Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate GFF1835 HP15_1792 B12-dependent methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__Marino:GFF1835
Length = 1232
Score = 1543 bits (3994), Expect = 0.0
Identities = 780/1230 (63%), Positives = 957/1230 (77%), Gaps = 11/1230 (0%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
+++++QL L ERI++LDGGMGTMIQ+ +L+E FRG+RFAD+ +++GNNDLL L++P
Sbjct: 5 TTRLDQLHKALQERIVILDGGMGTMIQNLKLDEKAFRGDRFADYEREVQGNNDLLNLTQP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
++ IH Y +AGADIIETNTFNST ++ ADY +E+++ E+N AAA+LAR ADE+TA+
Sbjct: 65 ALLRNIHADYLDAGADIIETNTFNSTQLSQADYGLEAIARELNVAAAELARQIADEYTAK 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
PEKPR+VAG +GPT+RTASISPDVN+P +RN+ F LV Y E+ LVEGG DLILIE
Sbjct: 125 NPEKPRFVAGAVGPTSRTASISPDVNNPGYRNVDFQTLVDNYYEAVGGLVEGGCDLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA++A + FE G+ LPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185 TIFDTLNAKAAIYATQQYFEDSGITLPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPI 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALG D LR YV+ELS AE YV+AHPNAGLPN FGEYD + MA+ I +A+
Sbjct: 245 SVGLNCALGADALRPYVEELSAKAETYVSAHPNAGLPNEFGEYDQTPEEMAEIIEGFARD 304
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
GFLNI+GGCCG+ P HI A+++AV PRK+PE P A RLSGLEP ++ LF+NVGE
Sbjct: 305 GFLNIIGGCCGSRPDHIEAIAQAVSKYPPRKIPERPKALRLSGLEPFTGDDNVLFINVGE 364
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTNVTGS +F RLIKEE+Y EAL VAR QVENGAQIIDINMDEGML+++ MV FLNL+A
Sbjct: 365 RTNVTGSKRFLRLIKEEQYEEALSVARDQVENGAQIIDINMDEGMLESKEVMVTFLNLVA 424
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
EPDI+RVPIMIDSSKWDVIE GL+CIQGK +VNSIS+KEG + F+ A+ RYGAAVV
Sbjct: 425 SEPDISRVPIMIDSSKWDVIEAGLRCIQGKAVVNSISLKEGEEEFVKRARDCMRYGAAVV 484
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDEQGQADT RK EIC+R+Y +LT +GF P DIIFDPNIFA+ATGIEEHNNYA D
Sbjct: 485 VMAFDEQGQADTYERKTEICKRSYDVLT-GIGFNPADIIFDPNIFAIATGIEEHNNYAVD 543
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI A I+ LPHA ISGGVSNVSFSFRGND VREAIH+VFLY+AI+ GM+MGIVN GQ
Sbjct: 544 FINATRWIRENLPHASISGGVSNVSFSFRGNDVVREAIHSVFLYHAIKAGMNMGIVNPGQ 603
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKY--RGSKTDDTANAQQAEWRSWEV 659
L IYD++ EL++ VEDV+LNRRDD T+RLLE+AE+Y +G KT + + WR W V
Sbjct: 604 LVIYDEIDPELKELVEDVVLNRRDDSTDRLLEIAERYKGKGGKTQE----EDLAWREWPV 659
Query: 660 NKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVV 719
KRLE++LVKGIT +I DTE RQ+AT PIEVIEGPLMDGMNVVGDLFG+GKMFLPQVV
Sbjct: 660 EKRLEHALVKGITTYIVDDTEACRQRATHPIEVIEGPLMDGMNVVGDLFGDGKMFLPQVV 719
Query: 720 KSARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIV 778
KSARVMKQAVA+L P+IEA K E K GK+++ATVKGDVHDIGKNIVGVVLQCNNYE++
Sbjct: 720 KSARVMKQAVAHLIPYIEAEKTEDQKAKGKILMATVKGDVHDIGKNIVGVVLQCNNYEVI 779
Query: 779 DLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTS 838
DLGVMVP +KIL AKE + DLIGLSGLITPSLDEMV+VA+EM+R F IPL+IGGATTS
Sbjct: 780 DLGVMVPCDKILAAAKEHDVDLIGLSGLITPSLDEMVHVAREMQRLDFNIPLMIGGATTS 839
Query: 839 KAHTAVKIEQNYSGP-TVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRK 897
KAHTAVKIE Y +YV +ASR V V + LLS + +FV R EY+ +R + +
Sbjct: 840 KAHTAVKIEPQYKNDIALYVSDASRCVNVASQLLSKNAKPEFVEAARTEYDEIRERRKNR 899
Query: 898 KPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSL 956
RT V+L+ ARD ++ Y PP G++ E + L +YIDWTPFFM+W +
Sbjct: 900 GDRTKLVSLKEARDRAPDISFEGYQPPKPAFTGIRVFEEYDLNELVDYIDWTPFFMSWDI 959
Query: 957 AGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRD 1016
+GKYP I +D G A+ LF DA +L ++ EK ++ RGV+G +PANR GDD+ +Y D
Sbjct: 960 SGKYPAIFDDPKRGEAARHLFDDAQKILHRMIDEKRVSARGVIGFWPANRRGDDVVLYTD 1019
Query: 1017 ETRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADA 1075
