Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_011159241.1 TX73_RS18905 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000195775.1:WP_011159241.1
Length = 1293
Score = 1485 bits (3844), Expect = 0.0
Identities = 759/1237 (61%), Positives = 923/1237 (74%), Gaps = 16/1237 (1%)
Query: 1 MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60
+S+K QL A +RILVLDG MGTMIQ +L+EA FRGERF D+ DL+GNNDLL+L++
Sbjct: 5 ISAKRTQLLALAAQRILVLDGAMGTMIQQLQLDEAAFRGERFKDFHRDLRGNNDLLILTQ 64
Query: 61 PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120
P+ I IH Y AGADI+ TNTF+ST+IA ADY+M L+ E++ A+LAR A + A
Sbjct: 65 PQAIEDIHAQYLRAGADIVATNTFSSTSIAQADYEMSELAYEMSRDGARLARNAAAKVEA 124
Query: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180
KPR+VAG +GPTNRTASISPDV +P +R +TFD L AY E L++GGAD++L+
Sbjct: 125 EDG-KPRFVAGAIGPTNRTASISPDVANPGYRAVTFDDLRIAYSEQINGLLDGGADILLL 183
Query: 181 ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240
ET+FDTLNAKAA++A+ EA G+++P+MISGTITD SGR LSGQ EAF+NS+RHA
Sbjct: 184 ETIFDTLNAKAALYAIAEITEARGIDVPVMISGTITDKSGRLLSGQMPEAFWNSVRHARP 243
Query: 241 LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300
+T G NCALG +LR ++ ++SR+A+ V A+PNAGLPN FG+YD + MA + E+A+
Sbjct: 244 ITIGFNCALGAKDLRAHIADISRVADTLVCAYPNAGLPNEFGQYDESPEYMASLVGEFAE 303
Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
AG +NIVGGCCGTTP HI A++ AV PR +P I RLSGLEP + +D FVNVG
Sbjct: 304 AGLVNIVGGCCGTTPAHIKAIAEAVAPHKPRVIPTIDPRLRLSGLEPFELTKDIPFVNVG 363
Query: 361 ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
ERTNVTGSAKF++LI Y+ AL VAR QVENGAQIID+NMDEG+LD+EAAM+ FLNL+
Sbjct: 364 ERTNVTGSAKFRKLITAGDYAAALQVARDQVENGAQIIDVNMDEGLLDSEAAMITFLNLV 423
Query: 421 AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
A EPDIA+VP+M+DSSK++VIE GLKC+QGK +VNSIS+KEG D F+H A++ RR+GAAV
Sbjct: 424 AAEPDIAKVPVMVDSSKFNVIEAGLKCLQGKPVVNSISLKEGEDKFLHEARIARRHGAAV 483
Query: 481 VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
VVMAFDE GQADT ARK EIC RAY IL VGFPPEDIIFDPNIFA+ATG+EEHNNY
Sbjct: 484 VVMAFDETGQADTYARKTEICARAYDILVNRVGFPPEDIIFDPNIFAIATGLEEHNNYGV 543
Query: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
DFI A I++ LPHA ISGGVSN+SFSFRGN+PVREA+H+VFLY+AI+ GMDMGIVNAG
Sbjct: 544 DFIEATRWIRQNLPHAHISGGVSNLSFSFRGNEPVREAMHSVFLYHAIKAGMDMGIVNAG 603
Query: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
Q+ +YDD+ ELR EDVILNR +ERLL LA+KYRG Q WRSW V
Sbjct: 604 QMIVYDDIDPELRQVCEDVILNRDPGASERLLALADKYRGQGKQQ--KEQDLAWRSWPVE 661
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
+RL ++LV GITEFIE DTEEAR +A RP+ VIEGPLM GMNVVGDLFG+GKMFLPQVVK
Sbjct: 662 QRLSHALVHGITEFIELDTEEARAKAERPLHVIEGPLMAGMNVVGDLFGDGKMFLPQVVK 721
Query: 721 SARVMKQAVAYLEPFIEASKEQG----------KTNGKMVIATVKGDVHDIGKNIVGVVL 770
SARVMKQAVAYL PF+E K + T GK+V+ATVKGDVHDIGKNIVG+VL
Sbjct: 722 SARVMKQAVAYLMPFMEEEKARNLAAGTDTGERATAGKIVLATVKGDVHDIGKNIVGIVL 781
Query: 771 QCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPL 830
QCNN+E++DLGVMVPA KI+ TAK NAD++GLSGLITPSLDEM +A E++R GF IPL
Sbjct: 782 QCNNFEVIDLGVMVPAAKIIETAKAENADIVGLSGLITPSLDEMSFLAGELQRSGFNIPL 841
Query: 831 LIGGATTSKAHTAVKIEQNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYET 889
LIGGATTS+ HTAVKI+ Y SG V+V +ASR VGV ++LLS + + A R +Y
Sbjct: 842 LIGGATTSRVHTAVKIDPAYPSGSVVHVNDASRAVGVASSLLSKDRGAAYAAEVRADYAK 901
Query: 890 VRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWT 948
+ H R + +TL AAR N DW A +P +G + S+ L YIDWT
Sbjct: 902 ISAAHHRAQADKKRLTLAAARANATKIDWAATSPVKPSFIGTRSFSGYSLAELAEYIDWT 961
Query: 949 PFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG 1008
