Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012501603.1 CPAR_RS01790 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000020505.1:WP_012501603.1
Length = 1227
Score = 1471 bits (3808), Expect = 0.0
Identities = 737/1225 (60%), Positives = 931/1225 (76%), Gaps = 7/1225 (0%)
Query: 6 EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
+ L + +RILVLDG MGTMIQ + L+E D+RGERFA LKGNNDLLV+++P++I
Sbjct: 3 DNLYGLIEQRILVLDGAMGTMIQRHGLDEQDYRGERFASHSHPLKGNNDLLVITQPDIIR 62
Query: 66 AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
+IH + +AGADI+ET TFN+ I+ +DYQ++ L+ E+N AAAK+AR+ ADE+TA+TP+K
Sbjct: 63 SIHCDFLDAGADIVETCTFNANPISQSDYQLQHLTKELNVAAAKVARSAADEFTAKTPDK 122
Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
PR+VAG +GPTN+T S+SPDVN+P FR +TF +V Y + L EGG DL+L+ETVFD
Sbjct: 123 PRFVAGSIGPTNKTLSLSPDVNNPGFRAVTFQEVVDNYTAQLEGLHEGGVDLLLVETVFD 182
Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL-TFG 244
TLN KAA++A++ G ++P+M+SGT+ DASGRTLSGQTTEAF+ S+ H +L + G
Sbjct: 183 TLNCKAALYAIEQYAAKTGWQVPVMVSGTVVDASGRTLSGQTTEAFWISISHMPSLLSVG 242
Query: 245 LNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFL 304
LNCALG ++R +++ LS IA YV+ +PNAGLPN FGEYD + MA QI +A++GF+
Sbjct: 243 LNCALGSKQMRPFIEALSNIAGSYVSVYPNAGLPNEFGEYDDSPEYMAAQIAGFAESGFV 302
Query: 305 NIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTN 364
NIVGGCCGTTP HI A++ AV+ L PRK P +LSGLEPL + E + F+NVGERTN
Sbjct: 303 NIVGGCCGTTPTHIRAIAEAVKTLTPRKRPANEHVLKLSGLEPLVVDETTGFINVGERTN 362
Query: 365 VTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEP 424
VTGS KF RLIKE Y EAL +ARQQVENGAQ+ID+N+DEGMLD+E +V FLNLIA EP
Sbjct: 363 VTGSRKFARLIKEANYDEALSIARQQVENGAQVIDVNLDEGMLDSEKVIVEFLNLIASEP 422
Query: 425 DIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMA 484
+IA+VP+MIDSSKW VIE GL+C QGK IVNSIS+KEG + F HA+ + +YGAA VVMA
Sbjct: 423 EIAKVPVMIDSSKWAVIENGLRCTQGKSIVNSISLKEGEEPFKEHARKIMQYGAATVVMA 482
Query: 485 FDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIG 544
FDEQGQAD+ R+IEIC RAYKILTEEVGFPPEDIIFDPN+ VATGI+EHNNYA DFI
Sbjct: 483 FDEQGQADSLHRRIEICSRAYKILTEEVGFPPEDIIFDPNVLTVATGIDEHNNYALDFIE 542
Query: 545 ACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAI 604
+ IK+ LPHA +SGG+SNVSFSFRGN+PVREA+H FLY+AI G+DMGIVNA QL I
Sbjct: 543 SVRWIKQNLPHAKVSGGISNVSFSFRGNEPVREAMHTAFLYHAIHAGLDMGIVNAAQLGI 602
Query: 605 YDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLE 664
Y+D+ EL VEDV+LNRRDD TERL+ AE R + A A+ AEWR+ V +RL+
Sbjct: 603 YEDIDPELLVYVEDVLLNRRDDATERLVAFAETIRDG--GEKAEAKTAEWRNAPVEERLK 660
Query: 665 YSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARV 724
++LVKGI ++I++DTEEARQ P+EVIEGPLM+GMN +GDLF EGKMFLPQVVKSARV
Sbjct: 661 HALVKGIVDYIDEDTEEARQLYPSPLEVIEGPLMNGMNHIGDLFAEGKMFLPQVVKSARV 720
Query: 725 MKQAVAYLEPFIEASKEQG---KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
MK++VA L P+IE K + K+++ATVKGDVHDIGKNIV VVL CNN+++VD+G
Sbjct: 721 MKRSVAVLVPYIEEEKAKSCDTSAKAKVLLATVKGDVHDIGKNIVSVVLACNNFDVVDIG 780
Query: 782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
VM+P +KIL + D++GLSGLITPSL+EM +VAKEMER G IPL+IGGATTSK H
Sbjct: 781 VMMPCDKILDAVVKEKPDVLGLSGLITPSLEEMAHVAKEMERLGMNIPLIIGGATTSKVH 840
Query: 842 TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
TAVK+ NYSG V+V +ASR+V VV+ L + QR+ ++A E E +R H +
Sbjct: 841 TAVKLAPNYSGAVVHVLDASRSVPVVSNLCNPAQREGYIAALNSEQEAMRKSHAERTAAK 900
Query: 902 PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKY 960
++L+AARDN A DW+A T + GV +E ++ LR+YIDWTPFF +W L G Y
Sbjct: 901 KYISLDAARDNRLAIDWEAETIDKPAQTGVTVLEDVTVGALRSYIDWTPFFRSWELHGVY 960
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
P+ILEDE VG EA +LF DA +LD++ +EK L +GV G+FPAN +GDDI +Y D+ R+
