Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012475469.1 CPHAMN1_RS10425 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000020545.1:WP_012475469.1
Length = 1227
Score = 1462 bits (3785), Expect = 0.0
Identities = 732/1225 (59%), Positives = 924/1225 (75%), Gaps = 8/1225 (0%)
Query: 6 EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
E L + L +RILVLDG MGT+IQ+Y+L E D+RGERFA LKGNND+LVL++P++I
Sbjct: 3 ESLASLLEKRILVLDGAMGTLIQTYKLEENDYRGERFASHGHSLKGNNDILVLTQPDIIH 62
Query: 66 AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
AIH + EAG+DIIETNTFN+ ++ +DY E+L IN AA+LAR AD ++ + P K
Sbjct: 63 AIHCEFLEAGSDIIETNTFNANPVSQSDYGTENLVKHINLEAARLARKAADAYSLKDPSK 122
Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
PR+VAG +GPTN+T S+SPDVN+P +R ++F + YRE + L+EGG DL+L+ETVFD
Sbjct: 123 PRFVAGSIGPTNKTLSLSPDVNNPGYRAVSFKEMADNYREQLEGLIEGGVDLLLVETVFD 182
Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL-TFG 244
TLN KAA+ A++ GV LPIMISGTI DASGRTLSGQTTEAF+ S+ H L + G
Sbjct: 183 TLNCKAAILAIEEISREKGVRLPIMISGTIVDASGRTLSGQTTEAFWISVAHTPGLLSVG 242
Query: 245 LNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFL 304
LNCALG ++R +++ LS +A V+ +PNAGLPN FGEYD + MA QI ++AQ+GF+
Sbjct: 243 LNCALGAKQMRPFLEALSHVAGSLVSVYPNAGLPNEFGEYDDSPEYMASQIADFAQSGFV 302
Query: 305 NIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTN 364
NIVGGCCGT P+HI A++ V + PRK P +P RL+GLEPL + + + F+N+GERTN
Sbjct: 303 NIVGGCCGTKPEHIRAIAETVATIEPRKKPSMPTELRLAGLEPLIVNKTTGFINIGERTN 362
Query: 365 VTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEP 424
VTGS KF RLI+EEKY EAL +ARQQVENGAQ+IDIN+DEGMLD+E M F+N+I EP
Sbjct: 363 VTGSRKFARLIREEKYDEALSIARQQVENGAQVIDINVDEGMLDSEKVMRDFVNMIGSEP 422
Query: 425 DIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMA 484
+IARVP+MIDSSKW VIE GL C+QGK IVNSIS+KEG D F AK + YGAA VVMA
Sbjct: 423 EIARVPLMIDSSKWSVIESGLCCVQGKSIVNSISLKEGEDLFRERAKKVMIYGAAAVVMA 482
Query: 485 FDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIG 544
FDE+GQAD+ R+IEIC RAY+IL +EVGF PE+IIFDPN+ VATGIEEH+NYA DFI
Sbjct: 483 FDEKGQADSLERRIEICERAYRILVDEVGFHPENIIFDPNVLTVATGIEEHDNYAVDFIE 542
Query: 545 ACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAI 604
+ IK LPHA +SGG+SNVSFSFRGN+PVREA+HA FL++AI G+DMGIVNAGQLA+
Sbjct: 543 SVRWIKENLPHARVSGGISNVSFSFRGNNPVREAMHAAFLFHAIHAGLDMGIVNAGQLAV 602
Query: 605 YDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLE 664
YDD+ EL + VEDV+LNRR D TERL+E AE + A A+QAEWR+ V +RL+
Sbjct: 603 YDDIEPELLERVEDVLLNRRKDATERLVEFAETIKDD--GQKAEAKQAEWRNGTVEERLQ 660
Query: 665 YSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARV 724
++LVKGI ++I+ DTEEARQ P+++IEGPLM GMNV+GDLF EGKMFLPQVVKSARV
Sbjct: 661 HALVKGIVDYIDSDTEEARQAYASPLDIIEGPLMGGMNVIGDLFAEGKMFLPQVVKSARV 720
Query: 725 MKQAVAYLEPFIEASKEQGKTN---GKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
