Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_010960817.1 MCA_RS07615 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000008325.1:WP_010960817.1
Length = 1237
Score = 1687 bits (4368), Expect = 0.0
Identities = 842/1224 (68%), Positives = 1002/1224 (81%), Gaps = 4/1224 (0%)
Query: 8 LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
L+ L ERIL LDG MGTMIQ Y+L EAD+RG+RFADWP DLKGNNDLL L++P+VI AI
Sbjct: 14 LKRLLKERILFLDGAMGTMIQRYKLAEADYRGQRFADWPRDLKGNNDLLSLTRPDVIEAI 73
Query: 68 HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
H AY EAGADI+ETN+FN+T I+MADY ME L EIN A+A+LAR AD + +TP++PR
Sbjct: 74 HWAYLEAGADIVETNSFNATRISMADYGMEPLVYEINVASARLARQVADRMSRQTPDRPR 133
Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
+VAGVLGPT+RTASISP VNDP FRNI FD LVA+Y E+ + LV+GGAD+ILIET+FDTL
Sbjct: 134 FVAGVLGPTSRTASISPSVNDPGFRNIGFDELVASYDEAVRGLVDGGADIILIETIFDTL 193
Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
NAKAAVFAV+ FE G LP+MISGTITDASGRTLSGQTTEAF+NSLRHA ++ GLNC
Sbjct: 194 NAKAAVFAVERFFEQEGYTLPVMISGTITDASGRTLSGQTTEAFWNSLRHARPISIGLNC 253
Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307
ALG +LRQ+V+ELSRIA+ YV+AHPNAGLPN FGEYD + MA++I +WA+ GFLNI+
Sbjct: 254 ALGAKQLRQHVEELSRIADTYVSAHPNAGLPNEFGEYDESPEAMAREIADWAEQGFLNII 313
Query: 308 GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTG 367
GGCCGTTP HI A+ AV+ PR++PEIP ACRL+GLEP NI SLFVNVGERTNVTG
Sbjct: 314 GGCCGTTPAHIEAIHDAVQHFPPRRIPEIPPACRLAGLEPCNITAGSLFVNVGERTNVTG 373
Query: 368 SAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIA 427
SA F+R+I+E KY EAL+VARQQVE+GAQIID+NMDEGMLD+ AAMV+FLNLIA EPDIA
Sbjct: 374 SAAFRRMIREAKYDEALEVARQQVESGAQIIDVNMDEGMLDSRAAMVQFLNLIAAEPDIA 433
Query: 428 RVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDE 487
RVP+MIDSSKW+++E GLKC+QGKGIVNSIS+KEG AF+HHA+L+RRYGAAV+VMAFDE
Sbjct: 434 RVPVMIDSSKWEILEAGLKCLQGKGIVNSISLKEGEAAFLHHARLVRRYGAAVIVMAFDE 493
Query: 488 QGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACE 547
QGQADTR RK+EIC RAY++LTE+ GFP EDIIFDPNIFAVATGIEEH+ Y DFI A
Sbjct: 494 QGQADTRERKVEICERAYRLLTEKAGFPAEDIIFDPNIFAVATGIEEHDRYGLDFIEAVA 553
Query: 548 DIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDD 607
+IK LPHAL+SGGVSNVSFSFRGND VREAIHAVFLY+AIR GMDMGIVNAGQLAIY++
Sbjct: 554 EIKSRLPHALVSGGVSNVSFSFRGNDAVREAIHAVFLYHAIRAGMDMGIVNAGQLAIYEE 613
Query: 608 LPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSL 667
+P ELRDAVEDVIL RR+D TERLL +A++YRG + + WRS V+KRLE++L
Sbjct: 614 VPEELRDAVEDVILARREDATERLLAIADRYRGEEGAGSERKADMAWRSLPVDKRLEHAL 673
Query: 668 VKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQ 727
VKGI EFIE DTEEAR+Q RP+ VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMK+
Sbjct: 674 VKGIDEFIEVDTEEARRQFERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKK 733
Query: 728 AVAYLEPFIEASK--EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVP 785
AVAYL P+++A K + TNGK+++ATVKGDVHDIGKNIVGVVLQCN +E++DLGVMVP
Sbjct: 734 AVAYLMPYMDAEKAGTEVGTNGKILMATVKGDVHDIGKNIVGVVLQCNGFEVIDLGVMVP 793
Query: 786 AEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVK 845
+KIL+TA+E N D+IGLSGLITPSLDEMV+VA+EMER GF IPL+IGGATTS+AHTAVK
Sbjct: 794 CDKILQTAREENVDIIGLSGLITPSLDEMVHVAREMERLGFEIPLMIGGATTSRAHTAVK 853
Query: 846 IEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVT 905
IE NY GPTVYV +ASR+VGV +LLS +D+F AR RKEYE VR H ++ + ++
Sbjct: 854 IEPNYHGPTVYVTDASRSVGVAGSLLSADLKDEFTARLRKEYEEVRRHHAGRRIQGTLLS 913
Query: 906 LEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPRIL 964
L+ AR F DW Y PP H LG++ +A +E + YIDW+PFF TW LAG YPRIL
Sbjct: 914 LQQARARAFHTDWAHYVPPAPHLLGLEVFDAYPLEEIAGYIDWSPFFHTWELAGSYPRIL 973
Query: 965 EDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVIN 1024
+DEVVG A+ L +DA ML L+ ++ L RGV+G FPAN GDD+ ++ DE+RT +
