Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_086511312.1 BZY95_RS18210 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_002151265.1:WP_086511312.1
Length = 1239
Score = 1645 bits (4261), Expect = 0.0
Identities = 829/1234 (67%), Positives = 992/1234 (80%), Gaps = 12/1234 (0%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
S+ L +L ERIL+LDGGMGTMIQ+ +L EADFRGERF DWP +LKGNNDLL L+ P
Sbjct: 6 SALTATLTERLGERILMLDGGMGTMIQNAKLEEADFRGERFGDWPSELKGNNDLLALTCP 65
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+++ +H AY EAGADIIETNTFNST ++ ADY ME+L EIN +A+LARA D A
Sbjct: 66 DLVTRLHRAYLEAGADIIETNTFNSTRLSQADYGMEALVPEINRESARLARAACDAVAAE 125
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
T PRYVAGVLGPT+RTAS+SPDVNDPA RN+TFD L Y E+ +AL+EGGADLILIE
Sbjct: 126 TGV-PRYVAGVLGPTSRTASLSPDVNDPAKRNVTFDQLRDNYYEAAEALIEGGADLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FA++ F+ G LP+MISGTITDASGRTLSGQTTEAF+NS+RHA+ L
Sbjct: 185 TIFDTLNAKAAIFALEALFDDRGERLPVMISGTITDASGRTLSGQTTEAFWNSVRHAQPL 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALG +ELR Y++ELS A+ +V+AHPNAGLPN FGEYD + MA + E+A +
Sbjct: 245 SIGLNCALGAEELRPYLEELSTKADTFVSAHPNAGLPNEFGEYDQTPEEMAAIVAEFASS 304
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
G +NI+GGCCG+TP+HIAA+ A++G+APRK+PE P ACRL+GLEP NI + SLFVNVGE
Sbjct: 305 GLVNIIGGCCGSTPEHIAAIHAAIQGMAPRKVPERPRACRLAGLEPFNIEKGSLFVNVGE 364
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTNVTGSA+FKRLI EE Y+ AL+VA QVENGAQIIDINMDEGML+++ AMVRFLNLIA
Sbjct: 365 RTNVTGSARFKRLIVEEDYTTALEVALDQVENGAQIIDINMDEGMLESQEAMVRFLNLIA 424
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
GEPDIARVPIMIDSSKW++IE GLKC+QGK +VNSIS+KEG +AF+ A L RRYGAAVV
Sbjct: 425 GEPDIARVPIMIDSSKWEIIEAGLKCVQGKAVVNSISLKEGEEAFLEQATLCRRYGAAVV 484
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDE GQADT ARK EIC+RAY++L E VGFPPEDIIFDPNIFA+ATGIEEH+NYA D
Sbjct: 485 VMAFDETGQADTFARKTEICQRAYELLIERVGFPPEDIIFDPNIFAIATGIEEHDNYAVD 544
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI A I+ LPHA++SGGVSNVSFSFRGNDPVREAIH+VFLY+AIR G+ MGIVNAGQ
Sbjct: 545 FIEATRWIREHLPHAMVSGGVSNVSFSFRGNDPVREAIHSVFLYHAIRAGLTMGIVNAGQ 604
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
LA+YDDLP ELR+AVEDV+LNRR DGTERL++LAEKY+G + A + EWRSWEV K
Sbjct: 605 LAVYDDLPEELREAVEDVVLNRRSDGTERLVDLAEKYKGDGS-GAAKKEDLEWRSWEVEK 663
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
R+E++LVKGIT FIE+DTE ARQ+A RPIEVIEGPLMDGMNVVGDLFG GKMFLPQVVKS
Sbjct: 664 RIEHALVKGITAFIEEDTELARQRAARPIEVIEGPLMDGMNVVGDLFGAGKMFLPQVVKS 723
Query: 722 ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
ARVMKQAVAYL PFIEA K E + GK+V+ATVKGDVHDIGKNIVGVVLQCNNYE++DL
Sbjct: 724 ARVMKQAVAYLIPFIEAEKSEDTQAKGKIVMATVKGDVHDIGKNIVGVVLQCNNYEVIDL 783
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPAEKIL+TA++VNAD+IGLSGLITPSLDEMV+VAKEM+RQGF +PLLIGGATTSKA
Sbjct: 784 GVMVPAEKILQTARDVNADIIGLSGLITPSLDEMVHVAKEMKRQGFKLPLLIGGATTSKA 843
Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
HTAVK+E Y P +YV +ASR VGV LLS T + +VA + EYE VR ++ +++P+
Sbjct: 844 HTAVKVEPQYDEPVIYVTDASRAVGVAGKLLSPTLKPAYVAEIKAEYEQVRERNAKRRPK 903
Query: 901 TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGK 959
++ AR DW +YTPP G++ E IE L IDWTPFFM+W LAGK
Sbjct: 904 AADLSYAEARQRKLPIDWDSYTPPRPAITGLKVFEGYDIEELVERIDWTPFFMSWELAGK 963
Query: 960 YPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDD-IEIYRDET 1018
YP+I +D VVG A+ LF DA ML KL K + RGV+GL+PAN V DD IE+Y DE+
Sbjct: 964 YPKIFDDAVVGEAARNLFADAQQMLRKLIDGKHVEARGVIGLWPANSVDDDVIEVYADES 1023
Query: 1019 RTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSG------KADYIGAFAVTGGLEEDA 1071
R+ VI HH+RQQT K Y LADFVAP+ + D++G FAVT G +A
Sbjct: 1024 RSEVIARLHHIRQQTTKNRDGVCYSLADFVAPRYDADGNERDQLDWVGGFAVTTGHGVEA 1083
Query: 1072 LADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQ 1131