E+ T + HHLRQQ EK G L+DFVAP+ SG DY+G FAVT G+ + +
Sbjct: 1020 ESCTEELTTLHHLRQQDEKAPGKPMMALSDFVAPEGSGTVDYVGGFAVTTGIGAEEFSVE 1079
Query: 1076 FEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRP 1135
F+ +DDYN IMVKALADRLAEAFAE +HERVR+ +WGYA +E L+N++LI+E Y+GIRP
Sbjct: 1080 FKDANDDYNAIMVKALADRLAEAFAERMHERVRQEFWGYAADEKLANDDLIKERYRGIRP 1139
Query: 1136 APGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQI 1195
APGYPACP+HTEKAT++ LLE G++LTE FAM+P A+VSGWYF+HP+SKY+AV +I
Sbjct: 1140 APGYPACPDHTEKATLFSLLEATDTAGIELTEHFAMFPTAAVSGWYFAHPESKYFAVGKI 1199
Query: 1196 QRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
DQVEDYA RKG+S E ERWLAP+L YD
Sbjct: 1200 GADQVEDYAERKGISKAEAERWLAPSLAYD 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: 3755
Number of extensions: 165
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: 1232
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1185
Effective search space: 1398300
Effective search space used: 1398300
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 GFF1835 HP15_1792 (B12-dependent 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.3052.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 1791.5 0.0 0 1791.4 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF1835 HP15_1792 B12-dependent methioni
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1835 HP15_1792 B12-dependent methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1791.4 0.0 0 0 1 1182 [] 15 1196 .. 15 1196 .. 0.99
Alignments for each domain:
== domain 1 score: 1791.4 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72
l++ri++lDG+mGt++q+ +L+e+ Frg+ +ad++re++GnndlLnlt+P ++++ih +y++aGaDi+etntF
lcl|FitnessBrowser__Marino:GFF1835 15 LQERIVILDGGMGTMIQNLKLDEKAFRGDrFADYEREVQGNNDLLNLTQPALLRNIHADYLDAGADIIETNTF 87
689********************************************************************** PP
TIGR02082 73 nsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtyd 144
nst++++adY+le+ a+eln +aa+lar++ade+t ++pek+RfvaG++GPt+++a++spdv++p++rnv+++
lcl|FitnessBrowser__Marino:GFF1835 88 NSTQLSQADYGLEAIARELNVAAAELARQIADEYTaKNPEKPRFVAGAVGPTSRTASISPDVNNPGYRNVDFQ 160
************************************************************************* PP
TIGR02082 145 elvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtlea 217
+lvd Y e+v gl++GG Dl+Liet+fDtlnakaa++a+++ fe+ g+ lPi+isg+i+d+sGrtLsGqt+ea
lcl|FitnessBrowser__Marino:GFF1835 161 TLVDNYYEAVGGLVEGGCDLILIETIFDTLNAKAAIYATQQYFEDSGITLPIMISGTITDASGRTLSGQTTEA 233
************************************************************************* PP
TIGR02082 218 flaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegl 290
f +s+ ha+ +++GLnCalGad lr++v+els++ae++vs++PnaGLPn++geYd+tpee+a++++ fa++g+
lcl|FitnessBrowser__Marino:GFF1835 234 FWNSVAHAKPISVGLNCALGADALRPYVEELSAKAETYVSAHPNAGLPNEFGEYDQTPEEMAEIIEGFARDGF 306
************************************************************************* PP
TIGR02082 291 lnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklik 363
lni+GGCCG++P+hi aia+av + prk +e +++++lsgle+++ +++ f+n+GeRtnv+Gsk+f +lik
lcl|FitnessBrowser__Marino:GFF1835 307 LNIIGGCCGSRPDHIEAIAQAVSKYPPRKIPERPKALRLSGLEPFTGDDNVLFINVGERTNVTGSKRFLRLIK 379
************************************************************************* PP
TIGR02082 364 aedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviq 436
+e+yeeal++a++qve+Gaqi+Din+De++l++++ m+++l+l+asepdi++vP+m+Dss+++v+eaGL++iq
lcl|FitnessBrowser__Marino:GFF1835 380 EEQYEEALSVARDQVENGAQIIDINMDEGMLESKEVMVTFLNLVASEPDISRVPIMIDSSKWDVIEAGLRCIQ 452
************************************************************************* PP
TIGR02082 437 GkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifD 509
Gka+vnsislk+Gee+F+++a+ +yGaavvvmafDe+Gqa+t+++k ei+kR y++lt +gf+p diifD
