Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate CA265_RS23440 CA265_RS23440 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__Pedo557:CA265_RS23440
Length = 1233
Score = 1476 bits (3822), Expect = 0.0
Identities = 741/1235 (60%), Positives = 927/1235 (75%), Gaps = 22/1235 (1%)
Query: 8 LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
+R +L +RILV+DG MGTMIQ Y L E DFRGERF + PCD+KGNNDLL +++P++I I
Sbjct: 3 IREELEKRILVIDGAMGTMIQRYTLTEEDFRGERFKNHPCDVKGNNDLLNITRPDIIKTI 62
Query: 68 HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
H Y +GADIIETNTF++ I+MADYQME LS E++F A++A+ +E+ A P++
Sbjct: 63 HLEYLASGADIIETNTFSTQRISMADYQMEDLSYEMSFEGARVAKEAVNEFMAANPDRKC 122
Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
+VAG +GPTNRT S+SP+VNDP FR + FD L AAY E + LV+GG+D++LIET+FDTL
Sbjct: 123 FVAGAIGPTNRTLSMSPNVNDPGFRAVYFDELEAAYYEQVRGLVDGGSDVLLIETIFDTL 182
Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
NAK A+ A+K E +G +L IMISGTITDASGRTLSGQT EAF NS+ HA+ L+ G NC
Sbjct: 183 NAKVAIVAIKKYEEVIGRKLEIMISGTITDASGRTLSGQTAEAFLNSVMHAKPLSIGFNC 242
Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307
ALG E+R +++EL+ A CYV+A+PNAGLPN FG YD A + ++ +GF+NIV
Sbjct: 243 ALGAKEMRPHIEELAAKAGCYVSAYPNAGLPNEFGAYDEQPHETAHLVDDFIASGFVNIV 302
Query: 308 GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTG 367
GGCCGTTP+HI +++ PRK+P + RLSGLEP+ I +S+FVN+GERTN+TG
Sbjct: 303 GGCCGTTPEHIGCIAKNARKAEPRKIPVLEPYMRLSGLEPVTITPESIFVNIGERTNITG 362
Query: 368 SAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIA 427
S KF +LI Y AL VA QQVE GAQ+ID+NMDEGMLD+EAAM +FLNLIA EPDIA
Sbjct: 363 SPKFSKLILGGDYEAALAVALQQVEGGAQVIDVNMDEGMLDSEAAMTKFLNLIASEPDIA 422
Query: 428 RVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDE 487
++PIM+DSSKW VIE GLKC+QGKGIVNSIS+KEG D F A+ + +YGAAVVVMAFDE
Sbjct: 423 KLPIMVDSSKWSVIENGLKCLQGKGIVNSISLKEGEDKFRESARKIMQYGAAVVVMAFDE 482
Query: 488 QGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACE 547
QGQAD R+ EIC+R+Y IL E+GFP EDIIFDPNI VATG+EEHNNYA DFI A
Sbjct: 483 QGQADNYERRKEICKRSYDILVNEIGFPAEDIIFDPNILTVATGLEEHNNYAVDFINATR 542
Query: 548 DIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDD 607
IK LPHA +SGGVSN+SFSFRGN+ VREA+H+ FLY+AI+ G+DMGIVNAG L +Y +
Sbjct: 543 WIKENLPHAKVSGGVSNISFSFRGNNTVREAMHSAFLYHAIQAGLDMGIVNAGMLEVYQE 602
Query: 608 LPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSL 667
+P EL + VEDV+LNRRDD TERL+E A+ K+ + EWR V +RL +SL
Sbjct: 603 IPPELLERVEDVLLNRRDDATERLVEYADTV---KSKGKEVVKDEEWRKGSVEERLSHSL 659
Query: 668 VKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQ 727
VKGI E+++ D EEARQ+ RPI+VIEGPLMDGMN+VGDLFG GKMFLPQVVKSARVMK+
Sbjct: 660 VKGIVEYLDDDVEEARQKYARPIQVIEGPLMDGMNIVGDLFGAGKMFLPQVVKSARVMKK 719
Query: 728 AVAYLEPFIEASK------EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
AVAYL PFIE K +Q + G++++ATVKGDVHDIGKNIVGVVL CNN+EIVD+G
Sbjct: 720 AVAYLLPFIEQEKLDNPDQDQNSSAGRVLMATVKGDVHDIGKNIVGVVLACNNFEIVDMG 779