Sbjct: 961 PQILEDEKVGEEATKLFNDATALLDRIDSEKLLGIKGVAGIFPANSIGDDIFVYSDDERS 1020
Query: 1021 HVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQH 1080
+ V H LRQQ+EK G AN LADFVAP+ SG D+IG F VT GL +L F A++
Sbjct: 1021 MIRTVLHTLRQQSEKHGEANLALADFVAPRESGVNDWIGCFTVTAGLGIQSLLQEFAAEN 1080
Query: 1081 DDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYP 1140
DDY++IM +ALADRLAEAFAE LHE+VR+ WGYAP E L +EELI E Y+GIRPAPGYP
Sbjct: 1081 DDYHRIMTQALADRLAEAFAEMLHEKVRRELWGYAPGEILGSEELIAEQYRGIRPAPGYP 1140
Query: 1141 ACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV 1200
ACP+HTEKATI++LL E TG+ LTE+FAM P ASV G YF++P SKY+ + +I +DQV
Sbjct: 1141 ACPDHTEKATIFDLLNAEAATGVTLTETFAMNPAASVCGLYFANPASKYFVLGKIGKDQV 1200
Query: 1201 EDYARRKGMSVTEVERWLAPNLGYD 1225
EDYA RKG+ V+E E+WLAP L YD
Sbjct: 1201 EDYANRKGLEVSEAEKWLAPALNYD 1225
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: 3529
Number of extensions: 139
Number of successful extensions: 8
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 WP_012501603.1 CPAR_RS01790 (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.15053.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 1732.1 0.0 0 1731.9 0.0 1.0 1 lcl|NCBI__GCF_000020505.1:WP_012501603.1 CPAR_RS01790 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012501603.1 CPAR_RS01790 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1731.9 0.0 0 0 2 1180 .. 10 1190 .. 9 1192 .. 0.98
Alignments for each domain:
== domain 1 score: 1731.9 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
++rilvlDGamGt++q++ L+e+d+rge +a ++ lkGnndlL++t+P++i++ih ++++aGaDiv
lcl|NCBI__GCF_000020505.1:WP_012501603.1 10 EQRILVLDGAMGTMIQRHGLDEQDYRGErFASHSHPLKGNNDLLVITQPDIIRSIHCDFLDAGADIV 76
79***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdv 133
et tFn+++i+++dY+l+++++eln +aak+ar +adeft +tp+k+RfvaGs+GPtnk+ +lspdv
lcl|NCBI__GCF_000020505.1:WP_012501603.1 77 ETCTFNANPISQSDYQLQHLTKELNVAAAKVARSAADEFTaKTPDKPRFVAGSIGPTNKTLSLSPDV 143
******************************************************************* PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p+fr vt++e+vd Y+ q +gl +GGvDllL+etvfDtln kaal+a+e+ ++ g ++P+++sg
lcl|NCBI__GCF_000020505.1:WP_012501603.1 144 NNPGFRAVTFQEVVDNYTAQLEGLHEGGVDLLLVETVFDTLNCKAALYAIEQYAAKTGWQVPVMVSG 210
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehae.ililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266
++vd+sGrtLsGqt+eaf +s++h++ +l++GLnCalG++++r+f+++ls++a +vsv+PnaGLPn
lcl|NCBI__GCF_000020505.1:WP_012501603.1 211 TVVDASGRTLSGQTTEAFWISISHMPsLLSVGLNCALGSKQMRPFIEALSNIAGSYVSVYPNAGLPN 277
************************973679************************************* PP
TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
++geYd pe +a++++ fae g++nivGGCCGttP hiraiaeavk ++prkr++ e+ + lsgle
lcl|NCBI__GCF_000020505.1:WP_012501603.1 278 EFGEYDDSPEYMAAQIAGFAESGFVNIVGGCCGTTPTHIRAIAEAVKTLTPRKRPANEHVLKLSGLE 344
******************************************************************* PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
+l +++ + f+n+GeRtnv+Gs+kf++lik+ +y+eal+ia+qqve+Gaq++D+n+De++lD+e+ +
lcl|NCBI__GCF_000020505.1:WP_012501603.1 345 PLVVDETTGFINVGERTNVTGSRKFARLIKEANYDEALSIARQQVENGAQVIDVNLDEGMLDSEKVI 411
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
+++l+l+asep+iakvP+m+Dss+++v+e GL++ qGk+ivnsislk+Gee F e+a++i +yGaa
lcl|NCBI__GCF_000020505.1:WP_012501603.1 412 VEFLNLIASEPEIAKVPVMIDSSKWAVIENGLRCTQGKSIVNSISLKEGEEPFKEHARKIMQYGAAT 478
******************************************************************* PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
vvmafDe+Gqa+ +++iei++Rayk+lte+vgfppediifDpn+lt+atGi+eh++ya+dfie++r