lcl|FitnessBrowser__Marino:GFF1835 453 GKAVVNSISLKEGEEEFVKRARDCMRYGAAVVVMAFDEQGQADTYERKTEICKRSYDVLTG-IGFNPADIIFD 524
************************************************************9.*********** PP
TIGR02082 510 pniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmg 582
pni++iatGieeh++ya+dfi+a+r+i+e+lP+a isgGvsnvsFs+rgnd vRea+hsvFLy+aikaG++mg
lcl|FitnessBrowser__Marino:GFF1835 525 PNIFAIATGIEEHNNYAVDFINATRWIRENLPHASISGGVSNVSFSFRGNDVVREAIHSVFLYHAIKAGMNMG 597
************************************************************************* PP
TIGR02082 583 ivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralv 655
ivn+g+l +yd+id+el+e+ved++l+rr+++t++Lle+ae+ykg+ k +++ +wr++pve+RLe+alv
lcl|FitnessBrowser__Marino:GFF1835 598 IVNPGQLVIYDEIDPELKELVEDVVLNRRDDSTDRLLEIAERYKGKGGK--TQEEDLAWREWPVEKRLEHALV 668
************************************************9..5567889*************** PP
TIGR02082 656 kGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728
kG++ +i +d+e+ r+++++p+e+iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+Py+e+ek+
lcl|FitnessBrowser__Marino:GFF1835 669 KGITTYIVDDTEACRQRATHPIEVIEGPLMDGMNVVGDLFGDGKMFLPQVVKSARVMKQAVAHLIPYIEAEKT 741
***********************************************************************98 PP
TIGR02082 729 ed.kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800
ed k+kGki++atvkGDvhDiGkniv+vvL+cn+yev+dlGv+vP++kil aak+++ D+iglsGLi++slde
lcl|FitnessBrowser__Marino:GFF1835 742 EDqKAKGKILMATVKGDVHDIGKNIVGVVLQCNNYEVIDLGVMVPCDKILAAAKEHDVDLIGLSGLITPSLDE 814
77599******************************************************************** PP
TIGR02082 801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkgev.vyvkdaseavkvvdkllsekkkaeelekike 872
mv+va+em+r ++iPl++GGa++skah+avki+++Yk ++ +yv das+ v+v+++lls+++k e++e+ ++
lcl|FitnessBrowser__Marino:GFF1835 815 MVHVAREMQRLDFNIPLMIGGATTSKAHTAVKIEPQYKNDIaLYVSDASRCVNVASQLLSKNAKPEFVEAART 887
**************************************99747****************************** PP
TIGR02082 873 eyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWel 944
ey+eire+ +++ ++++ +s+k+ar+ ++ + +++p+p f G++v+e++ ++el++yiDw+++F++W++
lcl|FitnessBrowser__Marino:GFF1835 888 EYDEIRERRKNRGDRTKLVSLKEARDRAPDISFE-GYQPPKPAFTGIRVFEEYdLNELVDYIDWTPFFMSWDI 959
*************************999999999.9************************************* PP
TIGR02082 945 rgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatv 1017
gkyp i++d+++g+ ar+lf+da+++l++++ ek + argv+G++Pa++ gdd+++ytde+ t++++t+
lcl|FitnessBrowser__Marino:GFF1835 960 SGKYPAIFDDPKRGEAARHLFDDAQKILHRMIDEKRVSARGVIGFWPANRRGDDVVLYTDESC---TEELTTL 1029
*************************************************************99...7888888 PP
TIGR02082 1018 rekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaea 1089
++ ++q ++ ++ +++l+Df+a+ sG++Dy+g ++vt+g+gaee++ ++++ +ddy++i+vkaladrlaea
lcl|FitnessBrowser__Marino:GFF1835 1030 HHLRQQDEKAPGKpMMALSDFVAPEGSGTVDYVGGFAVTTGIGAEEFSVEFKDANDDYNAIMVKALADRLAEA 1102
666677777777799********************************************************** PP
TIGR02082 1090 laellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslal 1161
+ae +hervR+e+wgya++e+l+++dl+kerYrGirpa+GYpacPdhtekatl++Llea G++lte +a+
lcl|FitnessBrowser__Marino:GFF1835 1103 FAERMHERVRQEFWGYAADEKLANDDLIKERYRGIRPAPGYPACPDHTEKATLFSLLEATDtAGIELTEHFAM 1175
**********************************************************98879********** PP
TIGR02082 1162 aPeasvsglyfahpeakYfav 1182
P+a+vsg+yfahpe+kYfav
lcl|FitnessBrowser__Marino:GFF1835 1176 FPTAAVSGWYFAHPESKYFAV 1196
*******************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1232 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: 00:00:00.11
# Mc/sec: 12.97
//
[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