LA+ ++A DDY+ IMV+AL DRLAEAFAE +HERVRK +WGY P+E L N+ LI E YQ
Sbjct: 1084 LAERYKAAGDDYSAIMVQALTDRLAEAFAERMHERVRKEFWGYVPDETLDNDALIAEKYQ 1143
Query: 1132 GIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYA 1191
GIRPAPGYPACP+HTEK T+++LL+ ++ G++LTE+FAMWP A+VSGWYFSHP +KY++
Sbjct: 1144 GIRPAPGYPACPDHTEKRTLFQLLDATENAGIELTENFAMWPAAAVSGWYFSHPQAKYFS 1203
Query: 1192 VAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
+I RDQVE A+RKGMS+ E+ERWL+P L YD
Sbjct: 1204 TGKITRDQVEALAQRKGMSLEELERWLSPVLSYD 1237
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: 3831
Number of extensions: 156
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: 1239
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1192
Effective search space: 1406560
Effective search space used: 1406560
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_086511312.1 BZY95_RS18210 (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.3558.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 1782.1 0.0 0 1781.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511312.1 BZY95_RS18210 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511312.1 BZY95_RS18210 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1781.9 0.0 0 0 3 1181 .. 18 1203 .. 16 1204 .. 0.98
Alignments for each domain:
== domain 1 score: 1781.9 bits; conditional E-value: 0
TIGR02082 3 krilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68
+ril+lDG+mGt++q+a+L+eadFrge + d+++elkGnndlL lt P++++ +hray+eaGaDi+e
lcl|NCBI__GCF_002151265.1:WP_086511312.1 18 ERILMLDGGMGTMIQNAKLEEADFRGErFGDWPSELKGNNDLLALTCPDLVTRLHRAYLEAGADIIE 84
89***************************************************************** PP
TIGR02082 69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135
tntFnst +++adY++e+++ e+n+++a+lar+++d + ++ +R+vaG+lGPt+++a+lspdv++
lcl|NCBI__GCF_002151265.1:WP_086511312.1 85 TNTFNSTRLSQADYGMEALVPEINRESARLARAACDAVAAETGVPRYVAGVLGPTSRTASLSPDVND 151
******************************************************************* PP
TIGR02082 136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202
p+ rnvt+d+l+d Y e++++l++GG+Dl+Liet+fDtlnakaa+fa+e +f+++g++lP++isg+i
lcl|NCBI__GCF_002151265.1:WP_086511312.1 152 PAKRNVTFDQLRDNYYEAAEALIEGGADLILIETIFDTLNAKAAIFALEALFDDRGERLPVMISGTI 218
******************************************************************* PP
TIGR02082 203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269
+d+sGrtLsGqt+eaf +s++ha+ l++GLnCalGa+elr++++els +a+++vs++PnaGLPn++g
lcl|NCBI__GCF_002151265.1:WP_086511312.1 219 TDASGRTLSGQTTEAFWNSVRHAQPLSIGLNCALGAEELRPYLEELSTKADTFVSAHPNAGLPNEFG 285
******************************************************************* PP
TIGR02082 270 eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealk 336
eYd+tpee+a++++efa+ gl+ni+GGCCG+tPehi+ai +a+++++prk++e + +++l+gle+++
lcl|NCBI__GCF_002151265.1:WP_086511312.1 286 EYDQTPEEMAAIVAEFASSGLVNIIGGCCGSTPEHIAAIHAAIQGMAPRKVPERPRACRLAGLEPFN 352
******************************************************************* PP
TIGR02082 337 iaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkl 403
i++ s fvn+GeRtnv+Gs++f++li +edy al++a +qve+Gaqi+Din+De++l+++++m+++
lcl|NCBI__GCF_002151265.1:WP_086511312.1 353 IEKGSLFVNVGERTNVTGSARFKRLIVEEDYTTALEVALDQVENGAQIIDINMDEGMLESQEAMVRF 419
******************************************************************* PP
TIGR02082 404 lsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvm 470
l+l+a+epdia+vP+m+Dss++e++eaGLk++qGka+vnsislk+Gee+Fle+a l ++yGaavvvm
lcl|NCBI__GCF_002151265.1:WP_086511312.1 420 LNLIAGEPDIARVPIMIDSSKWEIIEAGLKCVQGKAVVNSISLKEGEEAFLEQATLCRRYGAAVVVM 486
******************************************************************* PP
TIGR02082 471 afDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireik 537
