Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 5208198 Shew_0710 B12-dependent methionine synthase (RefSeq)
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__PV4:5208198
Length = 1240
Score = 1612 bits (4175), Expect = 0.0
Identities = 812/1227 (66%), Positives = 966/1227 (78%), Gaps = 9/1227 (0%)
Query: 6 EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
+ +RA+LN+ IL+LDG MGTMIQ+++L EADFRGERF WPCDLKGNNDLLVL++PE+I
Sbjct: 15 DAIRARLNKEILILDGAMGTMIQNHKLEEADFRGERFKQWPCDLKGNNDLLVLTQPELIK 74
Query: 66 AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
IH Y AGADIIETNTFN+T +AMADY+M+ LS EIN A+LAR DE A + +
Sbjct: 75 QIHRDYLLAGADIIETNTFNATQVAMADYEMQELSREINLEGARLARTACDEVAAESGRQ 134
Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
YVAGVLGPTNRT SISPDVNDP +RNI FD LV AY EST+AL+EGGAD+I++ET+FD
Sbjct: 135 C-YVAGVLGPTNRTCSISPDVNDPGYRNIHFDDLVEAYIESTQALIEGGADIIMVETIFD 193
Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245
TLNAKAA+FA++T F+ LG LP+MISGTITDASGRTL+GQTTEAFYNSLRH + L+ GL
Sbjct: 194 TLNAKAALFAIETLFDQLGQRLPVMISGTITDASGRTLTGQTTEAFYNSLRHVKPLSIGL 253
Query: 246 NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305
NCALGP ELR YV+ELS+IAECYV+AHPNAGLPN FG YD + MA+ I WA+ G LN
Sbjct: 254 NCALGPQELRPYVEELSKIAECYVSAHPNAGLPNEFGGYDETPEQMAEVIGPWAEEGLLN 313
Query: 306 IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNV 365
I+GGCCGTTP HI A+ AV R+LP++PVACRLSGLEPL I DSLFVNVGERTNV
Sbjct: 314 IIGGCCGTTPDHIKAIRAAVIKHGARELPDLPVACRLSGLEPLTIDADSLFVNVGERTNV 373
Query: 366 TGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPD 425
TGSAKF RLIK +Y EAL VAR QVENGAQIIDINMDEGMLD M +FLNLIA EPD
Sbjct: 374 TGSAKFLRLIKTGEYEEALSVARDQVENGAQIIDINMDEGMLDGVEVMQKFLNLIASEPD 433
Query: 426 IARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAF 485
I+RVPIMIDSSKW+VIE GLKCIQGKG+VNSIS+KEG FI A L++RYGAA ++MAF
Sbjct: 434 ISRVPIMIDSSKWEVIEAGLKCIQGKGVVNSISLKEGEAKFIEQATLVKRYGAAAIIMAF 493
Query: 486 DEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGA 545
DE GQADT ARKIEIC RAY++L ++VGFPPEDIIFDPNIFA+ATGI+EH+NYA DFI A
Sbjct: 494 DEVGQADTMARKIEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHDNYAVDFIEA 553
Query: 546 CEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIY 605
+IKR LPHA+ISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAGQLAIY
Sbjct: 554 TREIKRTLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQLAIY 613
Query: 606 DDLPAELRDAVEDVILN-----RRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
DD+ +L+ VE V+ N + + TE+LLE+AE+YRG A + EWRSW VN
Sbjct: 614 DDIDPDLKARVEAVVQNLPCPVQGSNNTEQLLEIAEQYRGDGAAG-AKKEDLEWRSWPVN 672
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
KRLE++LVKGITEFI+QDTEEARQ A+RP++VIEGPLMDGMNVVGDLFG GKMFLPQVVK
Sbjct: 673 KRLEHALVKGITEFIDQDTEEARQLASRPLDVIEGPLMDGMNVVGDLFGSGKMFLPQVVK 732
Query: 721 SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
SARVMK+AVAYL P+IEA K +G++NGK+++ TVKGDVHDIGKNIVGVVL CN YE+VDL
Sbjct: 733 SARVMKKAVAYLNPYIEAEKVEGESNGKILMVTVKGDVHDIGKNIVGVVLACNGYEVVDL 792
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVP EKI+ AK D+IG+SGLITPSLDEMV+ K + G IP +IGGAT SK
Sbjct: 793 GVMVPVEKIIEVAKAEKVDIIGMSGLITPSLDEMVHNVKAFHKAGLNIPSIIGGATCSKI 852
Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
HTAVKI + +Y+ +ASR V +VA L++ R + +EY +R + + R
Sbjct: 853 HTAVKIAPHAPEGAIYIADASRAVPMVAKLINKETRQATIDAAYEEYRVMRDKRNSQAKR 912
Query: 901 TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGK 959
V+LEAAR+N DW A+TP V ++LG Q + +E L + IDWTPFF +W L G
Sbjct: 913 KQIVSLEAARENRCQQDWNAHTPFVPNQLGRQVFDDYPLEDLVDRIDWTPFFRSWELHGH 972
Query: 960 YPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDET 1018
+P+IL+DEVVG EA++L++DA ML + EK L + V+GLFPAN V DDIEIY DE+
Sbjct: 973 FPKILDDEVVGEEARKLYQDAKAMLKTIIDEKWLTAKAVIGLFPANTVNYDDIEIYTDES 1032
