Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate GFF2059 Psest_2102 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__psRCH2:GFF2059
Length = 1230
Score = 1603 bits (4151), Expect = 0.0
Identities = 819/1229 (66%), Positives = 972/1229 (79%), Gaps = 9/1229 (0%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
SS+++ L+ L ERIL+LDGGMGTMIQSY+L E D+RG RFADWP D+KGNNDLL+LS+P
Sbjct: 5 SSRLQALQQALKERILILDGGMGTMIQSYKLEEEDYRGTRFADWPQDVKGNNDLLLLSRP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
++I AI AY +AGADI+ETNTFN+T ++ ADY ME L E+N A+LAR AD TA
Sbjct: 65 DIIQAIEKAYLDAGADILETNTFNATRVSQADYGMEELVYELNVEGARLAREVADAKTAE 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
TP++PR+VAGVLGPT+RT SISPDVN+P +RN+TFD LV Y E+T+ L+EGGADLILIE
Sbjct: 125 TPDRPRFVAGVLGPTSRTCSISPDVNNPGYRNVTFDLLVENYVEATRGLIEGGADLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FAV+ FE GVELPIMISGTITDASGRTLSGQTTEAF+NS+RHA+ +
Sbjct: 185 TIFDTLNAKAAIFAVQQVFEDEGVELPIMISGTITDASGRTLSGQTTEAFWNSVRHAKPI 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALG +LR Y++ELS AE +V+AHPNAGLPNAFGEYD MA + E+A +
Sbjct: 245 SVGLNCALGAKDLRPYLEELSSKAETFVSAHPNAGLPNAFGEYDESPAEMAAVVEEFAAS 304
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
GFLNI+GGCCGTTP HI A++ AV PR +P+IP ACRLSGLEP I SLFVNVGE
Sbjct: 305 GFLNIIGGCCGTTPAHIQAIAEAVSKYPPRAIPDIPKACRLSGLEPFTIDRSSLFVNVGE 364
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTN+TGSAKF RLI+EE Y+EAL+VA QQVE GAQ+IDINMDEGMLD++AAMV FLNLIA
Sbjct: 365 RTNITGSAKFARLIREENYTEALEVALQQVEAGAQVIDINMDEGMLDSKAAMVTFLNLIA 424
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ F A L +RYGAAVV
Sbjct: 425 GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFKQQAHLCKRYGAAVV 484
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDE GQADT ARK EIC+R+Y IL EVGFPPEDIIFDPNIFA+ATGIEEHNNYA D
Sbjct: 485 VMAFDEAGQADTAARKREICKRSYDILVNEVGFPPEDIIFDPNIFAIATGIEEHNNYAVD 544
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI AC I+ LP+AL SGGVSNVSFSFRGN+PVREAIH+VFL++AI+ G+ MGIVNAGQ
Sbjct: 545 FIEACAYIRDNLPYALTSGGVSNVSFSFRGNNPVREAIHSVFLFHAIKAGLTMGIVNAGQ 604
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
L IYD++P ELRDAVEDV+LNR +GTE LLELA+KY+G A+ EWRS V+K
Sbjct: 605 LEIYDEIPKELRDAVEDVVLNRSANGTEGLLELADKYKGD--GSVKEAETEEWRSLPVDK 662
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LVKGIT FI +DTEE RQQ RPIEVIEGPLM GMNVVGDLFG GKMFLPQVVKS
Sbjct: 663 RLEHALVKGITAFIVEDTEECRQQCKRPIEVIEGPLMSGMNVVGDLFGAGKMFLPQVVKS 722
Query: 722 ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
ARVMKQAVA+L PFIEA K ++ + GK+++ATVKGDVHDIGKNIVGVVL CN Y++VD+
Sbjct: 723 ARVMKQAVAHLIPFIEAEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDVVDM 782
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPAEKIL+TA D+IGLSGLITPSLDEMV+VAKEM+RQGF++PL+IGGATTSKA
Sbjct: 783 GVMVPAEKILQTAIAEKCDIIGLSGLITPSLDEMVHVAKEMQRQGFSLPLMIGGATTSKA 842
Query: 841 HTAVKIEQNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
HTAVKI+ Y + VYV +ASR VGV LLS + FV +TR+EY +R + +
Sbjct: 843 HTAVKIDPQYHNDAVVYVTDASRAVGVATTLLSKELKPAFVEKTREEYAMIRERTANRSA 902
Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
RT ++ A N FDW +YTP G Q +E + TL YIDWTPFF+ W LAG
Sbjct: 903 RTERLSYAQAVANKPQFDWASYTPVKPSFTGRQLLEDIDLRTLAEYIDWTPFFIAWDLAG 962
Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
KYPRILEDEVVG A LF DA ML+KL EK + R V G +PAN+V DD+E+Y D
Sbjct: 963 KYPRILEDEVVGEAATALFSDAQAMLNKLIDEKLIRARAVFGFWPANQVQDDDLEVYGDG 1022
Query: 1018 TRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
+ HHLRQQ K N LADFVAPK SG DY+G F T G+ + LA A+
Sbjct: 1023 GEK--LATLHHLRQQIIKPDAKPNLSLADFVAPKDSGITDYVGGFICTAGIGAEELAKAY 1080
Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
