Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_011767448.1 AZO_RS18695 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000061505.1:WP_011767448.1
Length = 1233
Score = 1503 bits (3892), Expect = 0.0
Identities = 773/1235 (62%), Positives = 938/1235 (75%), Gaps = 18/1235 (1%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
+ + E+LR QL +RIL+LDG MGTMIQ Y+L EAD+RG RF + P DLKGNNDLLVL++P
Sbjct: 3 ADRSEELRQQLAQRILILDGAMGTMIQQYKLGEADYRGTRFLEHPKDLKGNNDLLVLTRP 62
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+V+ IH AY +AGADIIET +FN+T ++ A+Y M ++ E+N A+A+L R DE+TAR
Sbjct: 63 DVVGEIHRAYLDAGADIIETCSFNATRVSQAEYGMADIAYELNVASARLVRELCDEFTAR 122
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
P KPRY AGVLGPT+RT SISPDVNDP +RNI FD LV Y ES K L+EGGADL+LIE
Sbjct: 123 NPAKPRYCAGVLGPTSRTLSISPDVNDPGYRNIEFDALVEDYYESAKGLMEGGADLLLIE 182
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAAVFAV+ F+ L LP+MISGTITDASGRTLSGQT EAF+NSL HA +
Sbjct: 183 TIFDTLNAKAAVFAVEKLFDDLDRRLPVMISGTITDASGRTLSGQTAEAFWNSLAHARPI 242
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADTMAKQIREWA 299
+FGLNCALG ELR YV ELS + + +V+AHPNAGLPN YD + +A+ + EWA
Sbjct: 243 SFGLNCALGAKELRAYVDELSNVCDTFVSAHPNAGLPNPLAPTGYDETPEQLAEAVVEWA 302
Query: 300 QAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNV 359
Q+G +NI+GGCCGTTP HIAA+++AV + PR++P+I RLSGLEP N+G DSLFVNV
Sbjct: 303 QSGLVNILGGCCGTTPAHIAAIAQAVAQVPPRRVPDIEKKLRLSGLEPFNVGADSLFVNV 362
Query: 360 GERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNL 419
GERTNVTGS F R+I E ++ +AL VARQQVENGAQ+IDINMDE MLD+ AAM RFL L
Sbjct: 363 GERTNVTGSKAFARMILEGRFDDALAVARQQVENGAQVIDINMDEAMLDSVAAMERFLKL 422
Query: 420 IAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAA 479
IA EPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEG ++F+ A+L RRYGAA
Sbjct: 423 IASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGEESFLRQARLARRYGAA 482
Query: 480 VVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYA 539
V+VMAFDE+GQADT ARKIEIC RAY++L +GFPPEDIIFDPNIFA+ATGIEEH+NYA
Sbjct: 483 VIVMAFDEKGQADTYARKIEICARAYELLV-GIGFPPEDIIFDPNIFAIATGIEEHDNYA 541
Query: 540 QDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNA 599
DFI + IK LPHA SGGVSNVSFSFRGN+PVREAIH VFLY+AI+ G+ MGIVNA
Sbjct: 542 VDFIQSVAWIKANLPHAKTSGGVSNVSFSFRGNEPVREAIHTVFLYHAIKAGLTMGIVNA 601
Query: 600 GQLAIYDDLPAELRDAVEDVILNRR----DDGTERLLELAEKYRGSKTDDTANAQQAEWR 655
G L +YDDL LR+ VEDV+LNR+ + E L+ELA+ + K DT WR
Sbjct: 602 GMLGVYDDLDPVLREKVEDVVLNRKPASGQNPGEALVELAQTVKEGKAKDT--GPDLAWR 659
Query: 656 SWEVNKRLEYSLVKGITEFIEQDTEEAR----QQATRPIEVIEGPLMDGMNVVGDLFGEG 711
W V +RL+++LVKGITEF+ DTEE R + P+ VIEGPLM GM+VVGDLFG G
Sbjct: 660 EWSVEERLKHALVKGITEFVVADTEEVRARLESEGKPPLAVIEGPLMAGMDVVGDLFGAG 719
Query: 712 KMFLPQVVKSARVMKQAVAYLEPFIEASKEQ--GKTNGKMVIATVKGDVHDIGKNIVGVV 769
KMFLPQVVKSARVMKQAVA+L P+IEA K + + G++VIATVKGDVHDIGKNIVGVV
Sbjct: 720 KMFLPQVVKSARVMKQAVAHLIPYIEAEKARTGATSKGRIVIATVKGDVHDIGKNIVGVV 779
Query: 770 LQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIP 829
L CN YE++DLGVMVP +KIL A+E A IGLSGLITPSL+EM +VA EM+RQGF +P
Sbjct: 780 LGCNGYEVIDLGVMVPTDKILNAAREHGAQAIGLSGLITPSLEEMSHVAAEMQRQGFDVP 839
Query: 830 LLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYET 889
LLIGGATTS+AHTA+KI +Y P VYV +ASR VGVV ALLS+ DF A+ +Y+
Sbjct: 840 LLIGGATTSRAHTAIKIAPHYQQPVVYVPDASRAVGVVTALLSEGGAGDFKAQLAADYDK 899
Query: 890 VRIQHGRKKPRTPPVTLEAARDNDF-AFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWT 948
+R QH KK V+LEAAR N + + Y P + LGV ++ ++ LR+YIDW
Sbjct: 900 IRAQHANKK-GVQLVSLEAARANAYNPLSVEGYEPVEPNTLGVMALDVDLDELRDYIDWG 958
Query: 949 PFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG 1008
PFF TW LAG +P+IL+DEVVG A+ +F DA ML+ L A + + + V GLFPAN VG
Sbjct: 959 PFFQTWDLAGSFPKILDDEVVGETARNVFNDAQAMLEDLIAGEWVQAKAVFGLFPANSVG 1018
Query: 1009 DDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGL 1067