Query: 1019 RTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEA 1078
R+ V +HHLR Q E+ G N+CLADFVAPK SG ADY+G FAVT G D FEA
Sbjct: 1033 RSKVEMTTHHLRMQIERVGNDNFCLADFVAPKDSGVADYMGGFAVTAGHGIDEHVARFEA 1092
Query: 1079 QHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPG 1138
HDDY+ IM+K LADRL EAFAE +HERVRK +WGYA +ENL NE LIRE Y+GIRPAPG
Sbjct: 1093 NHDDYSAIMLKCLADRLVEAFAERMHERVRKEFWGYAADENLDNEALIREKYKGIRPAPG 1152
Query: 1139 YPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRD 1198
YPACP+HTEK +WELL+ ++ +K+TES+AM+P A+VSGWYF+HP S+Y+ V I RD
Sbjct: 1153 YPACPDHTEKGLLWELLKPDETIDLKITESYAMFPTAAVSGWYFAHPQSRYFGVTNIGRD 1212
Query: 1199 QVEDYARRKGMSVTEVERWLAPNLGYD 1225
QVEDYA+RKGMSV E ERWLAP L YD
Sbjct: 1213 QVEDYAKRKGMSVEETERWLAPVLDYD 1239
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: 3712
Number of extensions: 143
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: 1240
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1192
Effective search space: 1405368
Effective search space used: 1405368
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 5208198 Shew_0710 (B12-dependent methionine synthase (RefSeq))
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.17482.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 1758.5 0.1 0 1758.3 0.1 1.0 1 lcl|FitnessBrowser__PV4:5208198 Shew_0710 B12-dependent methioni
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208198 Shew_0710 B12-dependent methionine synthase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1758.3 0.1 0 0 1 1182 [] 21 1206 .. 21 1206 .. 0.98
Alignments for each domain:
== domain 1 score: 1758.3 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFnst 75
lnk+il+lDGamGt++q+++L+eadFrge +++++++lkGnndlL+lt+Pe+i++ihr+y+ aGaDi+etntFn+t
lcl|FitnessBrowser__PV4:5208198 21 LNKEILILDGAMGTMIQNHKLEEADFRGErFKQWPCDLKGNNDLLVLTQPELIKQIHRDYLLAGADIIETNTFNAT 96
6899************************************************************************ PP
TIGR02082 76 eialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvtydelvdaYk 151
++a+adY+++++++e+n ++a+lar ++de+ ++ ++ +vaG+lGPtn++ ++spdv++p++rn+++d+lv+aY
lcl|FitnessBrowser__PV4:5208198 97 QVAMADYEMQELSREINLEGARLARTACDEVAAESGRQCYVAGVLGPTNRTCSISPDVNDPGYRNIHFDDLVEAYI 172
**************************************************************************** PP
TIGR02082 152 eqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtleaflaslehaei 227
e++++l++GG+D++++et+fDtlnakaalfa+e++f++ g++lP++isg+i+d+sGrtL+Gqt+eaf++sl+h +
lcl|FitnessBrowser__PV4:5208198 173 ESTQALIEGGADIIMVETIFDTLNAKAALFAIETLFDQLGQRLPVMISGTITDASGRTLTGQTTEAFYNSLRHVKP 248
**************************************************************************** PP
TIGR02082 228 lilGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPe 303
l++GLnCalG++elr++v+els++ae++vs++PnaGLPn++g Yd+tpe++a+++ +aeegllni+GGCCGttP+
lcl|FitnessBrowser__PV4:5208198 249 LSIGLNCALGPQELRPYVEELSKIAECYVSAHPNAGLPNEFGGYDETPEQMAEVIGPWAEEGLLNIIGGCCGTTPD 324
**************************************************************************** PP
TIGR02082 304 hiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqve 379
hi+ai +av + r+ ++l+ +++lsgle+l+i+ +s fvn+GeRtnv+Gs+kf +lik ++yeeal++a++qve
lcl|FitnessBrowser__PV4:5208198 325 HIKAIRAAVIKHGARELPDLPVACRLSGLEPLTIDADSLFVNVGERTNVTGSAKFLRLIKTGEYEEALSVARDQVE 400
**************************************************************************** PP
TIGR02082 380 eGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455
+Gaqi+Din+De++lDg++ m+k+l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk++vnsislk+Ge++F+e
lcl|FitnessBrowser__PV4:5208198 401 NGAQIIDINMDEGMLDGVEVMQKFLNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGVVNSISLKEGEAKFIE 476
**************************************************************************** PP
TIGR02082 456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfie 531
+a l+k+yGaa+++mafDe Gqa+t+++kiei++Ray++l++kvgfppediifDpni++iatGi+ehd+ya+dfie
lcl|FitnessBrowser__PV4:5208198 477 QATLVKRYGAAAIIMAFDEVGQADTMARKIEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHDNYAVDFIE 552
**************************************************************************** PP
TIGR02082 532 aireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedli 607
a+reik++lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+la+yddid++l+ ve ++
lcl|FitnessBrowser__PV4:5208198 553 ATREIKRTLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQLAIYDDIDPDLKARVEAVV 628
**************************************************************************** PP
TIGR02082 608 ldrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkaple 678
+ +++te+Lle+ae+y+g ++ + +++ ewr++pv++RLe+alvkG++e+i++d+eear+ +++pl+
lcl|FitnessBrowser__PV4:5208198 629 QNLPcpvqgSNNTEQLLEIAEQYRGDGAAGA-KKEDLEWRSWPVNKRLEHALVKGITEFIDQDTEEARQLASRPLD 703
*977777779*****************9955.58899*************************************** PP
TIGR02082 679 iiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivd 754
+iegpL+dGm+vvGdLFGsGkmfLPqvvksarvmkkavayL+Py+e+ek e +s+Gki++ tvkGDvhDiGkniv+
lcl|FitnessBrowser__PV4:5208198 704 VIEGPLMDGMNVVGDLFGSGKMFLPQVVKSARVMKKAVAYLNPYIEAEKVEGESNGKILMVTVKGDVHDIGKNIVG 779
**************************************************************************** PP
TIGR02082 755 vvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahva 830
vvL+cngyevvdlGv+vPveki+e+ak +k D+ig+sGLi++sldemv++++ +++ g++iP ++GGa+ sk h+a
lcl|FitnessBrowser__PV4:5208198 780 VVLACNGYEVVDLGVMVPVEKIIEVAKAEKVDIIGMSGLITPSLDEMVHNVKAFHKAGLNIPSIIGGATCSKIHTA 855
**************************************************************************** PP
TIGR02082 831 vkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrs 906
vkia++ +y das+av +v+kl++++++++ +++ eey +r k +++ ++++ +s++aar+++ + d++
lcl|FitnessBrowser__PV4:5208198 856 VKIAPHAPEGAIYIADASRAVPMVAKLINKETRQATIDAAYEEYRVMRDKRNSQAKRKQIVSLEAARENRCQQDWN 931
**************************************************************************** PP
TIGR02082 907 edlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekll 981
+ ++ +p++lG++v++++ +e+l++ iDw+++F +Wel+g++pkil+de++g+earkl++dak++l++++ ek l
lcl|FitnessBrowser__PV4:5208198 932 -AHTPFVPNQLGRQVFDDYpLEDLVDRIDWTPFFRSWELHGHFPKILDDEVVGEEARKLYQDAKAMLKTIIDEKWL 1006
.999************************************************************************ PP
TIGR02082 982 rargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvta 1056
+a++v+GlfPa++v+ ddieiytde++s +++t + + q+++ + + claDf+a+k+sG +Dy+g ++vta
lcl|FitnessBrowser__PV4:5208198 1007 TAKAVIGLFPANTVNyDDIEIYTDESRS--KVEMTTH-HLRMQIERVGNDNFCLADFVAPKDSGVADYMGGFAVTA 1079
************77549********993..3344444.4455555556669************************* PP
TIGR02082 1057 glgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpa 1132
g g++e ++ea++ddy++i++k ladrl ea+ae +hervRke+wgya++enld+e l++e+Y+Girpa+GYpa
lcl|FitnessBrowser__PV4:5208198 1080 GHGIDEHVARFEANHDDYSAIMLKCLADRLVEAFAERMHERVRKEFWGYAADENLDNEALIREKYKGIRPAPGYPA 1155
**************************************************************************** PP
TIGR02082 1133 cPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
cPdhtek l+eLl++++ i lk+tes+a+ P+a+vsg+yfahp+++Yf v
lcl|FitnessBrowser__PV4:5208198 1156 CPDHTEKGLLWELLKPDEtIDLKITESYAMFPTAAVSGWYFAHPQSRYFGV 1206
***************9888******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1240 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 0.04s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 11.50
//
[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