTTEAFYNSLRHADALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDA 288
********************************************************************* PP
TIGR02082 276 eelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfv 344
+++a++++e+ae+g+lnivGGCCGttPehi+a+++av+++ pr+ +e++ +++lsgle+l+i+++s fv
lcl|FitnessBrowser__Koxy:BWI76_RS01685 289 DTMAAQIREWAEAGFLNIVGGCCGTTPEHIAAMSHAVAGLPPRQLPEIPVACRLSGLEPLNIGDDSLFV 357
********************************************************************* PP
TIGR02082 345 niGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdi 413
n+GeRtnv+Gs+kf++lik+e+y+eal++a+qqve+Gaqi+Din+De++lD+ea+m+++l+l+a+epdi
lcl|FitnessBrowser__Koxy:BWI76_RS01685 358 NVGERTNVTGSAKFKRLIKEEKYNEALDVARQQVESGAQIIDINMDEGMLDAEAAMTRFLNLIAGEPDI 426
********************************************************************* PP
TIGR02082 414 akvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartad 482
a+vP+m+Dss++ev+e+GLk+iqGk+ivnsis+k+G+e F+++ak++++yGaavvvmafDe Gqa+t++
lcl|FitnessBrowser__Koxy:BWI76_RS01685 427 ARVPIMIDSSKWEVIEKGLKCIQGKGIVNSISMKEGVEPFIQHAKKVRRYGAAVVVMAFDEVGQADTRE 495
********************************************************************* PP
TIGR02082 483 kkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsn 551
+kiei++Rayk+lte+vgfppediifDpni+++atGieeh++ya+dfi a+++ik+elP+a isgGvsn
lcl|FitnessBrowser__Koxy:BWI76_RS01685 496 RKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSN 564
********************************************************************* PP
TIGR02082 552 vsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLle 620
vsFs+rgnd+vRea+h+vFLy+ai++G+Dmgivnag+la+ydd+++elr++ved+il+rr++ te+Ll+
lcl|FitnessBrowser__Koxy:BWI76_RS01685 565 VSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLD 633
********************************************************************* PP
TIGR02082 621 laelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmk 689
lae+y+g k++++++aq+aewr+++v++RLe++lvkG++e+ie d+eear+++ +p+e+iegpL+dGm+
lcl|FitnessBrowser__Koxy:BWI76_RS01685 634 LAEKYRGSKTDDTANAQQAEWRSWDVKKRLEYSLVKGITEFIELDTEEARQQAARPIEVIEGPLMDGMN 702
********************************************************************* PP
TIGR02082 690 vvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLs 758
vvGdLFG+GkmfLPqvvksarvmk+avayLePyle++ke+ +s+Gk+v+atvkGDvhDiGkniv+vvL+
lcl|FitnessBrowser__Koxy:BWI76_RS01685 703 VVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPYLEASKEKGSSNGKMVIATVKGDVHDIGKNIVGVVLQ 771
********************************************************************* PP
TIGR02082 759 cngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalska 827
cn+ye+vdlGv+vP++kil++a++ +aD+iglsGLi++sldemv+va+emer+g++iPll+GGa++ska
lcl|FitnessBrowser__Koxy:BWI76_RS01685 772 CNNYEIVDLGVMVPADKILKTAREVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
********************************************************************* PP
TIGR02082 828 hvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaa 896
h+avki+++Y+g++vyv++as++v vv++lls+++++++++++++eye++r ++g+kk ++ ++++aa
lcl|FitnessBrowser__Koxy:BWI76_RS01685 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSATQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAA 909
********************************************************************* PP
TIGR02082 897 rkevfaldrsedlevpapkflGtkvleasieellkyiDwkalFvqWelrgkypkilkdeleglearklf 965
r++++a+d++ +++p++++lG++++easie+l++yiDw+++F++W+l+gkyp+il+de++g+ea++lf
lcl|FitnessBrowser__Koxy:BWI76_RS01685 910 RDNDLAFDWE-SYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGEEAKRLF 977
**********.9********************************************************* PP
TIGR02082 966 kdakelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.... 1030
+da+elldklsaek+l++rgvvGlfPa++vgdd+eiy+det+ t+++++ ++lrqq+++
lcl|FitnessBrowser__Koxy:BWI76_RS01685 978 SDANELLDKLSAEKTLNPRGVVGLFPANRVGDDVEIYRDETR---THVLTVG----HHLRQQTEKvgfa 1039
****************************************99...7777777....6777777777777 PP
TIGR02082 1031 ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervR 1099
++claDf+a+k sG++Dy+ga++vt gl++++la+++ea++ddy++i+vka+adrlaea+ae+lhervR
lcl|FitnessBrowser__Koxy:BWI76_RS01685 1040 NYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAYEAQHDDYNKIMVKAIADRLAEAFAEYLHERVR 1108
********************************************************************* PP
TIGR02082 1100 kelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasv 1167
k +wgya++enl++e+l++e+Y+Girpa+GYpacP+htekat+++Lle+e+ +G+kltes+a++P asv
lcl|FitnessBrowser__Koxy:BWI76_RS01685 1109 KVYWGYAANENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWALLEVEKhTGMKLTESFAMWPGASV 1177
********************************************************************* PP
TIGR02082 1168 sglyfahpeakYfav 1182
sg+yf+hp++kYfav
lcl|FitnessBrowser__Koxy:BWI76_RS01685 1178 SGWYFSHPDSKYFAV 1192
*************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1227 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 0.04s 00:00:00.16 Elapsed: 00:00:00.16
# Mc/sec: 8.95
//
[ok]
This GapMind analysis is from Apr 09 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