afDe Gqa+t ++k ei++Ray+ll+e+vgfppediifDpni++iatGieehd+ya+dfiea+r+i+
lcl|NCBI__GCF_002151265.1:WP_086511312.1 487 AFDETGQADTFARKTEICQRAYELLIERVGFPPEDIIFDPNIFAIATGIEEHDNYAVDFIEATRWIR 553
******************************************************************* PP
TIGR02082 538 eelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevve 604
e+lP+a +sgGvsnvsFs+rgnd+vRea+hsvFLy+ai+aGl mgivnag+lavydd+++elre+ve
lcl|NCBI__GCF_002151265.1:WP_086511312.1 554 EHLPHAMVSGGVSNVSFSFRGNDPVREAIHSVFLYHAIRAGLTMGIVNAGQLAVYDDLPEELREAVE 620
******************************************************************* PP
TIGR02082 605 dlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleeark 671
d++l+rr++ te+L++lae+ykg + + +++ ewr+++ve+R+e+alvkG++ +ieed+e ar+
lcl|NCBI__GCF_002151265.1:WP_086511312.1 621 DVVLNRRSDGTERLVDLAEKYKGDGSGAA-KKEDLEWRSWEVEKRIEHALVKGITAFIEEDTELARQ 686
***********************999854.58889******************************** PP
TIGR02082 672 klkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkiv 737
++ +p+e+iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmk+avayL+P++e+ek+ed ++kGkiv
lcl|NCBI__GCF_002151265.1:WP_086511312.1 687 RAARPIEVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAYLIPFIEAEKSEDtQAKGKIV 753
********************************************************988689***** PP
TIGR02082 738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804
+atvkGDvhDiGkniv+vvL+cn+yev+dlGv+vP+ekil++a++ +aD+iglsGLi++sldemv+v
lcl|NCBI__GCF_002151265.1:WP_086511312.1 754 MATVKGDVHDIGKNIVGVVLQCNNYEVIDLGVMVPAEKILQTARDVNADIIGLSGLITPSLDEMVHV 820
******************************************************************* PP
TIGR02082 805 aeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekik 871
a+em+r+g+k+Pll+GGa++skah+avk++++Y+ +v+yv+das+av v+ klls + k +++++ik
lcl|NCBI__GCF_002151265.1:WP_086511312.1 821 AKEMKRQGFKLPLLIGGATTSKAHTAVKVEPQYDEPVIYVTDASRAVGVAGKLLSPTLKPAYVAEIK 887
******************************************************************* PP
TIGR02082 872 eeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwka 937
+eye++re+ +++ k +ls ++ar+ ++ +d+ +++p p G kv+e + ieel++ iDw++
lcl|NCBI__GCF_002151265.1:WP_086511312.1 888 AEYEQVRERNAKRRPKAADLSYAEARQRKLPIDWD-SYTPPRPAITGLKVFEGYdIEELVERIDWTP 953
**********************************9.9****************************** PP
TIGR02082 938 lFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgdd.ieiyt 1003
+F++Wel+gkypki++d ++g+ ar+lf+da+++l kl+ k ++argv+Gl+Pa+sv+dd ie+y+
lcl|NCBI__GCF_002151265.1:WP_086511312.1 954 FFMSWELAGKYPKIFDDAVVGEAARNLFADAQQMLRKLIDGKHVEARGVIGLWPANSVDDDvIEVYA 1020
**********************************************************999569*** PP
TIGR02082 1004 detvsqetkpiatvrekleqlrqqsdr.ylclaDfiask......esGikDylgallvtaglgaeel 1063
de++ ++ia +++ ++q+ +++d ++laDf+a++ e + D++g ++vt+g g+e+l
lcl|NCBI__GCF_002151265.1:WP_086511312.1 1021 DESR---SEVIARLHHIRQQTTKNRDGvCYSLADFVAPRydadgnERDQLDWVGGFAVTTGHGVEAL 1084
9999...66666666556666666665699*********75333222567999************** PP
TIGR02082 1064 akkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGY 1130
a++++a ddy++i+v+al+drlaea+ae +hervRke+wgy +e ld++ l+ e+Y+Girpa+GY
lcl|NCBI__GCF_002151265.1:WP_086511312.1 1085 AERYKAAGDDYSAIMVQALTDRLAEAFAERMHERVRKEFWGYVPDETLDNDALIAEKYQGIRPAPGY 1151
******************************************************************* PP
TIGR02082 1131 pacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfa 1181
pacPdhtek+tl++Ll+a + G++lte++a++P+a+vsg+yf+hp+akYf+
lcl|NCBI__GCF_002151265.1:WP_086511312.1 1152 PACPDHTEKRTLFQLLDATEnAGIELTENFAMWPAAAVSGWYFSHPQAKYFS 1203
****************98766******************************7 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1239 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: 9.29
//
[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