Sbjct: 974 DDEVVGEHARTLLQDARAMLALLTEQRWLTARGVIGFFPANSEGDDVVLWTDESRTERLA 1033
Query: 1025 VSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDY 1083
V HHLRQQ +K G YCLADFVAP SG ADY+G FAVT G +A + F HDDY
Sbjct: 1034 VLHHLRQQQDKPGGQPAYCLADFVAPVGSGVADYLGGFAVTVGHGIEAPLERFARVHDDY 1093
Query: 1084 NKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACP 1143
+ IM+KALADRLAEAFAE +H+RVR+ +WGYAP E+L NE LI E Y+GIRPAPGYPACP
Sbjct: 1094 SGIMLKALADRLAEAFAERMHQRVRREFWGYAPEESLDNEALIAEAYRGIRPAPGYPACP 1153
Query: 1144 EHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDY 1203
+HTEKAT++ LL+ E ++G+ LTESFAM+P +SVSGWYFSH +KY+ V +I RDQVEDY
Sbjct: 1154 DHTEKATLFRLLDAEANSGISLTESFAMYPASSVSGWYFSHASAKYFNVGKIGRDQVEDY 1213
Query: 1204 ARRKGMSVTEVERWLAPNLGYDAD 1227
ARRKGM+V EVERWLA +LGYDAD
Sbjct: 1214 ARRKGMTVREVERWLASSLGYDAD 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: 3795
Number of extensions: 162
Number of successful extensions: 6
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: 1237
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1190
Effective search space: 1404200
Effective search space used: 1404200
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_010960817.1 MCA_RS07615 (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.23923.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 1805.2 0.0 0 1805.0 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010960817.1 MCA_RS07615 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010960817.1 MCA_RS07615 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1805.0 0.0 0 0 1 1182 [] 18 1202 .. 18 1202 .. 0.99
Alignments for each domain:
== domain 1 score: 1805.0 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++ril lDGamGt++q+++L ead+rg+ +ad++r+lkGnndlL+lt+P+vi+aih ay+eaGaDi
lcl|NCBI__GCF_000008325.1:WP_010960817.1 18 LKERILFLDGAMGTMIQRYKLAEADYRGQrFADWPRDLKGNNDLLSLTRPDVIEAIHWAYLEAGADI 84
579**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
vetn Fn+t i++adY++e ++ye+n ++a+lar+vad ++ +tp+++RfvaG+lGPt+++a++sp+
lcl|NCBI__GCF_000008325.1:WP_010960817.1 85 VETNSFNATRISMADYGMEPLVYEINVASARLARQVADRMSrQTPDRPRFVAGVLGPTSRTASISPS 151
*****************************************899*********************** PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p+frn+ +delv++Y e+v+gl+dGG+D++Liet+fDtlnakaa+fave+ fe++g lP++is
lcl|NCBI__GCF_000008325.1:WP_010960817.1 152 VNDPGFRNIGFDELVASYDEAVRGLVDGGADIILIETIFDTLNAKAAVFAVERFFEQEGYTLPVMIS 218
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266
g+i+d+sGrtLsGqt+eaf +sl+ha +++GLnCalGa++lr++v+els++a+++vs++PnaGLPn
lcl|NCBI__GCF_000008325.1:WP_010960817.1 219 GTITDASGRTLSGQTTEAFWNSLRHARPISIGLNCALGAKQLRQHVEELSRIADTYVSAHPNAGLPN 285
******************************************************************* PP
TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
++geYd+ pe +a++++++ae+g+lni+GGCCGttP+hi ai +av+ pr+ +e++++++l+gle
lcl|NCBI__GCF_000008325.1:WP_010960817.1 286 EFGEYDESPEAMAREIADWAEQGFLNIIGGCCGTTPAHIEAIHDAVQHFPPRRIPEIPPACRLAGLE 352
******************************************************************* PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
+ +i+ s fvn+GeRtnv+Gs+ fr++i++ +y+eal++a+qqve+Gaqi+D+n+De++lD++a+m
lcl|NCBI__GCF_000008325.1:WP_010960817.1 353 PCNITAGSLFVNVGERTNVTGSAAFRRMIREAKYDEALEVARQQVESGAQIIDVNMDEGMLDSRAAM 419
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
+++l+l+a+epdia+vP+m+Dss++e+leaGLk++qGk+ivnsislk+Ge++Fl++a+l+++yGaav
lcl|NCBI__GCF_000008325.1:WP_010960817.1 420 VQFLNLIAAEPDIARVPVMIDSSKWEILEAGLKCLQGKGIVNSISLKEGEAAFLHHARLVRRYGAAV 486
******************************************************************* PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
+vmafDe+Gqa+t+++k+ei++Ray+lltek+gfp+ediifDpni+++atGieehdry++dfiea+
