Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_085217824.1 B9N75_RS05095 methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_900177405.1:WP_085217824.1 Length = 892 Score = 996 bits (2576), Expect = 0.0 Identities = 541/883 (61%), Positives = 646/883 (73%), Gaps = 30/883 (3%) Query: 354 SLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAM 413 S FVN+GERTNVTGSA FK+LI Y++A++VARQQVENGAQ+IDINMDEG+LDAEAAM Sbjct: 25 SSFVNIGERTNVTGSAAFKKLIMAGDYAKAVEVARQQVENGAQVIDINMDEGLLDAEAAM 84 Query: 414 VRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLL 473 FL LIA EPDIARVP MIDSSKW VIE GLKC+ GK IVNSIS+KEG F+ HA+ Sbjct: 85 TTFLKLIAAEPDIARVPFMIDSSKWSVIEAGLKCVSGKPIVNSISLKEGEAEFLAHARKC 144 Query: 474 RRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIE 533 R YGAAVVVMAFDE GQADT+ RK+EIC RAY +L + GF PEDIIFDPNIFAVATGI+ Sbjct: 145 RNYGAAVVVMAFDETGQADTKERKVEICARAYDMLVAD-GFAPEDIIFDPNIFAVATGID 203 Query: 534 EHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMD 593 EH YA DFI AC I+ PHA ISGG+SN+SFSFRGN+PVR A+H+VFLY+AI G+D Sbjct: 204 EHRRYALDFIEACRAIRIRCPHAHISGGLSNLSFSFRGNEPVRRAMHSVFLYHAIPAGLD 263 Query: 594 MGIVNAGQLAIYDDLPAELRDAVEDVILNRR----DDGTERLLELAEKYRGSKTDDTANA 649 M IVNAGQL +YD + AELR+A EDVIL+R D TERL+ LAEKY GS D Sbjct: 264 MAIVNAGQLDVYDTIDAELREACEDVILDREPKDGGDATERLVALAEKYLGS--DPVREK 321 Query: 650 QQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFG 709 + AEWR W V RL ++LVKGI + +DTEEARQ A RPI VIEGPLMDGMNVVGDLFG Sbjct: 322 EAAEWRGWPVAARLSHALVKGIDAHVVEDTEEARQSAERPIHVIEGPLMDGMNVVGDLFG 381 Query: 710 EGKMFLPQVVKSARVMKQAVAYLEPFIEASKE-QGKTNGK--MVIATVKGDVHDIGKNIV 766 GKMFLPQVVKSARVMK+AVA+L PFIEA KE G T GK +V+ATVKGDVHDIGKNIV Sbjct: 382 SGKMFLPQVVKSARVMKKAVAHLIPFIEAEKEATGATAGKGRIVMATVKGDVHDIGKNIV 441 Query: 767 GVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGF 826 GVVLQCN +EI+DLGVMV + IL+ A + AD+IGLSGLITPSLDEMV VA EM+R G Sbjct: 442 GVVLQCNGFEIIDLGVMVAWQDILQAANDNRADMIGLSGLITPSLDEMVTVADEMQRAGM 501 Query: 827 TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKE 886 T+PLLIGGATTS+ HTA+KI+ Y GP ++V +ASR VGV +AL+S+TQRD V++T + Sbjct: 502 TMPLLIGGATTSRVHTALKIDPAYEGPVIHVLDASRAVGVASALVSETQRDPLVSKTAGD 561 Query: 887 YETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYI 945 Y+ VR+ K + TL AR N FD + PP A G+ + ++ LR I Sbjct: 562 YDAVRVTRA-NKGQNELATLAEARANAQPFDPEGVAPPPAEP-GIHRFDDWPLDDLRQTI 619 Query: 946 DWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPAN 1005 DWTPFF W LAG YP IL+D VVG A+ LF DA MLD++ AEK + RGV GL+ Sbjct: 620 DWTPFFRAWELAGTYPAILDDAVVGESARNLFADAEAMLDRIVAEKWVTARGVAGLWRCR 679 Query: 1006 RVGDDIEIY--RDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFA 1062 R GDDI + DETR + LRQQ +K G N+ LADF+A D++G FA Sbjct: 680 RDGDDIMVLAGNDETRLPM------LRQQVKKREGRWNHSLADFIA----ADEDWMGGFA 729 Query: 1063 VTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSN 1122 V E LA F+A+ DDY+ I++KALADRLAEAFAE LH VR W YAP+E LSN Sbjct: 730 VAIHGLEPHLA-RFKAETDDYSDILLKALADRLAEAFAERLHRHVRTTLWAYAPDEALSN 788 Query: 1123 EELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKH---TGMKLTESFAMWPGASVSG 1179 +ELIRE Y+GIRPAPGYPACPEH+ K ++++L + G+ LT SFAM P A+VSG Sbjct: 789 DELIREKYRGIRPAPGYPACPEHSLKPILFDMLGGDGDAGPAGISLTSSFAMLPTAAVSG 848 Query: 1180 WYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222 +YF+H D+ Y+ VA+I RDQ+EDYA R+G+ + ERWL PNL Sbjct: 849 FYFAHRDASYFGVARIGRDQLEDYASRRGVDADQAERWLRPNL 891 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: 2655 Number of extensions: 106 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 1227 Length of database: 892 Length adjustment: 45 Effective length of query: 1182 Effective length of database: 847 Effective search space: 1001154 Effective search space used: 1001154 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: 58 (26.9 bits)
Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_085217823.1 B9N75_RS05090 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_900177405.1:WP_085217823.1 Length = 348 Score = 356 bits (914), Expect = e-102 Identities = 181/345 (52%), Positives = 239/345 (69%), Gaps = 3/345 (0%) Query: 6 EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65 E L A +RIL+ DG GT IQ +L EAD+ G D KGNNDLL L++P+++ Sbjct: 5 ETLIAAAKDRILIKDGPFGTEIQKRKLKEADYAGS--LGLARDQKGNNDLLALTRPDIVQ 62 Query: 66 AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125 AI + Y AGADII TNTF++ +I+ ADY E L EIN A+A++AR AD W A+ + Sbjct: 63 AITDDYLAAGADIIATNTFSANSISQADYAAEHLVREINTASARIARTAADTWAAKDG-R 121 Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185 PR+VAG +GPTN+T S+SPDVNDP +R I FD L A YRE T AL+ GGAD ILIET+FD Sbjct: 122 PRFVAGAIGPTNKTLSLSPDVNDPGYREIDFDQLKAVYREQTDALLAGGADFILIETIFD 181 Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245 TLNAKA + A + + LG ++P+MIS TITD +GR LSG T EAF+N++RHA +T GL Sbjct: 182 TLNAKAGIMAAREAADDLGRDVPLMISMTITDLAGRNLSGHTVEAFWNAVRHARPVTIGL 241 Query: 246 NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305 NC+ G ++LR +VQ L++IA+ + +PNAGLPN GEYD A I WA+ G +N Sbjct: 242 NCSFGAEQLRPHVQALAQIADALLMVYPNAGLPNEIGEYDELPVETAALIGAWAEKGLVN 301 Query: 306 IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNI 350 VGGCCG++P HIAA+++AV L R +P+ V RL+GLEP+ + Sbjct: 302 AVGGCCGSSPAHIAAIAKAVAALPARAVPKPAVRTRLAGLEPMTL 346 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: 944 Number of extensions: 34 Number of successful extensions: 3 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: 348 Length adjustment: 38 Effective length of query: 1189 Effective length of database: 310 Effective search space: 368590 Effective search space used: 368590 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: 54 (25.4 bits)
Align candidate WP_085217824.1 B9N75_RS05095 (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.147033.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 1115.0 0.0 0 1114.7 0.0 1.0 1 NCBI__GCF_900177405.1:WP_085217824.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085217824.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1114.7 0.0 0 0 341 1182 .] 25 861 .. 17 861 .. 0.95 Alignments for each domain: == domain 1 score: 1114.7 bits; conditional E-value: 0 TIGR02082 341 ssfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasep 411 ssfvniGeRtnv+Gs+ f+kli+a+dy +a+++a+qqve+Gaq++Din+De+llD+ea+m+++l+l+a+ep NCBI__GCF_900177405.1:WP_085217824.1 25 SSFVNIGERTNVTGSAAFKKLIMAGDYAKAVEVARQQVENGAQVIDINMDEGLLDAEAAMTTFLKLIAAEP 95 79********************************************************************* PP TIGR02082 412 diakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartad 482 dia+vP m+Dss++ v+eaGLk++ Gk ivnsislk+Ge++Fl +a++ ++yGaavvvmafDe Gqa+t++ NCBI__GCF_900177405.1:WP_085217824.1 96 DIARVPFMIDSSKWSVIEAGLKCVSGKPIVNSISLKEGEAEFLAHARKCRNYGAAVVVMAFDETGQADTKE 166 *********************************************************************** PP TIGR02082 483 kkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvs 553 +k+ei+ Ray++l++ gf pediifDpni+++atGi+eh+rya+dfiea+r i+ + P+a+isgG+sn+s NCBI__GCF_900177405.1:WP_085217824.1 167 