PFF W LAG++P IL+D VVG A+ L+ DA MLD++ E + +G +PAN G
Sbjct: 962 PFFQAWELAGRFPAILDDSVVGEAARSLYADARKMLDRIVTENWFTAKATIGFWPANADG 1021
Query: 1009 DDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGL 1067
DDI +Y DETRT I H LRQQ +K G AN L+DF+AP S ADYIG F VT G+
Sbjct: 1022 DDILVYADETRTTPIATLHTLRQQLDKREGRANAALSDFIAPVASSVADYIGGFVVTAGI 1081
Query: 1068 EEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIR 1127
ED +AD F+A+ DDY+ IMVKALADRLAEAFAE +H RVR+ +WGYA +ENLS E+LI
Sbjct: 1082 GEDVIADKFKAERDDYSSIMVKALADRLAEAFAERMHARVRREFWGYAADENLSAEDLIL 1141
Query: 1128 ENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDS 1187
E YQGIRPAPGYPA P+HTEKAT++ELL+ E G+ LTESFAMWPG+SVSG YFSHP S
Sbjct: 1142 EKYQGIRPAPGYPAQPDHTEKATLFELLDAEASAGVTLTESFAMWPGSSVSGLYFSHPQS 1201
Query: 1188 KYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGY 1224
Y+ V +I+RDQVEDYA RKG V ERWLAP L Y
Sbjct: 1202 AYFGVGKIERDQVEDYAARKGWDVATAERWLAPVLNY 1238
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: 3633
Number of extensions: 140
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: 1293
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1245
Effective search space: 1467855
Effective search space used: 1467855
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_011159241.1 TX73_RS18905 (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.16318.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 1764.1 0.0 0 1763.9 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011159241.1 TX73_RS18905 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195775.1:WP_011159241.1 TX73_RS18905 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1763.9 0.0 0 0 2 1182 .] 17 1206 .. 16 1206 .. 0.99
Alignments for each domain:
== domain 1 score: 1763.9 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+rilvlDGamGt++q+ +L+ea Frge ++d +r+l+GnndlL lt+P++i++ih +y+ aGaDiv
lcl|NCBI__GCF_000195775.1:WP_011159241.1 17 AQRILVLDGAMGTMIQQLQLDEAAFRGErFKDFHRDLRGNNDLLILTQPQAIEDIHAQYLRAGADIV 83
69***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
tntF+st+ia+adY++ ++aye+++ +a+lar++a++++ + k+RfvaG++GPtn++a++spdv
lcl|NCBI__GCF_000195775.1:WP_011159241.1 84 ATNTFSSTSIAQADYEMSELAYEMSRDGARLARNAAAKVEAEDGKPRFVAGAIGPTNRTASISPDVA 150
******************************************************************* PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p++r vt+d+l+ aY+eq++glldGG+D+lL+et+fDtlnakaal+a+ e+ e++g+++P++isg+
lcl|NCBI__GCF_000195775.1:WP_011159241.1 151 NPGYRAVTFDDLRIAYSEQINGLLDGGADILLLETIFDTLNAKAALYAIAEITEARGIDVPVMISGT 217
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+dksGr+LsGq eaf +s++ha +++G nCalGa++lr ++ +s+ a++lv ++PnaGLPn++
lcl|NCBI__GCF_000195775.1:WP_011159241.1 218 ITDKSGRLLSGQMPEAFWNSVRHARPITIGFNCALGAKDLRAHIADISRVADTLVCAYPNAGLPNEF 284
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g+Yd+ pe +a+ + efae+gl+nivGGCCGttP+hi+aiaeav+ kpr ++++++++lsgle++
lcl|NCBI__GCF_000195775.1:WP_011159241.1 285 GQYDESPEYMASLVGEFAEAGLVNIVGGCCGTTPAHIKAIAEAVAPHKPRVIPTIDPRLRLSGLEPF 351
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+++++ fvn+GeRtnv+Gs+kfrkli+a+dy +al++a++qve+Gaqi+D+n+De+llD+ea+m +
lcl|NCBI__GCF_000195775.1:WP_011159241.1 352 ELTKDIPFVNVGERTNVTGSAKFRKLITAGDYAAALQVARDQVENGAQIIDVNMDEGLLDSEAAMIT 418
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+a+epdiakvP+m+Dss+f+v+eaGLk++qGk +vnsislk+Ge++Fl++a++++++Gaavvv
lcl|NCBI__GCF_000195775.1:WP_011159241.1 419 FLNLVAAEPDIAKVPVMVDSSKFNVIEAGLKCLQGKPVVNSISLKEGEDKFLHEARIARRHGAAVVV 485
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe Gqa+t+++k ei+ Ray++l+++vgfppediifDpni++iatG+eeh++y++dfiea+r+i