Query: 782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
VMVPA++I++ AKE+NAD+IGLSGLITPSLDEMV+ AKEMER+GFTIPL+IGGATTS+ H
Sbjct: 780 VMVPAQEIIKKAKEINADIIGLSGLITPSLDEMVHFAKEMEREGFTIPLIIGGATTSRIH 839
Query: 842 TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
AVK+ NYSGP ++V +ASR+V V + L++ +D++VA R EY+ R H K+
Sbjct: 840 AAVKVAPNYSGPAIHVLDASRSVTVCSTLMNPETKDEYVAGIRAEYDKAREAHLNKRSDK 899
Query: 902 PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKY 960
TLE AR+N F D+Q PV G + + +E L YIDWTPFF TW L G Y
Sbjct: 900 RFKTLEEARENRFKIDFQP-NLPVPEFTGTRVFDNYPLEELVPYIDWTPFFHTWELRGSY 958
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRD---- 1016
P+I +D+ VG EA++LF DA +L ++ EK L R V+G +PAN VGDDI++ D
Sbjct: 959 PKIFDDKNVGDEAKKLFDDAQTLLKRILDEKLLTARAVIGFWPANTVGDDIQLTVDSSQL 1018
Query: 1017 ------ETRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEE 1069
+T + H LRQQ EK G Y L+DF+APK SG DY G FAVT G+
Sbjct: 1019 SNDSKLKTENSQLVTIHTLRQQAEKVDGQPYYALSDFIAPKESGIQDYFGGFAVTAGIGI 1078
Query: 1070 DALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIREN 1129
D L + FE+ +DDYN IM KALADRLAEAFAE +HERVRK YWGYA +ENLSN+ELI+E
Sbjct: 1079 DELVNEFESNYDDYNSIMAKALADRLAEAFAERMHERVRKEYWGYAQDENLSNQELIKEE 1138
Query: 1130 YQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKY 1189
Y GIRPAPGYPACPEHTEK T+++LL+ E G+ LTES+AM+P A+VSG+YF+HPDS+Y
Sbjct: 1139 YAGIRPAPGYPACPEHTEKGTLFQLLDAENKIGLHLTESYAMYPTAAVSGFYFAHPDSRY 1198
Query: 1190 YAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGY 1224
+ + +I +DQ+EDYA RK M V EVERWL+PNL Y
Sbjct: 1199 FGLGKITKDQIEDYAIRKNMPVEEVERWLSPNLAY 1233
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: 3661
Number of extensions: 153
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: 1233
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1186
Effective search space: 1399480
Effective search space used: 1399480
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 CA265_RS23440 CA265_RS23440 (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.2387.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 1780.3 0.1 0 1780.1 0.1 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS23440 CA265_RS23440 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS23440 CA265_RS23440 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1780.1 0.1 0 0 1 1181 [. 7 1200 .. 7 1201 .. 0.99
Alignments for each domain:
== domain 1 score: 1780.1 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaD 65
l+krilv+DGamGt++q++ Lte+dFrge ++++++++kGnndlLn+t+P++i++ih +y+ +GaD
lcl|FitnessBrowser__Pedo557:CA265_RS23440 7 LEKRILVIDGAMGTMIQRYTLTEEDFRGErFKNHPCDVKGNNDLLNITRPDIIKTIHLEYLASGAD 72
589*************************************************************** PP
TIGR02082 66 ivetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatls 130
i+etntF++ i++adY++ed++ye+++++a++a+e+ +ef +p++k fvaG++GPtn++ ++s
lcl|FitnessBrowser__Pedo557:CA265_RS23440 73 IIETNTFSTQRISMADYQMEDLSYEMSFEGARVAKEAVNEFMaANPDRKCFVAGAIGPTNRTLSMS 138