lcl|NCBI__GCF_000008325.1:WP_010960817.1 487 IVMAFDEQGQADTRERKVEICERAYRLLTEKAGFPAEDIIFDPNIFAVATGIEEHDRYGLDFIEAVA 553
******************************************************************* PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
eik +lP+a +sgGvsnvsFs+rgndavRea+h+vFLy+ai+aG+Dmgivnag+la+y+++++elr+
lcl|NCBI__GCF_000008325.1:WP_010960817.1 554 EIKSRLPHALVSGGVSNVSFSFRGNDAVREAIHAVFLYHAIRAGMDMGIVNAGQLAIYEEVPEELRD 620
******************************************************************* PP
TIGR02082 602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668
+ved+il+rr++ate+Ll +a++y+g + + s+ ++ +wr+lpv++RLe+alvkG+ e+ie d+ee
lcl|NCBI__GCF_000008325.1:WP_010960817.1 621 AVEDVILARREDATERLLAIADRYRGEEGAGSERKADMAWRSLPVDKRLEHALVKGIDEFIEVDTEE 687
******************************9**9********************************* PP
TIGR02082 669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed..ksk 733
ar++ ++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmkkavayL+Py+++ek+ + ++
lcl|NCBI__GCF_000008325.1:WP_010960817.1 688 ARRQFERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLMPYMDAEKAGTevGTN 754
***********************************************************8775579* PP
TIGR02082 734 GkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800
Gki++atvkGDvhDiGkniv+vvL+cng+ev+dlGv+vP++kil++a++++ D+iglsGLi++slde
lcl|NCBI__GCF_000008325.1:WP_010960817.1 755 GKILMATVKGDVHDIGKNIVGVVLQCNGFEVIDLGVMVPCDKILQTAREENVDIIGLSGLITPSLDE 821
******************************************************************* PP
TIGR02082 801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeel 867
mv+va+emer g++iPl++GGa++s+ah+avki+++Y+g++vyv+das++v v+ +lls++ k+e++
lcl|NCBI__GCF_000008325.1:WP_010960817.1 822 MVHVAREMERLGFEIPLMIGGATTSRAHTAVKIEPNYHGPTVYVTDASRSVGVAGSLLSADLKDEFT 888
******************************************************************* PP
TIGR02082 868 ekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyi 933
+++++eyee+r+++ ++ + + ls+++ar f++d+ ++ +pap+ lG +v++a+ +ee+ yi
lcl|NCBI__GCF_000008325.1:WP_010960817.1 889 ARLRKEYEEVRRHHAGRRIQGTLLSLQQARARAFHTDWA-HYVPPAPHLLGLEVFDAYpLEEIAGYI 954
***************************************.9************************** PP
TIGR02082 934 DwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddie 1000
Dw ++F +Wel+g+yp+il+de++g+ ar l +da+++l l++++ l+argv+G+fPa+s+gdd++
lcl|NCBI__GCF_000008325.1:WP_010960817.1 955 DWSPFFHTWELAGSYPRILDDEVVGEHARTLLQDARAMLALLTEQRWLTARGVIGFFPANSEGDDVV 1021
******************************************************************* PP
TIGR02082 1001 iytdetvsqetkpiatvrekleqlrqqsdr.....ylclaDfiaskesGikDylgallvtaglgaee 1062
++tde++ t+ +a+++ +lrqq+d+ +claDf+a+ sG +Dylg ++vt+g g+e+
lcl|NCBI__GCF_000008325.1:WP_010960817.1 1022 LWTDESR---TERLAVLH----HLRQQQDKpggqpAYCLADFVAPVGSGVADYLGGFAVTVGHGIEA 1081
****999...88888885....55555555555599******************************* PP
TIGR02082 1063 lakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafG 1129
+++ +ddy+ i++kaladrlaea+ae +h+rvR+e+wgya ee+ld+e l+ e YrGirpa+G
lcl|NCBI__GCF_000008325.1:WP_010960817.1 1082 PLERFARVHDDYSGIMLKALADRLAEAFAERMHQRVRREFWGYAPEESLDNEALIAEAYRGIRPAPG 1148
******************************************************************* PP
TIGR02082 1130 YpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
YpacPdhtekatl++Ll+ae G+ ltes+a++P++svsg+yf+h +akYf+v
lcl|NCBI__GCF_000008325.1:WP_010960817.1 1149 YPACPDHTEKATLFRLLDAEAnSGISLTESFAMYPASSVSGWYFSHASAKYFNV 1202
********************99******************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1237 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: 00:00:00.12
# Mc/sec: 11.97
//
[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