MK+AVA+L P+IE K + K K+++ATVKGDVHDIGKNIV VVL CNN+E+VD+G
Sbjct: 721 MKKAVAWLIPYIEEEKAKNKDTRPVAKVLLATVKGDVHDIGKNIVSVVLACNNFEVVDIG 780
Query: 782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
VM+P E IL A++ AD+IGLSGLITPSLDEMV+VAKEMER+G IPLLIGGATTS+ H
Sbjct: 781 VMMPCENILEAAEKEKADIIGLSGLITPSLDEMVHVAKEMERKGMRIPLLIGGATTSRVH 840
Query: 842 TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
TAVKI NYSGP V V +ASR+V V +LL+ + + FV + +E ++R H ++
Sbjct: 841 TAVKIAPNYSGPVVQVLDASRSVPAVNSLLTSSMKGAFVKKLTEEQHSLRESHAARQTSR 900
Query: 902 PPVTLEAARDNDFAFDWQAYTPPVAHRLGV-QEVEASIETLRNYIDWTPFFMTWSLAGKY 960
++ +R+N W T + + G+ ++ S+ LR YIDWTPFF W L GKY
Sbjct: 901 QHRSIGESRENRAKLSWSPETVTIPNHPGITEQANVSLSELREYIDWTPFFNVWELHGKY 960
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
P I E++ G EA++LF+DAN +LD++ EK+L +GV G+FPAN VGDDIEIY DE+R
Sbjct: 961 PDIFENKHCGSEARKLFEDANSLLDRICEEKSLVAKGVAGIFPANSVGDDIEIYTDESRA 1020
Query: 1021 HVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQ 1079
V+ H LRQQ EK TG AN LADF+APK SG+ DYIGAF +T G L FEA+
Sbjct: 1021 TVLTTLHTLRQQHEKNTGSANLALADFIAPKSSGRDDYIGAFTLTAGHGVKELMKRFEAE 1080
Query: 1080 HDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGY 1139
HDDY++IMV+ALADRLAEAFAE LH+RVRK WGYA +ENL+ ++L+ E Y+GIRPAPGY
Sbjct: 1081 HDDYHRIMVQALADRLAEAFAEMLHQRVRKELWGYAIDENLTKKQLLNEKYRGIRPAPGY 1140
Query: 1140 PACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199
PACP+HTEK I+ LL E TG+ LTE++AM P ASV G YF+HP++KY+ + I +DQ
Sbjct: 1141 PACPDHTEKPLIFNLLNSEAITGVTLTETYAMNPPASVCGLYFAHPEAKYFVLGSIGKDQ 1200
Query: 1200 VEDYARRKGMSVTEVERWLAPNLGY 1224
VE+YA RKGMS+ E E+WLAPNL Y
Sbjct: 1201 VEEYALRKGMSMAEAEKWLAPNLNY 1225
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: 3540
Number of extensions: 129
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: 1227
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1180
Effective search space: 1392400
Effective search space used: 1392400
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_012475469.1 CPHAMN1_RS10425 (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.7594.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 1745.3 0.0 0 1745.1 0.0 1.0 1 lcl|NCBI__GCF_000020545.1:WP_012475469.1 CPHAMN1_RS10425 methionine synth
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012475469.1 CPHAMN1_RS10425 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1745.1 0.0 0 0 1 1180 [. 9 1191 .. 9 1193 .. 0.98
Alignments for each domain:
== domain 1 score: 1745.1 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l+krilvlDGamGt +q+++L+e+d+rge +a + +lkGnnd+L+lt+P++i+aih +++eaG+Di
lcl|NCBI__GCF_000020545.1:WP_012475469.1 9 LEKRILVLDGAMGTLIQTYKLEENDYRGErFASHGHSLKGNNDILVLTQPDIIHAIHCEFLEAGSDI 75
589**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
+etntFn+++++++dY++e++++++n +aa+lar++ad ++ ++p k+RfvaGs+GPtnk+ +lspd