lcl|NCBI__GCF_000020505.1:WP_012501603.1 479 VVMAFDEQGQADSLHRRIEICSRAYKILTEEVGFPPEDIIFDPNVLTVATGIDEHNNYALDFIESVR 545
******************************************************************* PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
+ik++lP+ak+sgG+snvsFs+rgn++vRea+h+ FLy+ai+aGlDmgivna++l +y+did+el+
lcl|NCBI__GCF_000020505.1:WP_012501603.1 546 WIKQNLPHAKVSGGISNVSFSFRGNEPVREAMHTAFLYHAIHAGLDMGIVNAAQLGIYEDIDPELLV 612
******************************************************************* PP
TIGR02082 602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668
ved++l+rr++ate+L+ +ae+ ++ ek +ea++aewrn pveeRL++alvkG+ ++i+ed+ee
lcl|NCBI__GCF_000020505.1:WP_012501603.1 613 YVEDVLLNRRDDATERLVAFAETIRDGGEK--AEAKTAEWRNAPVEERLKHALVKGIVDYIDEDTEE 677
**************************9999..889******************************** PP
TIGR02082 669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed...ks 732
ar+ + +ple+iegpL++Gm+ +GdLF +GkmfLPqvvksarvmk++va+L Py+e+ek+++ ++
lcl|NCBI__GCF_000020505.1:WP_012501603.1 678 ARQLYPSPLEVIEGPLMNGMNHIGDLFAEGKMFLPQVVKSARVMKRSVAVLVPYIEEEKAKScdtSA 744
***********************************************************9888889* PP
TIGR02082 733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799
k k++latvkGDvhDiGkniv+vvL+cn+++vvd+Gv++P++kil+a k+k+Dv+glsGLi++sl+
lcl|NCBI__GCF_000020505.1:WP_012501603.1 745 KAKVLLATVKGDVHDIGKNIVSVVLACNNFDVVDIGVMMPCDKILDAVVKEKPDVLGLSGLITPSLE 811
******************************************************************* PP
TIGR02082 800 emvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaee 866
em++va+emer g++iPl++GGa++sk h+avk+a++Y+g vv+v das++v vv++l + +++ +
lcl|NCBI__GCF_000020505.1:WP_012501603.1 812 EMAHVAKEMERLGMNIPLIIGGATTSKVHTAVKLAPNYSGAVVHVLDASRSVPVVSNLCNPAQREGY 878
******************************************************************* PP
TIGR02082 867 lekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellky 932
++++++e+e +r+++ e+ ++++s++aar++++a+d++ + ++ +p + G+ vle++ + l++y
lcl|NCBI__GCF_000020505.1:WP_012501603.1 879 IAALNSEQEAMRKSHAERTAAKKYISLDAARDNRLAIDWE-AETIDKPAQTGVTVLEDVtVGALRSY 944
****************************************.999*********************** PP
TIGR02082 933 iDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddi 999
iDw+++F +Wel+g yp+il+de++g+ea+klf+da++lld++ +ekll +gv G+fPa+s+gddi
lcl|NCBI__GCF_000020505.1:WP_012501603.1 945 IDWTPFFRSWELHGVYPQILEDEKVGEEATKLFNDATALLDRIDSEKLLGIKGVAGIFPANSIGDDI 1011
******************************************************************* PP
TIGR02082 1000 eiytdetvsqetkpiatvrekleqlrqqsdr....ylclaDfiaskesGikDylgallvtaglgaee 1062
+y+d+ +s+ i tv l++lrqqs++ +l+laDf+a++esG +D++g + vtaglg++
lcl|NCBI__GCF_000020505.1:WP_012501603.1 1012 FVYSDDERSM----IRTV---LHTLRQQSEKhgeaNLALADFVAPRESGVNDWIGCFTVTAGLGIQS 1071
****888844....4444...35555555554545******************************** PP
TIGR02082 1063 lakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafG 1129
l +++ a++ddy+ i+ +aladrlaea+ae+lhe+vR+elwgya e l e+l+ e+YrGirpa+G
lcl|NCBI__GCF_000020505.1:WP_012501603.1 1072 LLQEFAAENDDYHRIMTQALADRLAEAFAEMLHEKVRRELWGYAPGEILGSEELIAEQYRGIRPAPG 1138
******************************************************************* PP
TIGR02082 1130 YpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYf 1180
YpacPdhtekat+++Ll+ae +G++lte +a++P+asv+glyfa+p++kYf
lcl|NCBI__GCF_000020505.1:WP_012501603.1 1139 YPACPDHTEKATIFDLLNAEAaTGVTLTETFAMNPAASVCGLYFANPASKYF 1190
*********************9****************************** 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 13.26
//
[ok]
This GapMind analysis is from Apr 10 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