Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_036374656.1 MVAN_RS17445 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000015305.1:WP_036374656.1
Length = 1253
Score = 1549 bits (4011), Expect = 0.0
Identities = 784/1237 (63%), Positives = 952/1237 (76%), Gaps = 20/1237 (1%)
Query: 6 EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
++L+ L RI+V+DG MGT IQ R +EA +RGERF DWP DL GNNDLL L++P++I
Sbjct: 21 DELKVALGRRIVVIDGAMGTAIQRDRPDEAGYRGERFKDWPSDLVGNNDLLTLTQPQIIE 80
Query: 66 AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
IH Y EAGADI+ETNTFN+ ++++DY ME LS E+N+A A LAR DE++ TP+K
Sbjct: 81 GIHREYLEAGADILETNTFNANAVSLSDYGMEKLSYELNYAGAALARKACDEFS--TPDK 138
Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
PRYVAG LGPT RTASISPDVNDP RN+++D LVAAY ++ LV+GGADL+++ET+FD
Sbjct: 139 PRYVAGALGPTTRTASISPDVNDPGARNVSYDQLVAAYLDAASGLVDGGADLLIVETIFD 198
Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245
TLNAKAAVFA++T FE G P++ISGTITDASGRTLSGQ TEAF+NS+RHA L GL
Sbjct: 199 TLNAKAAVFAIETLFEDRGRRWPVIISGTITDASGRTLSGQVTEAFWNSVRHARPLAVGL 258
Query: 246 NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305
NCALG E+R Y+ E+SRIA+ +V+ +PNAGLPNAFGEYD A + E+A+AG +N
Sbjct: 259 NCALGAPEMRPYLAEMSRIADTFVSCYPNAGLPNAFGEYDESPTRQAGYVAEFAEAGLVN 318
Query: 306 IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNV 365
+VGGCCGTTP HIA ++R V+G PRK+PEIPVA RL+GLEPLNI +DSLFVN+GERTN+
Sbjct: 319 LVGGCCGTTPAHIAEIARVVDGKPPRKVPEIPVATRLAGLEPLNITDDSLFVNIGERTNI 378
Query: 366 TGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPD 425
TGSA+F+ LIK E Y AL VA QQVE GAQ+IDINMDEGM+D AAM RF LIA EPD
Sbjct: 379 TGSARFRNLIKAEDYDTALSVALQQVEVGAQVIDINMDEGMIDGVAAMDRFTKLIAAEPD 438
Query: 426 IARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAF 485
I+RVP+MIDSSKW+VIE GLK +QGK IVNSISMKEG + FI A+L R+YGAAVVVMAF
Sbjct: 439 ISRVPVMIDSSKWEVIEAGLKNVQGKPIVNSISMKEGEEKFIREARLCRKYGAAVVVMAF 498
Query: 486 DEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGA 545
DEQGQAD R+ +IC RAY+ILTEEVGFP EDIIFDPN FA+ATGIEEH +Y DFI A
Sbjct: 499 DEQGQADNLERRKQICGRAYRILTEEVGFPAEDIIFDPNCFALATGIEEHASYGIDFIEA 558
Query: 546 CEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIY 605
C IK LP ISGG+SNVSFSFRGN+PVREAIHAVFL++AI+ G+DMGIVNAG L Y
Sbjct: 559 CAWIKENLPGVHISGGISNVSFSFRGNNPVREAIHAVFLFHAIKAGLDMGIVNAGALVPY 618
Query: 606 DDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEY 665
D + ELRD +EDV+LNRR+D ERLLE+AE++ + +T +A AEWRS V +R+ +
Sbjct: 619 DSIDPELRDRIEDVVLNRREDAAERLLEIAERF--NSKGETEDAGVAEWRSLPVRERITH 676
Query: 666 SLVKGITEFIEQDTEEARQQAT----RPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
+LVKGI ++ DTEE R + RPIEVIEGPLMDGMNVVGDLFG GKMFLPQVVKS
Sbjct: 677 ALVKGIDAHVDDDTEELRAEIADAGGRPIEVIEGPLMDGMNVVGDLFGAGKMFLPQVVKS 736
Query: 722 ARVMKQAVAYLEPFIEASKEQG------KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNY 775
ARVMK+AVAYL PFIEA K + TNG +V+ATVKGDVHDIGKNIVGVVLQCNN+