lcl|NCBI__GCF_000020545.1:WP_012475469.1 76 IETNTFNANPVSQSDYGTENLVKHINLEAARLARKAADAYSlKDPSKPRFVAGSIGPTNKTLSLSPD 142
*****************************************99************************ PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p++r v + e+ d Y+eq +gl++GGvDllL+etvfDtln kaa++a+ee+ ekg++lPi+is
lcl|NCBI__GCF_000020545.1:WP_012475469.1 143 VNNPGYRAVSFKEMADNYREQLEGLIEGGVDLLLVETVFDTLNCKAAILAIEEISREKGVRLPIMIS 209
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflasleha.eililGLnCalGadelrefvkelsetaealvsviPnaGLP 265
g+ivd+sGrtLsGqt+eaf +s+ h+ ++l++GLnCalGa+++r+f+++ls+ a lvsv+PnaGLP
lcl|NCBI__GCF_000020545.1:WP_012475469.1 210 GTIVDASGRTLSGQTTEAFWISVAHTpGLLSVGLNCALGAKQMRPFLEALSHVAGSLVSVYPNAGLP 276
***********************99835899************************************ PP
TIGR02082 266 nalgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgl 332
n++geYd pe +a+++++fa+ g++nivGGCCGt+Pehiraiae v+ i+prk+++++++++l+gl
lcl|NCBI__GCF_000020545.1:WP_012475469.1 277 NEFGEYDDSPEYMASQIADFAQSGFVNIVGGCCGTKPEHIRAIAETVATIEPRKKPSMPTELRLAGL 343
******************************************************************* PP
TIGR02082 333 ealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgead 399
e+l +++ + f+niGeRtnv+Gs+kf++li++e+y+eal+ia+qqve+Gaq++DinvDe++lD+e+
lcl|NCBI__GCF_000020545.1:WP_012475469.1 344 EPLIVNKTTGFINIGERTNVTGSRKFARLIREEKYDEALSIARQQVENGAQVIDINVDEGMLDSEKV 410
******************************************************************* PP
TIGR02082 400 mkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaa 466
m+ +++++ sep+ia+vPlm+Dss++ v+e GL ++qGk+ivnsislk+Ge+ F e+ak++ yGaa
lcl|NCBI__GCF_000020545.1:WP_012475469.1 411 MRDFVNMIGSEPEIARVPLMIDSSKWSVIESGLCCVQGKSIVNSISLKEGEDLFRERAKKVMIYGAA 477
******************************************************************* PP
TIGR02082 467 vvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieai 533
+vvmafDe+Gqa+ +++iei++Ray++l+++vgf pe+iifDpn+lt+atGieehd+ya+dfie++
lcl|NCBI__GCF_000020545.1:WP_012475469.1 478 AVVMAFDEKGQADSLERRIEICERAYRILVDEVGFHPENIIFDPNVLTVATGIEEHDNYAVDFIESV 544
******************************************************************* PP
TIGR02082 534 reikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelr 600
r+ike+lP+a++sgG+snvsFs+rgn++vRea+h+ FL++ai+aGlDmgivnag+lavyddi++el+
lcl|NCBI__GCF_000020545.1:WP_012475469.1 545 RWIKENLPHARVSGGISNVSFSFRGNNPVREAMHAAFLFHAIHAGLDMGIVNAGQLAVYDDIEPELL 611
******************************************************************* PP
TIGR02082 601 evvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedle 667
e ved++l+rr++ate+L+e+ae+ k+ +k +ea++aewrn veeRL++alvkG+ ++i+ d+e
lcl|NCBI__GCF_000020545.1:WP_012475469.1 612 ERVEDVLLNRRKDATERLVEFAETIKDDGQK--AEAKQAEWRNGTVEERLQHALVKGIVDYIDSDTE 676
***************************9999..889******************************* PP
TIGR02082 668 earkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed...k 731