*****************************************999********************** PP
TIGR02082 131 pdverpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPi 196
p+v++p+fr v +del +aY eqv+gl+dGG D+lLiet+fDtlnak a++a+++ e gr+l i
lcl|FitnessBrowser__Pedo557:CA265_RS23440 139 PNVNDPGFRAVYFDELEAAYYEQVRGLVDGGSDVLLIETIFDTLNAKVAIVAIKKYEEVIGRKLEI 204
****************************************************************** PP
TIGR02082 197 lisgvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPna 262
+isg+i+d+sGrtLsGqt eafl+s+ ha+ l++G nCalGa+e+r++++el+++a ++vs++Pna
lcl|FitnessBrowser__Pedo557:CA265_RS23440 205 MISGTITDASGRTLSGQTAEAFLNSVMHAKPLSIGFNCALGAKEMRPHIEELAAKAGCYVSAYPNA 270
****************************************************************** PP
TIGR02082 263 GLPnalgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksv 328
GLPn++g Yd++p+e+a+ + +f++ g++nivGGCCGttPehi ia+ +++ +prk + le++++
lcl|FitnessBrowser__Pedo557:CA265_RS23440 271 GLPNEFGAYDEQPHETAHLVDDFIASGFVNIVGGCCGTTPEHIGCIAKNARKAEPRKIPVLEPYMR 336
****************************************************************** PP
TIGR02082 329 lsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevll 394
lsgle+++i++es fvniGeRtn++Gs kf+kli +dye+al +a qqve Gaq++D+n+De++l
lcl|FitnessBrowser__Pedo557:CA265_RS23440 337 LSGLEPVTITPESIFVNIGERTNITGSPKFSKLILGGDYEAALAVALQQVEGGAQVIDVNMDEGML 402
****************************************************************** PP
TIGR02082 395 DgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekakli 460
D+ea+m+k+l+l+asepdiak+P+m+Dss++ v+e GLk++qGk+ivnsislk+Ge++F e+a++i
lcl|FitnessBrowser__Pedo557:CA265_RS23440 403 DSEAAMTKFLNLIASEPDIAKLPIMVDSSKWSVIENGLKCLQGKGIVNSISLKEGEDKFRESARKI 468
****************************************************************** PP
TIGR02082 461 keyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdrya 526
+yGaavvvmafDe+Gqa++++++ ei+kR y++l++++gfp+ediifDpnilt+atG+eeh++ya
lcl|FitnessBrowser__Pedo557:CA265_RS23440 469 MQYGAAVVVMAFDEQGQADNYERRKEICKRSYDILVNEIGFPAEDIIFDPNILTVATGLEEHNNYA 534
****************************************************************** PP
TIGR02082 527 idfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavy 592
+dfi+a+r+ike+lP+ak+sgGvsn+sFs+rgn++vRea+hs FLy+ai+aGlDmgivnag+l+vy
lcl|FitnessBrowser__Pedo557:CA265_RS23440 535 VDFINATRWIKENLPHAKVSGGVSNISFSFRGNNTVREAMHSAFLYHAIQAGLDMGIVNAGMLEVY 600
****************************************************************** PP
TIGR02082 593 ddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGe 658
++i++el+e ved++l+rr++ate+L+e+a++ k + ++ + + +ewr+ +veeRL+++lvkG+
lcl|FitnessBrowser__Pedo557:CA265_RS23440 601 QEIPPELLERVEDVLLNRRDDATERLVEYADTVKSKGKE---VVKDEEWRKGSVEERLSHSLVKGI 663
********************************8888777...6789******************** PP
TIGR02082 659 regieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePyle 724
e++++d+eear+k+ +p+++iegpL+dGm++vGdLFG+GkmfLPqvvksarvmkkavayL P++e