lcl|NCBI__GCF_000195775.1:WP_011159241.1 486 MAFDETGQADTYARKTEICARAYDILVNRVGFPPEDIIFDPNIFAIATGLEEHNNYGVDFIEATRWI 552
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
+++lP+a+isgGvsn+sFs+rgn++vRea+hsvFLy+aikaG+Dmgivnag++ vyddid+elr+v+
lcl|NCBI__GCF_000195775.1:WP_011159241.1 553 RQNLPHAHISGGVSNLSFSFRGNEPVREAMHSVFLYHAIKAGMDMGIVNAGQMIVYDDIDPELRQVC 619
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed+il+r++ a+e+Ll la++y+g+ ++ +++q +wr++pve+RL++alv+G++e+ie d+eear
lcl|NCBI__GCF_000195775.1:WP_011159241.1 620 EDVILNRDPGASERLLALADKYRGQGKQ--QKEQDLAWRSWPVEQRLSHALVHGITEFIELDTEEAR 684
*************************999..5578899****************************** PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed....... 730
k+++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+avayL+P++e+ek+ +
lcl|NCBI__GCF_000195775.1:WP_011159241.1 685 AKAERPLHVIEGPLMAGMNVVGDLFGDGKMFLPQVVKSARVMKQAVAYLMPFMEEEKARNlaagtdt 751
**********************************************************99******* PP
TIGR02082 731 ...kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLi 794
++GkivlatvkGDvhDiGkniv++vL+cn++ev+dlGv+vP++ki+e+ak ++aD++glsGLi
lcl|NCBI__GCF_000195775.1:WP_011159241.1 752 gerATAGKIVLATVKGDVHDIGKNIVGIVLQCNNFEVIDLGVMVPAAKIIETAKAENADIVGLSGLI 818
**999************************************************************** PP
TIGR02082 795 vksldemvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllse 860
++sldem + a e++r g++iPll+GGa++s+ h+avki+++Y +g+vv+v+das+av v+++lls+
lcl|NCBI__GCF_000195775.1:WP_011159241.1 819 TPSLDEMSFLAGELQRSGFNIPLLIGGATTSRVHTAVKIDPAYpSGSVVHVNDASRAVGVASSLLSK 885
*******************************************779********************* PP
TIGR02082 861 kkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.i 926
++ a+++++++++y +i +++ + ++ l+++aar + ++d+ ++++++p f+Gt+ + + +
lcl|NCBI__GCF_000195775.1:WP_011159241.1 886 DRGAAYAAEVRADYAKISAAHHRAQADKKRLTLAAARANATKIDWA-ATSPVKPSFIGTRSFSGYsL 951
**********************************************.******************** PP
TIGR02082 927 eellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaq 993
+el +yiDw+++F +Wel+g++p il+d+++g+ ar l++da+++ld++++e+ +a++ +G++Pa+
lcl|NCBI__GCF_000195775.1:WP_011159241.1 952 AELAEYIDWTPFFQAWELAGRFPAILDDSVVGEAARSLYADARKMLDRIVTENWFTAKATIGFWPAN 1018
******************************************************************* PP
TIGR02082 994 svgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglg 1059
gddi +y+det+ t+piat+++ ++ql + ++r + +l+Dfia+ +s +Dy+g ++vtag+g
lcl|NCBI__GCF_000195775.1:WP_011159241.1 1019 ADGDDILVYADETR---TTPIATLHTLRQQLDKREGRaNAALSDFIAPVASSVADYIGGFVVTAGIG 1082
************99...99*****9999999999999999*************************** PP
TIGR02082 1060 aeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirp 1126
++ +a+k++a++ddy+si+vkaladrlaea+ae +h rvR+e+wgya++enl+ edl+ e+Y+Girp
lcl|NCBI__GCF_000195775.1:WP_011159241.1 1083 EDVIADKFKAERDDYSSIMVKALADRLAEAFAERMHARVRREFWGYAADENLSAEDLILEKYQGIRP 1149
******************************************************************* PP
TIGR02082 1127 afGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
a+GYpa+Pdhtekatl+eLl+ae G++ltes+a++P +svsglyf+hp++ Yf v
lcl|NCBI__GCF_000195775.1:WP_011159241.1 1150 APGYPAQPDHTEKATLFELLDAEAsAGVTLTESFAMWPGSSVSGLYFSHPQSAYFGV 1206
***********************99******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1293 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: 0.09u 0.04s 00:00:00.13 Elapsed: 00:00:00.11
# Mc/sec: 12.77
//
[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