DDI Y DE+R + H LRQQ E+ G ++CLADFVAPK SG D+ GAFAVT GL
Sbjct: 1019 DDIAFYADESRDEPMMTWHGLRQQHERPAGKPHWCLADFVAPKASGVRDWCGAFAVTAGL 1078
Query: 1068 EEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIR 1127
+ FEA HDDY IM+K+LADRLAEA AE+LHERVRK YWGYA +E L N LI+
Sbjct: 1079 GIEHKLAEFEAAHDDYRAIMLKSLADRLAEATAEWLHERVRKEYWGYAADEQLDNAALIK 1138
Query: 1128 ENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDS 1187
E Y+GIRPAPGYPACP+HT KA +++LL+ + GM LTES AM P ASVSG+YF+HP+S
Sbjct: 1139 EQYKGIRPAPGYPACPDHTVKAALFQLLDAPTNAGMGLTESMAMTPAASVSGFYFAHPES 1198
Query: 1188 KYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
Y+A+++I RDQV D+A+R G++ RWLAP L
Sbjct: 1199 HYFAISKIGRDQVTDWAQRTGLTEEAAARWLAPLL 1233
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: 3703
Number of extensions: 145
Number of successful extensions: 10
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: 1233
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1186
Effective search space: 1399480
Effective search space used: 1399480
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_011767448.1 AZO_RS18695 (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.2404.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 1704.5 0.0 0 1704.3 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011767448.1 AZO_RS18695 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011767448.1 AZO_RS18695 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1704.3 0.0 0 0 2 1182 .] 14 1203 .. 13 1203 .. 0.98
Alignments for each domain:
== domain 1 score: 1704.3 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+ril+lDGamGt++q+++L ead+rg + +++++lkGnndlL+lt+P+v+ +ihray++aGaDi+
lcl|NCBI__GCF_000061505.1:WP_011767448.1 14 AQRILILDGAMGTMIQQYKLGEADYRGTrFLEHPKDLKGNNDLLVLTRPDVVGEIHRAYLDAGADII 80
79**************************9************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdv 133
et Fn+t +++a+Y+++d ayeln ++a+l re +deft ++p k+R+ aG+lGPt+++ ++spdv
lcl|NCBI__GCF_000061505.1:WP_011767448.1 81 ETCSFNATRVSQAEYGMADIAYELNVASARLVRELCDEFTaRNPAKPRYCAGVLGPTSRTLSISPDV 147
******************************************************************* PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p++rn+++d lv+ Y e++kgl++GG+DllLiet+fDtlnakaa+fave++f++ r+lP++isg
lcl|NCBI__GCF_000061505.1:WP_011767448.1 148 NDPGYRNIEFDALVEDYYESAKGLMEGGADLLLIETIFDTLNAKAAVFAVEKLFDDLDRRLPVMISG 214
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267
+i+d+sGrtLsGqt eaf +sl ha +++GLnCalGa+elr +v els+ +++vs++PnaGLPn
lcl|NCBI__GCF_000061505.1:WP_011767448.1 215 TITDASGRTLSGQTAEAFWNSLAHARPISFGLNCALGAKELRAYVDELSNVCDTFVSAHPNAGLPNP 281
******************************************************************* PP
TIGR02082 268 lg..eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgl 332
l+ Yd+tpe+la+a+ e+a+ gl+ni+GGCCGttP+hi+aia+av+++ pr+++++e+k++lsgl
lcl|NCBI__GCF_000061505.1:WP_011767448.1 282 LAptGYDETPEQLAEAVVEWAQSGLVNILGGCCGTTPAHIAAIAQAVAQVPPRRVPDIEKKLRLSGL 348
*9999************************************************************** PP
TIGR02082 333 ealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgead 399
e+++++ +s fvn+GeRtnv+Gsk f+++i ++ +++al +a+qqve+Gaq++Din+De++lD++a+
lcl|NCBI__GCF_000061505.1:WP_011767448.1 349 EPFNVGADSLFVNVGERTNVTGSKAFARMILEGRFDDALAVARQQVENGAQVIDINMDEAMLDSVAA 415
******************************************************************* PP
TIGR02082 400 mkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaa 466
m+++l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk+ivnsis+k+Gee Fl++a+l+++yGaa
lcl|NCBI__GCF_000061505.1:WP_011767448.1 416 MERFLKLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGEESFLRQARLARRYGAA 482
******************************************************************* PP
TIGR02082 467 vvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieai 533