Sbjct: 737 ARVMKKAVAYLLPFIEAEKAENGTSDSKDTNGTIVMATVKGDVHDIGKNIVGVVLQCNNF 796
Query: 776 EIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGA 835
E++DLGVMVPA+KIL AKE NAD+IGLSGLITPSLDEM N A EMER+G IPLLIGGA
Sbjct: 797 EVIDLGVMVPAQKILDAAKEHNADIIGLSGLITPSLDEMANFAVEMEREGLEIPLLIGGA 856
Query: 836 TTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHG 895
TTS+AHTAVKI GP V+V++ASR+V V AALL D QR + T +Y ++R +H
Sbjct: 857 TTSRAHTAVKIAPRRGGPVVWVKDASRSVPVAAALLDDRQRPALLEATEADYASLRERHA 916
Query: 896 RKKPRTPPVTLEAARDNDFAFDWQAYTPPV-AHRLGVQEV-EASIETLRNYIDWTPFFMT 953
+K R P +TLE AR N +W YTPPV A LGV+E + + LR YIDW PFF
Sbjct: 917 QKNER-PMLTLEKARANRTPVEWDGYTPPVPAQGLGVREFKDYDLAELREYIDWQPFFNA 975
Query: 954 WSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV--GDDI 1011
W + G++P IL + G A++L+ DA +MLD L EK L GV+G FPAN GDDI
Sbjct: 976 WEMKGRFPDILNNPATGEAARKLYDDAQEMLDTLIKEKWLTANGVIGFFPANASPGGDDI 1035
Query: 1012 EIYRDETRTHVINVSHHLRQQTE-KTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEED 1070
+Y D+TRT V+ H+LRQQ E ++G N L DF+APK SG DYIGAFAVT GL
Sbjct: 1036 VVYTDDTRTEVLTTLHNLRQQGEHRSGIPNRSLGDFIAPKESGLRDYIGAFAVTAGLGSQ 1095
Query: 1071 ALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENY 1130
F+A DDY+ I++++LADRLAEAFAE +HERVRK +WGY P+E L N+ LI E Y
Sbjct: 1096 DKIMEFKAALDDYSAILLESLADRLAEAFAERMHERVRKEFWGYQPDEQLDNDALIGEKY 1155
Query: 1131 QGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYY 1190
GIRPAPGYPACPEHTEKAT+W+L++V++ TG++LTES AMWPGA+VSGWYFSHP S+Y+
Sbjct: 1156 VGIRPAPGYPACPEHTEKATLWKLMDVKERTGIELTESMAMWPGAAVSGWYFSHPQSQYF 1215
Query: 1191 AVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
V ++ +DQV DYA+RKG ++ E ERWLAPNLGY+ +
Sbjct: 1216 VVGRLAQDQVADYAKRKGWTLAEAERWLAPNLGYNPE 1252
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: 3863
Number of extensions: 176
Number of successful extensions: 11
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: 1253
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1205
Effective search space: 1420695
Effective search space used: 1420695
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_036374656.1 MVAN_RS17445 (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.19114.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 1722.7 0.0 0 1722.5 0.0 1.0 1 lcl|NCBI__GCF_000015305.1:WP_036374656.1 MVAN_RS17445 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_036374656.1 MVAN_RS17445 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1722.5 0.0 0 0 3 1182 .] 29 1217 .. 27 1217 .. 0.98
Alignments for each domain:
== domain 1 score: 1722.5 bits; conditional E-value: 0
TIGR02082 3 krilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68
+ri+v+DGamGt +q+ + +ea +rge ++d++++l GnndlL+lt+P++i+ ihr+y+eaGaDi+e
lcl|NCBI__GCF_000015305.1:WP_036374656.1 29 RRIVVIDGAMGTAIQRDRPDEAGYRGErFKDWPSDLVGNNDLLTLTQPQIIEGIHREYLEAGADILE 95
89***************************************************************** PP
TIGR02082 69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135
