Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate AO353_21615 AO353_21615 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_21615
Length = 1236
Score = 1608 bits (4165), Expect = 0.0
Identities = 820/1235 (66%), Positives = 975/1235 (78%), Gaps = 15/1235 (1%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
S+++ L+ L ERIL+LDGGMGTMIQS++L E D+RG+RFADWP D+KGNNDLLVLS+P
Sbjct: 5 SARLHVLKQALKERILILDGGMGTMIQSFKLEEQDYRGKRFADWPSDVKGNNDLLVLSRP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+VI AI Y +AGADI+ETNTFN+T ++ ADY M+ L+ E+N A+LAR AD T
Sbjct: 65 DVIGAIEKQYLDAGADILETNTFNATQVSQADYGMQGLAYELNVEGARLARKVADAKTLE 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
TP+KPR+VAGVLGPT+RT S+SPDVN+P +RN+TFD LV Y E+TK L+EGGADLILIE
Sbjct: 125 TPDKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FAV+ FE +G ELPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185 TIFDTLNAKAAIFAVQGVFEEVGFELPIMISGTITDASGRTLSGQTTEAFWNSIAHAKPI 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALG ELR Y++ELS A YV+AHPNAGLPN FGEYD AK I E+AQ+
Sbjct: 245 SVGLNCALGARELRPYLEELSNKASTYVSAHPNAGLPNEFGEYDELPVETAKVIEEFAQS 304
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
GFLNIVGGCCGTTP HI A+++AV G APR++P+IP ACRLSGLEP I SLFVNVGE
Sbjct: 305 GFLNIVGGCCGTTPGHIEAIAKAVAGYAPRQIPDIPKACRLSGLEPFTIDRSSLFVNVGE 364
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTN+TGSAKF RLI+E+ Y+EAL+VA QQVE GAQ+IDINMDEGMLD++ AMV FLNLIA
Sbjct: 365 RTNITGSAKFARLIREDNYTEALEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIA 424
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ FIHHAKL +RYGAAVV
Sbjct: 425 GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVV 484
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDE GQADT ARK EIC+R+Y IL EV FPPEDIIFDPNIFAVATGIEEHNNYA D
Sbjct: 485 VMAFDEAGQADTEARKKEICKRSYDILVNEVDFPPEDIIFDPNIFAVATGIEEHNNYAVD 544
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI AC I+ ELP+AL SGGVSNVSFSFRGN+PVREAIH+VFL YAIRNG+ MGIVNAGQ
Sbjct: 545 FINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRNGLTMGIVNAGQ 604
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
L IYD +PAELRDAVEDVILNR DGT+ LL +A+KY+G A+ EWR+W+VNK
Sbjct: 605 LEIYDQIPAELRDAVEDVILNRTPDGTDALLAIADKYKGD--GSVKEAETEEWRAWDVNK 662
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LVKGIT I +DTEE+R RPIEVIEGPLM GMN+VGDLFG GKMFLPQVVKS
Sbjct: 663 RLEHALVKGITTHIVEDTEESRLSFARPIEVIEGPLMSGMNIVGDLFGAGKMFLPQVVKS 722
Query: 722 ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
ARVMKQAVA+L PFIE K ++ + GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVDL
Sbjct: 723 ARVMKQAVAHLIPFIELEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDL 782
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPAEKIL+ AKE D+IGLSGLITPSLDEMV+VA+EM+RQ F +PL+IGGATTSKA
Sbjct: 783 GVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVHVAREMQRQDFHLPLMIGGATTSKA 842
Query: 841 HTAVKIEQNYSG-PTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
HTAVKIE YS VYV +ASR VGV LLS + FV RTR+EY VR + +
Sbjct: 843 HTAVKIEPKYSNDAVVYVTDASRAVGVATQLLSKELKAGFVERTREEYIEVRERTANRSA 902
Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
RT ++ AA FDW +Y P G + ++ ++ L YIDWTPFF++W LAG
Sbjct: 903 RTERLSYPAAIAKKPQFDWSSYEPVKPTFTGAKVLDNIDLKVLAEYIDWTPFFISWDLAG 962
Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
K+PRIL+DEVVG A L+ DA +ML KL EK ++ R V G +PAN+V DD+E+Y D+
Sbjct: 963 KFPRILQDEVVGEAATALYADAQEMLAKLIDEKLISARAVFGFWPANQVHDDDLEVYGDD 1022
Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
+ + HHLRQQ KT G N+ LADFVAPK SG DY+G F T G+ + +A A+
Sbjct: 1023 GKP--LARLHHLRQQIIKTDGKPNFSLADFVAPKESGITDYVGGFITTAGIGAEEVAKAY 1080
Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
+ DDYN IMVKALADRLAEA AE+LH++VRK YWGYA +E L NE LI+E Y GIRPA
Sbjct: 1081 QDAGDDYNSIMVKALADRLAEACAEWLHQQVRKNYWGYAKDETLDNEALIKEQYTGIRPA 1140
Query: 1137 PGYPACPEHTEKATIWELLEVEK------HTGMKLTESFAMWPGASVSGWYFSHPDSKYY 1190