+ + DDYN IMVKALADRLAEA AE+LH++VRK YWGYA +E LSNEELIRE Y+GIRPA
Sbjct: 1081 QDKGDDYNSIMVKALADRLAEACAEWLHQQVRKQYWGYAKDEQLSNEELIREQYKGIRPA 1140
Query: 1137 PGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQ 1196
PGYPACP+HTEK T+++LL+ + + + LTE +AM P A+VSGWYF+HP+++Y+AV +I
Sbjct: 1141 PGYPACPDHTEKGTLFQLLDADGISQVTLTEHYAMLPTAAVSGWYFAHPEAQYFAVGKID 1200
Query: 1197 RDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
+DQVE Y++RKG + ERWL PNLGYD
Sbjct: 1201 KDQVESYSQRKGEDIAVSERWLMPNLGYD 1229
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: 3711
Number of extensions: 164
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: 1230
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1183
Effective search space: 1395940
Effective search space used: 1395940
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 GFF2059 Psest_2102 (5-methyltetrahydrofolate--homocysteine methyltransferase)
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.3717.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 1783.6 0.0 0 1783.4 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF2059 Psest_2102 5-methyltetrahydrofol
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2059 Psest_2102 5-methyltetrahydrofolate--homocysteine methyltransferase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1783.4 0.0 0 0 1 1182 [] 15 1196 .. 15 1196 .. 0.98
Alignments for each domain:
== domain 1 score: 1783.4 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72
l++ril+lDG+mGt++qs++L+e+d+rg +ad+++++kGnndlL l++P++i+ai +ay++aGaDi+etntF
lcl|FitnessBrowser__psRCH2:GFF2059 15 LKERILILDGGMGTMIQSYKLEEEDYRGTrFADWPQDVKGNNDLLLLSRPDIIQAIEKAYLDAGADILETNTF 87
579********************************************************************** PP
TIGR02082 73 nsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtyd 144
n+t +++adY++e+++yeln ++a+larevad t tp+++RfvaG+lGPt+++ ++spdv++p++rnvt+d
lcl|FitnessBrowser__psRCH2:GFF2059 88 NATRVSQADYGMEELVYELNVEGARLAREVADAKTaETPDRPRFVAGVLGPTSRTCSISPDVNNPGYRNVTFD 160
********************************99999************************************ PP
TIGR02082 145 elvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtlea 217
lv+ Y+e+++gl++GG+Dl+Liet+fDtlnakaa+fav++vfe++g+elPi+isg+i+d+sGrtLsGqt+ea
lcl|FitnessBrowser__psRCH2:GFF2059 161 LLVENYVEATRGLIEGGADLILIETIFDTLNAKAAIFAVQQVFEDEGVELPIMISGTITDASGRTLSGQTTEA 233
************************************************************************* PP
TIGR02082 218 flaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegl 290
f +s++ha+ +++GLnCalGa++lr++++els +ae++vs++PnaGLPna+geYd+ p e+a++++efa+ g+
lcl|FitnessBrowser__psRCH2:GFF2059 234 FWNSVRHAKPISVGLNCALGAKDLRPYLEELSSKAETFVSAHPNAGLPNAFGEYDESPAEMAAVVEEFAASGF 306
************************************************************************* PP
TIGR02082 291 lnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklik 363
lni+GGCCGttP+hi+aiaeav + pr ++++++++lsgle+++i++ s fvn+GeRtn++Gs+kf++li+
lcl|FitnessBrowser__psRCH2:GFF2059 307 LNIIGGCCGTTPAHIQAIAEAVSKYPPRAIPDIPKACRLSGLEPFTIDRSSLFVNVGERTNITGSAKFARLIR 379
************************************************************************* PP
TIGR02082 364 aedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviq 436
+e+y eal++a qqve Gaq++Din+De++lD++a+m+++l+l+a+epdi++vP+m+Dss++ev+eaGLk+iq
lcl|FitnessBrowser__psRCH2:GFF2059 380 EENYTEALEVALQQVEAGAQVIDINMDEGMLDSKAAMVTFLNLIAGEPDISRVPIMIDSSKWEVIEAGLKCIQ 452
************************************************************************* PP
TIGR02082 437 GkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifD 509
Gk+ivnsis+k+G+e+F ++a+l k+yGaavvvmafDe Gqa+ta++k ei+kR y++l+++vgfppediifD
lcl|FitnessBrowser__psRCH2:GFF2059 453 GKGIVNSISMKEGVEQFKQQAHLCKRYGAAVVVMAFDEAGQADTAARKREICKRSYDILVNEVGFPPEDIIFD 525