v+vmafDe+Gqa+t+++kiei+ Ray+ll+ +gfppediifDpni++iatGieehd+ya+dfi+++
lcl|NCBI__GCF_000061505.1:WP_011767448.1 483 VIVMAFDEKGQADTYARKIEICARAYELLVG-IGFPPEDIIFDPNIFAIATGIEEHDNYAVDFIQSV 548
*******************************.*********************************** PP
TIGR02082 534 reikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelr 600
+ik +lP+ak+sgGvsnvsFs+rgn++vRea+h+vFLy+aikaGl mgivnag+l vydd+d+ lr
lcl|NCBI__GCF_000061505.1:WP_011767448.1 549 AWIKANLPHAKTSGGVSNVSFSFRGNEPVREAIHTVFLYHAIKAGLTMGIVNAGMLGVYDDLDPVLR 615
******************************************************************* PP
TIGR02082 601 evvedlildrr....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregie 663
e+ved++l+r+ ++ e L+ela++ k+ k+k++ +wr+++veeRL++alvkG++e++
lcl|NCBI__GCF_000061505.1:WP_011767448.1 616 EKVEDVVLNRKpasgQNPGEALVELAQTVKEGKAKDT--GPDLAWREWSVEERLKHALVKGITEFVV 680
***********777778889********999999954..47789*********************** PP
TIGR02082 664 edleear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePyleke 726
+d+ee r + k+pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+Py+e+e
lcl|NCBI__GCF_000061505.1:WP_011767448.1 681 ADTEEVRarleSEGKPPLAVIEGPLMAGMDVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPYIEAE 747
*****98666667789*************************************************** PP
TIGR02082 727 keed..kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDvigls 791
k+ + +skG+iv+atvkGDvhDiGkniv+vvL+cngyev+dlGv+vP++kil+aa+++ a igls
lcl|NCBI__GCF_000061505.1:WP_011767448.1 748 KARTgaTSKGRIVIATVKGDVHDIGKNIVGVVLGCNGYEVIDLGVMVPTDKILNAAREHGAQAIGLS 814
*9988899*********************************************************** PP
TIGR02082 792 GLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkll 858
GLi++sl+em +va em+r+g+++Pll+GGa++s+ah+a kia++Y+++vvyv das+av vv +ll
lcl|NCBI__GCF_000061505.1:WP_011767448.1 815 GLITPSLEEMSHVAAEMQRQGFDVPLLIGGATTSRAHTAIKIAPHYQQPVVYVPDASRAVGVVTALL 881
******************************************************************* PP
TIGR02082 859 sekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas 925
se ++ +++ ++y++ir ++ + k+ ++ +s++aar + +++ e +e+++p+ lG+ l+
lcl|NCBI__GCF_000061505.1:WP_011767448.1 882 SEGGAGDFKAQLAADYDKIRAQHAN-KKGVQLVSLEAARANAYNPLSVEGYEPVEPNTLGVMALDVD 947
***********************98.778999*********************************** PP
TIGR02082 926 ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPa 992
++el++yiDw ++F +W+l+g++pkil+de++g+ ar++f+da+++l+ l+a + ++a++v+GlfPa
lcl|NCBI__GCF_000061505.1:WP_011767448.1 948 LDELRDYIDWGPFFQTWDLAGSFPKILDDEVVGETARNVFNDAQAMLEDLIAGEWVQAKAVFGLFPA 1014
******************************************************************* PP
TIGR02082 993 qsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtagl 1058
+svgddi+ y+de++ +p+ t + ++q ++ ++ + claDf+a+k+sG +D+ ga++vtagl
lcl|NCBI__GCF_000061505.1:WP_011767448.1 1015 NSVGDDIAFYADESR---DEPMMTWHGLRQQHERPAGKpHWCLADFVAPKASGVRDWCGAFAVTAGL 1078
*************99...5666666666677777777679*************************** PP
TIGR02082 1059 gaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGir 1125
g+e+ ++ea +ddy +i++k+ladrlaea ae+lhervRke+wgya++e+ld++ l+ke+Y+Gir
lcl|NCBI__GCF_000061505.1:WP_011767448.1 1079 GIEHKLAEFEAAHDDYRAIMLKSLADRLAEATAEWLHERVRKEYWGYAADEQLDNAALIKEQYKGIR 1145
******************************************************************* PP
TIGR02082 1126 pafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
pa+GYpacPdht ka l++Ll+a + G+ ltes+a++P+asvsg+yfahpe++Yfa+
lcl|NCBI__GCF_000061505.1:WP_011767448.1 1146 PAPGYPACPDHTVKAALFQLLDAPTnAGMGLTESMAMTPAASVSGFYFAHPESHYFAI 1203
**********************9999******************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1233 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: 9.14
//
[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