Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_106713177.1 CU102_RS21440 methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_003010955.1:WP_106713177.1 Length = 1262 Score = 1506 bits (3898), Expect = 0.0 Identities = 765/1220 (62%), Positives = 926/1220 (75%), Gaps = 11/1220 (0%) Query: 14 ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73 ERIL+LDG MGT IQ LNE FRG+RFAD C L+GNNDLL+L++P+ I IH AY Sbjct: 35 ERILILDGAMGTQIQGLNLNEESFRGDRFADCSCHLQGNNDLLILTQPQAIEDIHYAYAM 94 Query: 74 AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133 AGADI+ETNTF+STTIA ADY ME + E+N A+LAR A + + K R+VAG L Sbjct: 95 AGADILETNTFSSTTIAQADYSMEEVVYELNRDGARLARRAAIK-AEQKDGKRRFVAGAL 153 Query: 134 GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193 GPTNRTASISPDVN+P +R +TFD L AY E + L++GGAD+ILIET+FDTLNAKAA+ Sbjct: 154 GPTNRTASISPDVNNPGYRAVTFDDLRIAYAEQVRGLIDGGADIILIETIFDTLNAKAAI 213 Query: 194 FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253 FA + FE G+ LPIMISGTITD SGRTLSGQT AF+ S+RHA+ T GLNCALG + Sbjct: 214 FATQEVFEEKGITLPIMISGTITDRSGRTLSGQTPTAFWYSVRHAKPFTIGLNCALGANA 273 Query: 254 LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313 +R ++ E++ +A+ +V A+PNAGLPN FG+YD + MA Q+ E+A+ G LNIVGGCCG+ Sbjct: 274 MRDHLAEIASVADAFVCAYPNAGLPNEFGQYDESPEAMAAQLEEFAREGLLNIVGGCCGS 333 Query: 314 TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373 TP+HI A++ AV PR++PE + RLSGLEP + +D FVNVGERTN+TGSAKF++ Sbjct: 334 TPEHIKAIAEAVGKYGPREIPETEIHMRLSGLEPFTLTKDIAFVNVGERTNITGSAKFRK 393 Query: 374 LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433 LI ++ ALDVAR QV NGAQIIDINMDEG++D+E AMV FLNLIA EPDIARVP+MI Sbjct: 394 LITSGDFATALDVARDQVANGAQIIDINMDEGLIDSEKAMVEFLNLIAAEPDIARVPVMI 453 Query: 434 DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493 DSSKWDVIE GLKC+QGK +VNSISMKEG AFI HAK +R YGAAVVVMAFD QGQADT Sbjct: 454 DSSKWDVIEAGLKCVQGKPLVNSISMKEGEQAFIDHAKRVRAYGAAVVVMAFDTQGQADT 513 Query: 494 RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553 RK+ I RAY++LT E GFPPEDI+FDPN+FAVATGIEEHN Y FI A I L Sbjct: 514 LERKVAISTRAYELLTREAGFPPEDIVFDPNVFAVATGIEEHNGYGVAFIEATRQITETL 573 Query: 554 PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613 PH ISGG+SN+SFSFRGN+PVREA+HAVFLY+AI+ GMDMGIVNAGQLA+Y+ + ELR Sbjct: 574 PHVHISGGISNLSFSFRGNEPVREAMHAVFLYHAIQVGMDMGIVNAGQLAVYESIDPELR 633 Query: 614 DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673 +A EDV+LNRRDD TERLL+LAE+Y+G+ + A + WR W V KR+E++LV GITE Sbjct: 634 EACEDVVLNRRDDATERLLDLAERYKGAAGKE-ARERDLAWREWSVEKRIEHALVNGITE 692 Query: 674 FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733 FIE DTEEAR +A RP+ VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMKQAVA L Sbjct: 693 FIEADTEEARLEAERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAVLL 752 Query: 734 PFIEASK------EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAE 787 P++EA K Q ++ GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGVMVP+ Sbjct: 753 PYMEAEKLANGGSGQRESAGKVLMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPSA 812 Query: 788 KILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIE 847 KIL+TA++ D+IGLSGLITPSLDEMV+VA EMER+GF IPLLIGGATTS+ HTAVKI Sbjct: 813 KILQTARDEKVDIIGLSGLITPSLDEMVHVAAEMEREGFDIPLLIGGATTSRVHTAVKIN 872 Query: 848 QNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTL 906 Y G TVYV +ASR VGVV+ LLS + +V R EY V H R + ++L Sbjct: 873 PRYHKGQTVYVTDASRAVGVVSNLLSLEAKPGYVDGVRAEYTKVAEAHARNEADKQRLSL 932 Query: 907 EAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILE 965 AR N DW +YTPP LG + E + + YIDWTPFF TW L G+YP ILE Sbjct: 933 AKARANAQMVDWVSYTPPKPSFLGTRVFENYDLAEIARYIDWTPFFQTWELKGRYPAILE 992 Query: 966 DEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINV 1025 DE G A++LF DA ML K+ AEK NP+ V+GL+PA VGDDI ++ DE R + Sbjct: 993 DEKQGPAARQLFDDAQAMLKKIIAEKWFNPKAVIGLWPAGAVGDDIRLFTDEARGQELAT 1052 Query: 