Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012046873.1 BBTA_RS33075 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000015165.1:WP_012046873.1
Length = 1287
Score = 1473 bits (3814), Expect = 0.0
Identities = 758/1221 (62%), Positives = 925/1221 (75%), Gaps = 13/1221 (1%)
Query: 14 ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73
ERIL+LDG MGTMIQ+ + +EA FR ERF D+ DL+GNNDLL+L++PE I IH Y
Sbjct: 18 ERILILDGAMGTMIQALQFDEAAFRSERFKDFHRDLRGNNDLLILTQPEAIEDIHAQYLR 77
Query: 74 AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133
AGADI+ TNTF++T+IA ADY + + E+N A+LAR A A K R+VAG +
Sbjct: 78 AGADIVATNTFSATSIAQADYDLSDIIYELNREGARLARNAATR-VAAEDGKQRFVAGAM 136
Query: 134 GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193
GPTNRTASISPDV++P +R +TFD L AY E + L++GGADL+L+ET+FDTLNAKAA+
Sbjct: 137 GPTNRTASISPDVSNPGYRAVTFDDLRIAYGEQARGLLDGGADLLLVETIFDTLNAKAAL 196
Query: 194 FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253
+A+ EA G+++P+MISGTITD SGR LSGQ EAF+NS+RHA+ LT G NCALG ++
Sbjct: 197 YAIAELCEARGIDVPVMISGTITDKSGRLLSGQMPEAFWNSVRHAKPLTIGFNCALGAED 256
Query: 254 LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313
LR +V ++ R+A+ V A+PNAGLPN FG+YD MA+ I E+A+ G +NIVGGCCGT
Sbjct: 257 LRAHVADIGRVADTLVCAYPNAGLPNEFGQYDETPAYMARLIGEFARDGLVNIVGGCCGT 316
Query: 314 TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373
TP HIAA++ AV PR +PEI RLSGLEP + + FVNVGERTNVTGSAKF++
Sbjct: 317 TPDHIAAIAAAVAPHKPRAVPEIAPRLRLSGLEPFELTPEIPFVNVGERTNVTGSAKFRK 376
Query: 374 LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433
LI Y+ AL VAR QVENGAQ+ID+NMDEG+LD+EAAM FLNL+A EPDIARVP+M+
Sbjct: 377 LITAGDYTAALQVARDQVENGAQVIDVNMDEGLLDSEAAMRTFLNLVAAEPDIARVPVMV 436
Query: 434 DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493
DSSK+ VIE GLKC+QGK +VNSIS+KEG + FIH AK+ RR+GAAVVVMAFDE GQADT
Sbjct: 437 DSSKFHVIEAGLKCVQGKPVVNSISLKEGEEKFIHEAKIARRHGAAVVVMAFDETGQADT 496
Query: 494 RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553
RK EIC RAYKIL E++GFPPEDIIFDPNIFA+ATGIEEHNNY DFI A I+ L
Sbjct: 497 YKRKTEICARAYKILVEQIGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATRWIRSNL 556
Query: 554 PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613
PHA +SGGVSN+SFSFRGN+PVREA+H+VFLY+AI+ GMDMGIVNAGQ+ +YDD+ ELR
Sbjct: 557 PHAHVSGGVSNLSFSFRGNEPVREAMHSVFLYHAIKAGMDMGIVNAGQMIVYDDIDPELR 616
Query: 614 DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673
EDV+LNR +ERLL LAEK+RG + T A A WR W V+KRL ++LV GITE
Sbjct: 617 QVCEDVVLNRDPGASERLLALAEKFRG-QGKQTKEADLA-WRDWPVDKRLSHALVHGITE 674
Query: 674 FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733
FIE DTEEAR +TRP++VIEGPLM GMNVVGDLFG+GKMFLPQVVKSARVMKQAVAYL
Sbjct: 675 FIEVDTEEARAASTRPLDVIEGPLMAGMNVVGDLFGDGKMFLPQVVKSARVMKQAVAYLM 734
Query: 734 PFIEASK--EQGKTN-----GKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPA 786
PF+EA K +G+ N GK+V+ATVKGDVHDIGKNIVG+VLQCNN+E++DLGVMVPA
Sbjct: 735 PFMEAEKAANKGRANERSNAGKIVLATVKGDVHDIGKNIVGIVLQCNNFEVIDLGVMVPA 794
Query: 787 EKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKI 846
KI+ TAK NAD+IGLSGLITPSLDEM +A EMERQG +PLLIGGATTS+ HTAVKI
Sbjct: 795 AKIIETAKTENADIIGLSGLITPSLDEMAYLASEMERQGLNMPLLIGGATTSRVHTAVKI 854
Query: 847 EQNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVT 905
+ NY SGP V+V +ASR VGV ++LLS ++D + A R EY+ + H R + +
Sbjct: 855 DPNYQSGPVVHVNDASRAVGVASSLLSAERKDAYAAEIRTEYQKIAAAHLRGQADKKRLK 914
Query: 906 LEAARDNDFAFDWQAYTPPVAHRLGVQE-VEASIETLRNYIDWTPFFMTWSLAGKYPRIL 964
L AR N D+ P LGV+ + + L YIDWTPFF TW LAG++P IL
Sbjct: 915 LSDARANAPKIDFAKARPVKPTFLGVKTFADYDLAELVPYIDWTPFFQTWELAGRFPAIL 974