RKVEICARAYDMLVA-DGFAPEDIIFDPNIFAVATGIDEHRRYALDFIEACRAIRIRCPHAHISGGLSNLS 236 **************9.7****************************************************** PP TIGR02082 554 FslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrr....reatekLle 620 Fs+rgn++vR+a+hsvFLy+ai aGlDm+ivnag+l+vyd id+elre++ed+ildr+ +ate+L+ NCBI__GCF_900177405.1:WP_085217824.1 237 FSFRGNEPVRRAMHSVFLYHAIPAGLDMAIVNAGQLDVYDTIDAELREACEDVILDREpkdgGDATERLVA 307 **********************************************************7766689****** PP TIGR02082 621 laelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvv 691 lae+y g +e++ aewr++pv RL++alvkG+ ++ ed+eear+ +++p+++iegpL+dGm+vv NCBI__GCF_900177405.1:WP_085217824.1 308 LAEKYLGSDPV--REKEAAEWRGWPVAARLSHALVKGIDAHVVEDTEEARQSAERPIHVIEGPLMDGMNVV 376 ******99998..66699***************************************************** PP TIGR02082 692 GdLFGsGkmfLPqvvksarvmkkavayLePylekekeed...kskGkivlatvkGDvhDiGknivdvvLsc 759 GdLFGsGkmfLPqvvksarvmkkava+L+P++e+eke++ kG+iv+atvkGDvhDiGkniv+vvL+c NCBI__GCF_900177405.1:WP_085217824.1 377 GDLFGSGKMFLPQVVKSARVMKKAVAHLIPFIEAEKEATgatAGKGRIVMATVKGDVHDIGKNIVGVVLQC 447 ************************************99888799*************************** PP TIGR02082 760 ngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahva 830 ng+e++dlGv+v + il+aa++++aD+iglsGLi++sldemv+va em+r g+++Pll+GGa++s+ h+a NCBI__GCF_900177405.1:WP_085217824.1 448 NGFEIIDLGVMVAWQDILQAANDNRADMIGLSGLITPSLDEMVTVADEMQRAGMTMPLLIGGATTSRVHTA 518 *********************************************************************** PP TIGR02082 831 vkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgek.keklialsekaarkev 900 ki+++Y+g+v++v das+av v+++l+se+++++ ++k+ +y+ +r + +k +++l +l+e++a+ + NCBI__GCF_900177405.1:WP_085217824.1 519 LKIDPAYEGPVIHVLDASRAVGVASALVSETQRDPLVSKTAGDYDAVRVTRANKgQNELATLAEARANAQP 589 ************************************************87655314555555555555555 PP TIGR02082 901 faldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdake 970 f+++ p p G++ +++ +++l++ iDw+++F +Wel+g+yp il+d ++g+ ar+lf+da++ NCBI__GCF_900177405.1:WP_085217824.1 590 FDPE----GVAPPPAEPGIHRFDDWpLDDLRQTIDWTPFFRAWELAGTYPAILDDAVVGESARNLFADAEA 656 5444....457889999*******9********************************************** PP TIGR02082 971 lldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfias 1040 +ld+++aek ++argv Gl+ +++ gddi++++++ + + + ++q+++ ++r + +laDfia NCBI__GCF_900177405.1:WP_085217824.1 657 MLDRIVAEKWVTARGVAGLWRCRRDGDDIMVLAGNDE----TRLPML---RQQVKKREGRwNHSLADFIAA 720 ********************************95544....333333...588888888889********9 PP TIGR02082 1041 kesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenl 1111 +D++g ++v+ + g e +++a++ddy+ il+kaladrlaea+ae lh++vR lw+ya +e+l NCBI__GCF_900177405.1:WP_085217824.1 721 ----DEDWMGGFAVA-IHGLEPHLARFKAETDDYSDILLKALADRLAEAFAERLHRHVRTTLWAYAPDEAL 786 ....99*****9998.7778888889********************************************* PP TIGR02082 1112 dkedllkerYrGirpafGYpacPdhtekatlleLleaer....iGlklteslalaPeasvsglyfahpeak 1178 ++++l++e+YrGirpa+GYpacP+h+ k l+++l + G+ lt s+a+ P+a+vsg+yfah +a NCBI__GCF_900177405.1:WP_085217824.1 787 SNDELIREKYRGIRPAPGYPACPEHSLKPILFDMLGGDGdagpAGISLTSSFAMLPTAAVSGFYFAHRDAS 857 ***********************************6543224589************************** PP TIGR02082 1179 Yfav 1182 Yf v NCBI__GCF_900177405.1:WP_085217824.1 858 YFGV 861 **86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (892 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: 00:00:00.02 # Mc/sec: 41.01 // [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