1026 SHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYN 1084 LRQQ +++ G N L+DFVAP SGK DY+G F VT G+EE A+A+ FE +DDY+ Sbjct: 1053 FFTLRQQLSKRDGRPNVALSDFVAPVDSGKEDYVGGFVVTAGIEEVAIAERFERANDDYS 1112 Query: 1085 KIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPE 1144 I+VKALADR AEAFAE +H+RVRK +WGYAP ENL++++LI E Y+GIRPAPGYPA P+ Sbjct: 1113 SILVKALADRFAEAFAELMHQRVRKEFWGYAPEENLASDDLIGEAYRGIRPAPGYPAQPD 1172 Query: 1145 HTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYA 1204 HTEK T++ LL+ E ++LTESFAMWPG+SVSG Y +HPDS Y+ VA+++RDQVEDYA Sbjct: 1173 HTEKETLFRLLDAEAKIDVRLTESFAMWPGSSVSGIYIAHPDSYYFGVAKVERDQVEDYA 1232 Query: 1205 RRKGMSVTEVERWLAPNLGY 1224 RK M V +VERWL P L Y Sbjct: 1233 ARKSMPVADVERWLGPILNY 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: 3669 Number of extensions: 125 Number of successful extensions: 9 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: 1262 Length adjustment: 48 Effective length of query: 1179 Effective length of database: 1214 Effective search space: 1431306 Effective search space used: 1431306 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_106713177.1 CU102_RS21440 (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.2578274.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 1754.0 0.0 0 1753.8 0.0 1.0 1 NCBI__GCF_003010955.1:WP_106713177.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106713177.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1753.8 0.0 0 0 2 1182 .] 34 1220 .. 33 1220 .. 0.99 Alignments for each domain: == domain 1 score: 1753.8 bits; conditional E-value: 0 TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetnt 71 ++ril+lDGamGtq+q nL+e+ Frg+ +ad++++l+GnndlL lt+P++i++ih ay aGaDi+etnt NCBI__GCF_003010955.1:WP_106713177.1 34 RERILILDGAMGTQIQGLNLNEESFRGDrFADCSCHLQGNNDLLILTQPQAIEDIHYAYAMAGADILETNT 104 68********************************************************************* PP TIGR02082 72 FnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvt 142 F+st+ia+adY +e+ +yeln+ +a+lar++a + +++ k+RfvaG+lGPtn++a++spdv++p++r vt NCBI__GCF_003010955.1:WP_106713177.1 105 FSSTTIAQADYSMEEVVYELNRDGARLARRAAIKAEQKDGKRRFVAGALGPTNRTASISPDVNNPGYRAVT 175 ************************************999999***************************** PP TIGR02082 143 ydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGq 213 +d+l+ aY eqv+gl+dGG+D++Liet+fDtlnakaa+fa++evfeekg+ lPi+isg+i+d+sGrtLsGq NCBI__GCF_003010955.1:WP_106713177.1 176 FDDLRIAYAEQVRGLIDGGADIILIETIFDTLNAKAAIFATQEVFEEKGITLPIMISGTITDRSGRTLSGQ 246 *********************************************************************** PP TIGR02082 214 tleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalke 284 t af s++ha+ +++GLnCalGa+ +r+++ e++ a+a+v ++PnaGLPn++g+Yd+ pe +a++l+e NCBI__GCF_003010955.1:WP_106713177.1 247 TPTAFWYSVRHAKPFTIGLNCALGANAMRDHLAEIASVADAFVCAYPNAGLPNEFGQYDESPEAMAAQLEE 317 *********************************************************************** PP TIGR02082 285 faeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGs 355 fa+egllnivGGCCG+tPehi+aiaeav + pr+ +e+e +++lsgle+++++++ fvn+GeRtn++Gs NCBI__GCF_003010955.1:WP_106713177.1 318 FAREGLLNIVGGCCGSTPEHIKAIAEAVGKYGPREIPETEIHMRLSGLEPFTLTKDIAFVNVGERTNITGS 388 *********************************************************************** PP TIGR02082 356 kkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefe 426 +kfrkli+ +d+ al++a++qv +Gaqi+Din+De+l D+e++m+++l+l+a+epdia+vP+m+Dss+++ NCBI__GCF_003010955.1:WP_106713177.1 389 AKFRKLITSGDFATALDVARDQVANGAQIIDINMDEGLIDSEKAMVEFLNLIAAEPDIARVPVMIDSSKWD 459 *********************************************************************** PP TIGR02082 427 vleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykllte 497 v+eaGLk++qGk +vnsis+k+Ge++F+++ak ++ yGaavvvmafD +Gqa+t ++k+ i +Ray+llt NCBI__GCF_003010955.1:WP_106713177.1 460 