PGYPACP+HTEK T++ LL+ E +G+ LTE +AM+P A+VSGWYF+HP ++Y+
Sbjct: 1141 PGYPACPDHTEKGTLFALLDPEASEMHAGRSGVFLTEHYAMFPAAAVSGWYFAHPQAQYF 1200
Query: 1191 AVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
AV +I +DQV+ Y RKG ++ ERWLAPNLGYD
Sbjct: 1201 AVGKIDKDQVQSYTARKGQELSVSERWLAPNLGYD 1235
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: 3816
Number of extensions: 169
Number of successful extensions: 9
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: 1236
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1189
Effective search space: 1403020
Effective search space used: 1403020
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 AO353_21615 AO353_21615 (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.26271.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 1755.7 0.0 0 1755.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 AO353_21615 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 AO353_21615 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1755.5 0.0 0 0 1 1182 [] 15 1202 .. 15 1202 .. 0.98
Alignments for each domain:
== domain 1 score: 1755.5 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfea 62
l++ril+lDG+mGt++qs++L+e+d+rg+ +ad+++++kGnndlL+l++P+vi ai ++y++a
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 15 LKERILILDGGMGTMIQSFKLEEQDYRGKrFADWPSDVKGNNDLLVLSRPDVIGAIEKQYLDA 77
579************************************************************ PP
TIGR02082 63 GaDivetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtn 124
GaDi+etntFn+t++++adY+++ +ayeln ++a+lar+vad t tp+k+RfvaG+lGPt+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 78 GADILETNTFNATQVSQADYGMQGLAYELNVEGARLARKVADAKTlETPDKPRFVAGVLGPTS 140
*******************************************99899*************** PP
TIGR02082 125 klatlspdverpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevf 187
++ +lspdv++p++rnvt+delv+ Y+e++kgl++GG+Dl+Liet+fDtlnakaa+fav+ vf
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 141 RTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIETIFDTLNAKAAIFAVQGVF 203
*************************************************************** PP
TIGR02082 188 eekgrelPilisgvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelse 250
ee g elPi+isg+i+d+sGrtLsGqt+eaf +s+ ha+ +++GLnCalGa elr++++els+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 204 EEVGFELPIMISGTITDASGRTLSGQTTEAFWNSIAHAKPISVGLNCALGARELRPYLEELSN 266
*************************************************************** PP
TIGR02082 251 taealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavk 313
+a+++vs++PnaGLPn++geYd++p e+ak+++efa+ g+lnivGGCCGttP hi aia+av+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 267 KASTYVSAHPNAGLPNEFGEYDELPVETAKVIEEFAQSGFLNIVGGCCGTTPGHIEAIAKAVA 329
*************************************************************** PP
TIGR02082 314 dikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakq 376
+ +pr+ ++++++++lsgle+++i++ s fvn+GeRtn++Gs+kf++li++++y eal++a q
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 330 GYAPRQIPDIPKACRLSGLEPFTIDRSSLFVNVGERTNITGSAKFARLIREDNYTEALEVALQ 392
*************************************************************** PP
TIGR02082 377 qveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGka 439
qve Gaq++Din+De++lD++++m+++l+l+a+epdi++vP+m+Dss++ev+eaGLk+iqGk+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 393 QVEAGAQVIDINMDEGMLDSKKAMVTFLNLIAGEPDISRVPIMIDSSKWEVIEAGLKCIQGKG 455
*************************************************************** PP
TIGR02082 440 ivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfp 502
ivnsis+k+G+e+F+++akl k+yGaavvvmafDe Gqa+t ++k ei+kR y++l+++v+fp
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 456 IVNSISMKEGVEQFIHHAKLCKRYGAAVVVMAFDEAGQADTEARKKEICKRSYDILVNEVDFP 518
*************************************************************** PP
TIGR02082 503 pediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRea 565