tntFn++ ++l+dY++e+++yeln ++a+lar+++def+ tp+k+R+vaG+lGPt+++a++spdv++
lcl|NCBI__GCF_000015305.1:WP_036374656.1 96 TNTFNANAVSLSDYGMEKLSYELNYAGAALARKACDEFS-TPDKPRYVAGALGPTTRTASISPDVND 161
***************************************.*************************** PP
TIGR02082 136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202
p+ rnv yd+lv+aY +++ gl+dGG+Dll++et+fDtlnakaa+fa+e++fe++gr+ P++isg+i
lcl|NCBI__GCF_000015305.1:WP_036374656.1 162 PGARNVSYDQLVAAYLDAASGLVDGGADLLIVETIFDTLNAKAAVFAIETLFEDRGRRWPVIISGTI 228
******************************************************************* PP
TIGR02082 203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269
+d+sGrtLsGq +eaf +s++ha l++GLnCalGa e+r+++ e+s++a+++vs++PnaGLPna+g
lcl|NCBI__GCF_000015305.1:WP_036374656.1 229 TDASGRTLSGQVTEAFWNSVRHARPLAVGLNCALGAPEMRPYLAEMSRIADTFVSCYPNAGLPNAFG 295
******************************************************************* PP
TIGR02082 270 eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealk 336
eYd+ p++ a ++efae+gl+n+vGGCCGttP+hi++ia++v++ prk++e++ +++l+gle+l+
lcl|NCBI__GCF_000015305.1:WP_036374656.1 296 EYDESPTRQAGYVAEFAEAGLVNLVGGCCGTTPAHIAEIARVVDGKPPRKVPEIPVATRLAGLEPLN 362
******************************************************************* PP
TIGR02082 337 iaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkl 403
i+++s fvniGeRtn++Gs++fr+likaedy+ al++a qqve Gaq++Din+De++ Dg+a+m ++
lcl|NCBI__GCF_000015305.1:WP_036374656.1 363 ITDDSLFVNIGERTNITGSARFRNLIKAEDYDTALSVALQQVEVGAQVIDINMDEGMIDGVAAMDRF 429
******************************************************************* PP
TIGR02082 404 lsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvm 470
++l+a+epdi++vP+m+Dss++ev+eaGLk +qGk ivnsis+k+Gee+F+++a+l ++yGaavvvm
lcl|NCBI__GCF_000015305.1:WP_036374656.1 430 TKLIAAEPDISRVPVMIDSSKWEVIEAGLKNVQGKPIVNSISMKEGEEKFIREARLCRKYGAAVVVM 496
******************************************************************* PP
TIGR02082 471 afDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireik 537
afDe+Gqa++ +++ +i+ Ray++lte+vgfp+ediifDpn +++atGieeh y+idfiea+ +ik
lcl|NCBI__GCF_000015305.1:WP_036374656.1 497 AFDEQGQADNLERRKQICGRAYRILTEEVGFPAEDIIFDPNCFALATGIEEHASYGIDFIEACAWIK 563
******************************************************************* PP
TIGR02082 538 eelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevve 604
e+lP ++isgG+snvsFs+rgn++vRea+h+vFL++aikaGlDmgivnag l +yd id+elr+ +e
lcl|NCBI__GCF_000015305.1:WP_036374656.1 564 ENLPGVHISGGISNVSFSFRGNNPVREAIHAVFLFHAIKAGLDMGIVNAGALVPYDSIDPELRDRIE 630
******************************************************************* PP
TIGR02082 605 dlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear. 670
d++l+rr++a e+Lle+ae+++ + e+ ++a aewr+lpv+eR+++alvkG+ ++++d+ee r
lcl|NCBI__GCF_000015305.1:WP_036374656.1 631 DVVLNRREDAAERLLEIAERFNSKGET--EDAGVAEWRSLPVRERITHALVKGIDAHVDDDTEELRa 695