VIEAGLKCVQGKPLVNSISMKEGEQAFIDHAKRVRAYGAAVVVMAFDTQGQADTLERKVAISTRAYELLTR 530 *********************************************************************** PP TIGR02082 498 kvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhs 568 ++gfppedi+fDpn++++atGieeh+ y+++fiea+r+i e+lP+++isgG+sn+sFs+rgn++vRea+h+ NCBI__GCF_003010955.1:WP_106713177.1 531 EAGFPPEDIVFDPNVFAVATGIEEHNGYGVAFIEATRQITETLPHVHISGGISNLSFSFRGNEPVREAMHA 601 *********************************************************************** PP TIGR02082 569 vFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqea 639 vFLy+ai++G+Dmgivnag+lavy+ id+elre++ed++l+rr++ate+Ll+lae+ykg k ++ ++ NCBI__GCF_003010955.1:WP_106713177.1 602 VFLYHAIQVGMDMGIVNAGQLAVYESIDPELREACEDVVLNRRDDATERLLDLAERYKGAAGK-EARERDL 671 **************************************************************9.5558899 PP TIGR02082 640 ewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksar 710 +wr+++ve+R+e+alv+G++e+ie+d+eear ++++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksar NCBI__GCF_003010955.1:WP_106713177.1 672 AWREWSVEKRIEHALVNGITEFIEADTEEARLEAERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSAR 742 9********************************************************************** PP TIGR02082 711 vmkkavayLePylekekeed......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvek 775 vmk+ava+L Py+e+ek ++ +s+Gk+++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP +k NCBI__GCF_003010955.1:WP_106713177.1 743 VMKQAVAVLLPYMEAEKLANggsgqrESAGKVLMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPSAK 813 *****************9999999999******************************************** PP TIGR02082 776 ileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvk 845 il++a+++k D+iglsGLi++sldemv+va emer+g++iPll+GGa++s+ h+avki+++Y kg++vyv+ NCBI__GCF_003010955.1:WP_106713177.1 814 ILQTARDEKVDIIGLSGLITPSLDEMVHVAAEMEREGFDIPLLIGGATTSRVHTAVKINPRYhKGQTVYVT 884 *************************************************************9669****** PP TIGR02082 846 daseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkf 916 das+av vv++lls ++k +++ +++ey ++ e + +++ ++ ls+++ar + +d+ +++p+p f NCBI__GCF_003010955.1:WP_106713177.1 885 DASRAVGVVSNLLSLEAKPGYVDGVRAEYTKVAEAHARNEADKQRLSLAKARANAQMVDWV-SYTPPKPSF 954 *************************************************************.9******** PP TIGR02082 917 lGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargv 986 lGt+v+e++ ++e+ yiDw+++F +Wel+g+yp il+de++g ar+lf+da+++l+k++aek ++++v NCBI__GCF_003010955.1:WP_106713177.1 955 LGTRVFENYdLAEIARYIDWTPFFQTWELKGRYPAILEDEKQGPAARQLFDDAQAMLKKIIAEKWFNPKAV 1025 *********************************************************************** PP TIGR02082 987 vGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvta 1056 +Gl+Pa vgddi ++tde++ +++at+ + ++ql + +r +++l+Df+a+ +sG++Dy+g ++vta NCBI__GCF_003010955.1:WP_106713177.1 1026 IGLWPAGAVGDDIRLFTDEAR---GQELATFFTLRQQLSKRDGRpNVALSDFVAPVDSGKEDYVGGFVVTA 1093 ********************9...556677777778888888888************************** PP TIGR02082 1057 glgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpa 1127 g+++ ++a+++e +ddy+silvkaladr+aea+ael+h+rvRke+wgya eenl+ +dl+ e YrGirpa NCBI__GCF_003010955.1:WP_106713177.1 1094 GIEEVAIAERFERANDDYSSILVKALADRFAEAFAELMHQRVRKEFWGYAPEENLASDDLIGEAYRGIRPA 1164 *********************************************************************** PP TIGR02082 1128 fGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182 +GYpa+Pdhtek tl++Ll+ae i ++ltes+a++P +svsg+y+ahp++ Yf v NCBI__GCF_003010955.1:WP_106713177.1 1165 PGYPAQPDHTEKETLFRLLDAEAkIDVRLTESFAMWPGSSVSGIYIAHPDSYYFGV 1220 **********************99******************************76 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1262 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 43.67 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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