lcl|FitnessBrowser__Pedo557:CA265_RS23440 664 VEYLDDDVEEARQKYARPIQVIEGPLMDGMNIVGDLFGAGKMFLPQVVKSARVMKKAVAYLLPFIE 729
****************************************************************** PP
TIGR02082 725 kekeed......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkk 784
+ek ++ +s+G++++atvkGDvhDiGkniv+vvL+cn++e+vd+Gv+vP+++i+++ak+ +
lcl|FitnessBrowser__Pedo557:CA265_RS23440 730 QEKLDNpdqdqnSSAGRVLMATVKGDVHDIGKNIVGVVLACNNFEIVDMGVMVPAQEIIKKAKEIN 795
**988888888899**************************************************** PP
TIGR02082 785 aDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdasea 850
aD+iglsGLi++sldemv+ a+emer+g++iPl++GGa++s+ h avk+a++Y+g+ ++v das++
lcl|FitnessBrowser__Pedo557:CA265_RS23440 796 ADIIGLSGLITPSLDEMVHFAKEMEREGFTIPLIIGGATTSRIHAAVKVAPNYSGPAIHVLDASRS 861
****************************************************************** PP
TIGR02082 851 vkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkf 916
v+v+++l++ ++k+e+++ i++ey+++re + +k++ ++ ++++ar+++f++d + + p+p+f
lcl|FitnessBrowser__Pedo557:CA265_RS23440 862 VTVCSTLMNPETKDEYVAGIRAEYDKAREAHLNKRSDKRFKTLEEARENRFKIDFQ--PNLPVPEF 925
*******************************************************9..99****** PP
TIGR02082 917 lGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekll 981
Gt+v++++ +eel++yiDw+++F +Welrg+ypki++d+ +g ea+klf+da+ ll+++ ekll
lcl|FitnessBrowser__Pedo557:CA265_RS23440 926 TGTRVFDNYpLEELVPYIDWTPFFHTWELRGSYPKIFDDKNVGDEAKKLFDDAQTLLKRILDEKLL 991
****************************************************************** PP
TIGR02082 982 rargvvGlfPaqsvgddieiytdetvsq...etkpiatvrekleqlrqqsdr.....ylclaDfia 1039
+ar+v+G++Pa++vgddi++ d + + k+ ++ + ++lrqq ++ y++l+Dfia
lcl|FitnessBrowser__Pedo557:CA265_RS23440 992 TARAVIGFWPANTVGDDIQLTVDSSQLSndsKLKTENSQLVTIHTLRQQAEKvdgqpYYALSDFIA 1057
********************98876533233677788888889*******999999********** PP
TIGR02082 1040 skesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgy 1105
+kesGi+Dy+g ++vtag+g++el +++e + ddy+si+ kaladrlaea+ae +hervRke+wgy
lcl|FitnessBrowser__Pedo557:CA265_RS23440 1058 PKESGIQDYFGGFAVTAGIGIDELVNEFESNYDDYNSIMAKALADRLAEAFAERMHERVRKEYWGY 1123
****************************************************************** PP
TIGR02082 1106 aeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsgl 1170
a++enl++++l+ke+Y Girpa+GYpacP+htek tl++Ll+ae+ iGl+ltes+a++P+a+vsg+
lcl|FitnessBrowser__Pedo557:CA265_RS23440 1124 AQDENLSNQELIKEEYAGIRPAPGYPACPEHTEKGTLFQLLDAENkIGLHLTESYAMYPTAAVSGF 1189
********************************************99******************** PP
TIGR02082 1171 yfahpeakYfa 1181
yfahp+++Yf
lcl|FitnessBrowser__Pedo557:CA265_RS23440 1190 YFAHPDSRYFG 1200
**********5 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1233 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: 0.11u 0.05s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 9.11
//
[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