ear+ + +pl+iiegpL+ Gm+v+GdLF +GkmfLPqvvksarvmkkava+L+Py+e+ek+++ +
lcl|NCBI__GCF_000020545.1:WP_012475469.1 677 EARQAYASPLDIIEGPLMGGMNVIGDLFAEGKMFLPQVVKSARVMKKAVAWLIPYIEEEKAKNkdtR 743
************************************************************9984444 PP
TIGR02082 732 skGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksl 798
k++latvkGDvhDiGkniv+vvL+cn++evvd+Gv++P+e+ileaa+k+kaD+iglsGLi++sl
lcl|NCBI__GCF_000020545.1:WP_012475469.1 744 PVAKVLLATVKGDVHDIGKNIVSVVLACNNFEVVDIGVMMPCENILEAAEKEKADIIGLSGLITPSL 810
568**************************************************************** PP
TIGR02082 799 demvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkae 865
demv+va+emer+g++iPll+GGa++s+ h+avkia++Y+g+vv v das++v v++ll+ k +
lcl|NCBI__GCF_000020545.1:WP_012475469.1 811 DEMVHVAKEMERKGMRIPLLIGGATTSRVHTAVKIAPNYSGPVVQVLDASRSVPAVNSLLTSSMKGA 877
******************************************************************* PP
TIGR02082 866 elekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellk 931
+++k++ee++++re++ +++ +++ s+ + r+++ +l +s +v+ p++ G+ + ++ + el++
lcl|NCBI__GCF_000020545.1:WP_012475469.1 878 FVKKLTEEQHSLRESHAARQTSRQHRSIGESRENRAKLSWS-PETVTIPNHPGITEQANVsLSELRE 943
*****************************************.7889999999999888888****** PP
TIGR02082 932 yiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgdd 998
yiDw+++F +Wel+gkyp i++++ g earklf+da++lld++ +ek+l a+gv G+fPa+svgdd
lcl|NCBI__GCF_000020545.1:WP_012475469.1 944 YIDWTPFFNVWELHGKYPDIFENKHCGSEARKLFEDANSLLDRICEEKSLVAKGVAGIFPANSVGDD 1010
******************************************************************* PP
TIGR02082 999 ieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeela 1064
ieiytde++ +++++t+++ ++q ++++++ +l+laDfia+k+sG Dy+ga+ tag g++el
lcl|NCBI__GCF_000020545.1:WP_012475469.1 1011 IEIYTDESR---ATVLTTLHTLRQQHEKNTGSaNLALADFIAPKSSGRDDYIGAFTLTAGHGVKELM 1074
******999...5555555555666667766679********************************* PP
TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
k++ea++ddy+ i+v+aladrlaea+ae+lh+rvRkelwgya +enl k++ll e+YrGirpa+GYp
lcl|NCBI__GCF_000020545.1:WP_012475469.1 1075 KRFEAEHDDYHRIMVQALADRLAEAFAEMLHQRVRKELWGYAIDENLTKKQLLNEKYRGIRPAPGYP 1141
******************************************************************* PP
TIGR02082 1132 acPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYf 1180
acPdhtek +++Ll+ e +G++lte +a++P asv+glyfahpeakYf
lcl|NCBI__GCF_000020545.1:WP_012475469.1 1142 ACPDHTEKPLIFNLLNSEAiTGVTLTETYAMNPPASVCGLYFAHPEAKYF 1191
*******************99***************************** PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1227 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 0.04s 00:00:00.12 Elapsed: 00:00:00.11
# Mc/sec: 12.20
//
[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