pediifDpni+++atGieeh++ya+dfi+a+ i+ elP+a +sgGvsnvsFs+rgn++vRea
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 519 PEDIIFDPNIFAVATGIEEHNNYAVDFINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREA 581
*************************************************************** PP
TIGR02082 566 lhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgt 628
+hsvFL +ai++Gl mgivnag+l++yd+i++elr++ved+il+r ++ t+ Ll +a++ykg
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 582 IHSVFLLYAIRNGLTMGIVNAGQLEIYDQIPAELRDAVEDVILNRTPDGTDALLAIADKYKGD 644
**************************************************************9 PP
TIGR02082 629 keksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvv 691
+ kea+++ewr ++v++RLe+alvkG++ +i ed+ee+r +p+e+iegpL+ Gm++v
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 645 GSV--KEAETEEWRAWDVNKRLEHALVKGITTHIVEDTEESRLSFARPIEVIEGPLMSGMNIV 705
998..999******************************************************* PP
TIGR02082 692 GdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivlatvkGDvhDiGkniv 753
GdLFG+GkmfLPqvvksarvmk+ava+L+P++e ek ++ ++kGki++atvkGDvhDiGkniv
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 706 GDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIELEKGDKpEAKGKILMATVKGDVHDIGKNIV 768
***********************************9877689********************* PP
TIGR02082 754 dvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiP 816
+vvL+cngy++vdlGv+vP+ekil++ak++k D+iglsGLi++sldemv+va+em+r+ +++P
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 769 GVVLGCNGYDIVDLGVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVHVAREMQRQDFHLP 831
*************************************************************** PP
TIGR02082 817 lllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkkaeelekikeeyeeir 878
l++GGa++skah+avki++kY+ vvyv+das+av v+ +lls++ ka ++e+++eey e+r
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 832 LMIGGATTSKAHTAVKIEPKYSNdAVVYVTDASRAVGVATQLLSKELKAGFVERTREEYIEVR 894
*********************872699************************************ PP
TIGR02082 879 ekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFv 940
e+ ++ +++ ls aa ++ ++d+s +e+++p+f G kvl+++ ++ l +yiDw+++F+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 895 ERTANRSARTERLSYPAAIAKKPQFDWS-SYEPVKPTFTGAKVLDNIdLKVLAEYIDWTPFFI 956
****************************.9********************************* PP
TIGR02082 941 qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsv.gddieiy 1002
+W+l+gk+p+il+de++g+ a+ l++da+e+l kl+ ekl+ ar+v+G++Pa++v +dd+e+y
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 957 SWDLAGKFPRILQDEVVGEAATALYADAQEMLAKLIDEKLISARAVFGFWPANQVhDDDLEVY 1019
****************************************************9761578**** PP
TIGR02082 1003 tdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeela 1064
d++ p+a +++ ++q+ + ++ + +laDf+a+kesGi+Dy+g +++tag+gaee a
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 1020 GDDGK-----PLARLHHLRQQIIKTDGKpNFSLADFVAPKESGITDYVGGFITTAGIGAEEVA 1077
*8876.....8888888888888888878********************************** PP
TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpa 1127
k++++ ddy+si+vkaladrlaea ae+lh++vRk++wgya++e ld+e l+ke+Y Girpa
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 1078 KAYQDAGDDYNSIMVKALADRLAEACAEWLHQQVRKNYWGYAKDETLDNEALIKEQYTGIRPA 1140
*************************************************************** PP
TIGR02082 1128 fGYpacPdhtekatlleLleae.......riGlklteslalaPeasvsglyfahpeakYfav 1182
+GYpacPdhtek tl++Ll++e r G+ lte +a+ P+a+vsg+yfahp+a+Yfav
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21615 1141 PGYPACPDHTEKGTLFALLDPEasemhagRSGVFLTEHYAMFPAAAVSGWYFAHPQAQYFAV 1202
*******************9885545444579****************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1236 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: 0.10u 0.03s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 11.54
//
[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