Query: 965 EDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVIN 1024
+D VG A+ L+ DA ML ++ EK R +G +PAN GDDI +Y D++RT I
Sbjct: 975 DDAKVGEAARALYDDALKMLKRIVDEKWFTARAAIGFWPANAEGDDIVLYADDSRTERIA 1034
Query: 1025 VSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDY 1083
H LRQQ EK G N L+DFVAP S DY+G F VT GL EDA+AD F+ +DDY
Sbjct: 1035 TLHTLRQQLEKREGRFNTALSDFVAPVGSSVPDYVGGFVVTAGLGEDAVADRFKNANDDY 1094
Query: 1084 NKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACP 1143
+ I+VKALADRLAEAFAE LH RVR+ +W YAP+E LS ++LI E YQGIRPAPGYPA P
Sbjct: 1095 SSILVKALADRLAEAFAERLHARVRREFWAYAPDEALSPDDLILEKYQGIRPAPGYPAQP 1154
Query: 1144 EHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDY 1203
+HTEKAT++ELL+ E + G++LTESFAMWPG+SVSG YF+ P+S Y+ V +I+RDQVEDY
Sbjct: 1155 DHTEKATLFELLDAENNAGVRLTESFAMWPGSSVSGLYFASPESFYFGVGKIERDQVEDY 1214
Query: 1204 ARRKGMSVTEVERWLAPNLGY 1224
A RKGM+V EVERWLAP L Y
Sbjct: 1215 ATRKGMTVAEVERWLAPILNY 1235
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: 3768
Number of extensions: 144
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: 1287
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1239
Effective search space: 1460781
Effective search space used: 1460781
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_012046873.1 BBTA_RS33075 (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.18830.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 1752.8 0.0 0 1752.6 0.0 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012046873.1 BBTA_RS33075 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012046873.1 BBTA_RS33075 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1752.6 0.0 0 0 2 1182 .] 17 1203 .. 16 1203 .. 0.99
Alignments for each domain:
== domain 1 score: 1752.6 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
++ril+lDGamGt++q+ + +ea Fr e ++d +r+l+GnndlL lt+Pe+i++ih +y+ aGaDiv
lcl|NCBI__GCF_000015165.1:WP_012046873.1 17 RERILILDGAMGTMIQALQFDEAAFRSErFKDFHRDLRGNNDLLILTQPEAIEDIHAQYLRAGADIV 83
68***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
tntF++t+ia+adYdl d +yeln+++a+lar++a+ + + k+RfvaG++GPtn++a++spdv
lcl|NCBI__GCF_000015165.1:WP_012046873.1 84 ATNTFSATSIAQADYDLSDIIYELNREGARLARNAATRVAAEDGKQRFVAGAMGPTNRTASISPDVS 150
****************************************9************************** PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p++r vt+d+l+ aY eq++glldGG+DllL+et+fDtlnakaal+a+ e+ e++g+++P++isg+
lcl|NCBI__GCF_000015165.1:WP_012046873.1 151 NPGYRAVTFDDLRIAYGEQARGLLDGGADLLLVETIFDTLNAKAALYAIAELCEARGIDVPVMISGT 217
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+dksGr+LsGq eaf +s++ha+ l++G nCalGa++lr +v +++ a++lv ++PnaGLPn++
lcl|NCBI__GCF_000015165.1:WP_012046873.1 218 ITDKSGRLLSGQMPEAFWNSVRHAKPLTIGFNCALGAEDLRAHVADIGRVADTLVCAYPNAGLPNEF 284
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g+Yd+tp +a+ + efa++gl+nivGGCCGttP+hi+aia+av+ kpr ++e+ ++++lsgle++
lcl|NCBI__GCF_000015165.1:WP_012046873.1 285 GQYDETPAYMARLIGEFARDGLVNIVGGCCGTTPDHIAAIAAAVAPHKPRAVPEIAPRLRLSGLEPF 351
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
++++e fvn+GeRtnv+Gs+kfrkli+a+dy +al++a++qve+Gaq++D+n+De+llD+ea+m++
lcl|NCBI__GCF_000015165.1:WP_012046873.1 352 ELTPEIPFVNVGERTNVTGSAKFRKLITAGDYTAALQVARDQVENGAQVIDVNMDEGLLDSEAAMRT 418
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+a+epdia+vP+m+Dss+f+v+eaGLk++qGk +vnsislk+Gee+F+++ak+++++Gaavvv
lcl|NCBI__GCF_000015165.1:WP_012046873.1 419 FLNLVAAEPDIARVPVMVDSSKFHVIEAGLKCVQGKPVVNSISLKEGEEKFIHEAKIARRHGAAVVV 485
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe Gqa+t+++k ei+ Rayk+l+e++gfppediifDpni++iatGieeh++y++dfiea+r+i