************************************************************************* PP
TIGR02082 510 pniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmg 582
pni++iatGieeh++ya+dfiea+ i+ +lP+a +sgGvsnvsFs+rgn++vRea+hsvFL++aikaGl mg
lcl|FitnessBrowser__psRCH2:GFF2059 526 PNIFAIATGIEEHNNYAVDFIEACAYIRDNLPYALTSGGVSNVSFSFRGNNPVREAIHSVFLFHAIKAGLTMG 598
************************************************************************* PP
TIGR02082 583 ivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralv 655
ivnag+l++yd+i+kelr++ved++l+r+ + te Llela++ykg + kea+++ewr+lpv++RLe+alv
lcl|FitnessBrowser__psRCH2:GFF2059 599 IVNAGQLEIYDEIPKELRDAVEDVVLNRSANGTEGLLELADKYKGDGSV--KEAETEEWRSLPVDKRLEHALV 669
*********************************************9998..999******************* PP
TIGR02082 656 kGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728
kG++ +i ed+ee r++ k+p+e+iegpL+ Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+ek
lcl|FitnessBrowser__psRCH2:GFF2059 670 KGITAFIVEDTEECRQQCKRPIEVIEGPLMSGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIEAEKG 742
************************************************************************8 PP
TIGR02082 729 ed.kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800
++ ++kGki++atvkGDvhDiGkniv+vvL+cngy+vvd+Gv+vP+ekil++a +k D+iglsGLi++slde
lcl|FitnessBrowser__psRCH2:GFF2059 743 DKpEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDVVDMGVMVPAEKILQTAIAEKCDIIGLSGLITPSLDE 815
87689******************************************************************** PP
TIGR02082 801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkkaeelekike 872
mv+va+em+r+g+++Pl++GGa++skah+avki+++Y+ vvyv+das+av v+ +lls++ k +++ek++e
lcl|FitnessBrowser__psRCH2:GFF2059 816 MVHVAKEMQRQGFSLPLMIGGATTSKAHTAVKIDPQYHNdAVVYVTDASRAVGVATTLLSKELKPAFVEKTRE 888
*************************************86269******************************* PP
TIGR02082 873 eyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWel 944
ey ire+ ++ +++ ls ++a ++ ++d+ +++++p f G++ le++ + +l +yiDw+++F++W+l
lcl|FitnessBrowser__psRCH2:GFF2059 889 EYAMIRERTANRSARTERLSYAQAVANKPQFDWA-SYTPVKPSFTGRQLLEDIdLRTLAEYIDWTPFFIAWDL 960
**********************************.9************************************* PP
TIGR02082 945 rgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiat 1016
+gkyp+il+de++g+ a+ lf+da+++l+kl+ ekl+rar+v+G++Pa++v+ dd+e+y d + ++at
lcl|FitnessBrowser__psRCH2:GFF2059 961 AGKYPRILEDEVVGEAATALFSDAQAMLNKLIDEKLIRARAVFGFWPANQVQdDDLEVYGDGGE-----KLAT 1028
************************************************97652689***97766.....7777 PP
TIGR02082 1017 vrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlae 1088
+++ ++q+ + ++ +l+laDf+a+k+sGi+Dy+g ++ tag+gaeelak++++k ddy+si+vkaladrlae
lcl|FitnessBrowser__psRCH2:GFF2059 1029 LHHLRQQIIKPDAKpNLSLADFVAPKDSGITDYVGGFICTAGIGAEELAKAYQDKGDDYNSIMVKALADRLAE 1101
777767766665556********************************************************** PP
TIGR02082 1089 alaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlkltesla 1160
a ae+lh++vRk++wgya++e+l++e+l++e+Y+Girpa+GYpacPdhtek tl++Ll+a+ ++lte +a
lcl|FitnessBrowser__psRCH2:GFF2059 1102 ACAEWLHQQVRKQYWGYAKDEQLSNEELIREQYKGIRPAPGYPACPDHTEKGTLFQLLDADGiSQVTLTEHYA 1174
**************************************************************567******** PP
TIGR02082 1161 laPeasvsglyfahpeakYfav 1182
+ P+a+vsg+yfahpea+Yfav
lcl|FitnessBrowser__psRCH2:GFF2059 1175 MLPTAAVSGWYFAHPEAQYFAV 1196
********************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1230 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: 0.07u 0.04s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 13.53
//
[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