**********************99999..55699******************************994 PP
TIGR02082 671 ...kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.... 730
+p+e+iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkavayL P++e+ek+e+
lcl|NCBI__GCF_000015305.1:WP_036374656.1 696 eiaDAGGRPIEVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLLPFIEAEKAENgtsd 762
44445579*****************************************************999999 PP
TIGR02082 731 ..kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLiv 795
+++G+iv+atvkGDvhDiGkniv+vvL+cn++ev+dlGv+vP++kil+aak+++aD+iglsGLi+
lcl|NCBI__GCF_000015305.1:WP_036374656.1 763 skDTNGTIVMATVKGDVHDIGKNIVGVVLQCNNFEVIDLGVMVPAQKILDAAKEHNADIIGLSGLIT 829
9999*************************************************************** PP
TIGR02082 796 ksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekk 862
+sldem++ a emer+g++iPll+GGa++s+ah+avkia++ g+vv+vkdas++v v+++ll++++
lcl|NCBI__GCF_000015305.1:WP_036374656.1 830 PSLDEMANFAVEMEREGLEIPLLIGGATTSRAHTAVKIAPRRGGPVVWVKDASRSVPVAAALLDDRQ 896
******************************************************************* PP
TIGR02082 863 kaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpap.kflGtkvleas.ie 927
+ + le+++++y ++re++ + k+++ l++++ar ++ +++ +++p+p + lG+++++++ ++
lcl|NCBI__GCF_000015305.1:WP_036374656.1 897 RPALLEATEADYASLRERHAQ-KNERPMLTLEKARANRTPVEWD-GYTPPVPaQGLGVREFKDYdLA 961
*******************98.788899***************9.7777776267************ PP
TIGR02082 928 ellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaq. 993
el++yiDw+++F +We++g++p il+++ +g+ arkl++da+e+ld+l++ek l+a+gv+G+fPa+
lcl|NCBI__GCF_000015305.1:WP_036374656.1 962 ELREYIDWQPFFNAWEMKGRFPDILNNPATGEAARKLYDDAQEMLDTLIKEKWLTANGVIGFFPANa 1028
*****************************************************************94 PP
TIGR02082 994 .svgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtagl 1058
gddi++ytd+t+ t++++t+++ ++q ++ s+ + +l Dfia+kesG +Dy+ga++vtagl
lcl|NCBI__GCF_000015305.1:WP_036374656.1 1029 sPGGDDIVVYTDDTR---TEVLTTLHNLRQQGEHRSGIpNRSLGDFIAPKESGLRDYIGAFAVTAGL 1092
3469*******9999...888888887778887777778**************************** PP
TIGR02082 1059 gaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGir 1125
g ++ +++a ddy++il+++ladrlaea+ae +hervRke+wgy +e+ld++ l+ e+Y Gir
lcl|NCBI__GCF_000015305.1:WP_036374656.1 1093 GSQDKIMEFKAALDDYSAILLESLADRLAEAFAERMHERVRKEFWGYQPDEQLDNDALIGEKYVGIR 1159
******************************************************************* PP
TIGR02082 1126 pafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
pa+GYpacP+htekatl++L+++++ +G++ltes+a++P a+vsg+yf+hp+++Yf v
lcl|NCBI__GCF_000015305.1:WP_036374656.1 1160 PAPGYPACPEHTEKATLWKLMDVKErTGIELTESMAMWPGAAVSGWYFSHPQSQYFVV 1217
**********************9877******************************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1253 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 0.05s 00:00:00.14 Elapsed: 00:00:00.13
# Mc/sec: 10.88
//
[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