lcl|NCBI__GCF_000015165.1:WP_012046873.1 486 MAFDETGQADTYKRKTEICARAYKILVEQIGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATRWI 552
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
+ +lP+a++sgGvsn+sFs+rgn++vRea+hsvFLy+aikaG+Dmgivnag++ vyddid+elr+v+
lcl|NCBI__GCF_000015165.1:WP_012046873.1 553 RSNLPHAHVSGGVSNLSFSFRGNEPVREAMHSVFLYHAIKAGMDMGIVNAGQMIVYDDIDPELRQVC 619
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l+r++ a+e+Ll lae+++g+ ++ +k ++ +wr++pv++RL++alv+G++e+ie d+eear
lcl|NCBI__GCF_000015165.1:WP_012046873.1 620 EDVVLNRDPGASERLLALAEKFRGQGKQ-TK-EADLAWRDWPVDKRLSHALVHGITEFIEVDTEEAR 684
************************9999.45.67789****************************** PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed....... 730
++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+avayL+P++e+ek+++
lcl|NCBI__GCF_000015165.1:WP_012046873.1 685 AASTRPLDVIEGPLMAGMNVVGDLFGDGKMFLPQVVKSARVMKQAVAYLMPFMEAEKAANkgraner 751
*********************************************************9999999999 PP
TIGR02082 731 kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivks 797
+++GkivlatvkGDvhDiGkniv++vL+cn++ev+dlGv+vP++ki+e+ak ++aD+iglsGLi++s
lcl|NCBI__GCF_000015165.1:WP_012046873.1 752 SNAGKIVLATVKGDVHDIGKNIVGIVLQCNNFEVIDLGVMVPAAKIIETAKTENADIIGLSGLITPS 818
999**************************************************************** PP
TIGR02082 798 ldemvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkk 863
ldem++ a emer+g+++Pll+GGa++s+ h+avki+++Y+ g+vv+v+das+av v+++lls+++k
lcl|NCBI__GCF_000015165.1:WP_012046873.1 819 LDEMAYLASEMERQGLNMPLLIGGATTSRVHTAVKIDPNYQsGPVVHVNDASRAVGVASSLLSAERK 885
****************************************7489*********************** PP
TIGR02082 864 aeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieel 929
++++++i++ey++i + + + ++ l++++ar + ++d ++++++p+flG+k++ ++ ++el
lcl|NCBI__GCF_000015165.1:WP_012046873.1 886 DAYAAEIRTEYQKIAAAHLRGQADKKRLKLSDARANAPKIDFA-KARPVKPTFLGVKTFADYdLAEL 951
******************************************9.9********************** PP
TIGR02082 930 lkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg 996
++yiDw+++F +Wel+g++p il+d ++g+ ar l++da ++l++++ ek +ar+ +G++Pa+ +g
lcl|NCBI__GCF_000015165.1:WP_012046873.1 952 VPYIDWTPFFQTWELAGRFPAILDDAKVGEAARALYDDALKMLKRIVDEKWFTARAAIGFWPANAEG 1018
******************************************************************* PP
TIGR02082 997 ddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaee 1062
ddi++y+d+++ t+ iat+++ ++ql++ ++r +++l+Df+a+ s Dy+g ++vtaglg+++
lcl|NCBI__GCF_000015165.1:WP_012046873.1 1019 DDIVLYADDSR---TERIATLHTLRQQLEKREGRfNTALSDFVAPVGSSVPDYVGGFVVTAGLGEDA 1082
*******9998...99999999999*********99******************************* PP
TIGR02082 1063 lakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafG 1129
a+++++ +ddy+silvkaladrlaea+ae lh rvR+e+w+ya +e+l+ +dl+ e+Y+Girpa+G
lcl|NCBI__GCF_000015165.1:WP_012046873.1 1083 VADRFKNANDDYSSILVKALADRLAEAFAERLHARVRREFWAYAPDEALSPDDLILEKYQGIRPAPG 1149
******************************************************************* PP
TIGR02082 1130 YpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
Ypa+Pdhtekatl+eLl+ae+ G++ltes+a++P +svsglyfa pe+ Yf v
lcl|NCBI__GCF_000015165.1:WP_012046873.1 1150 YPAQPDHTEKATLFELLDAENnAGVRLTESFAMWPGSSVSGLYFASPESFYFGV 1203
*********************9******************************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1287 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 0.04s 00:00:00.15 Elapsed: 00:00:00.14
# Mc/sec: 10.22
//
[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