Align homocysteine methyltransferase Met26; EC 2.1.1.14 (characterized)
to candidate WP_069664705.1 BCR25_RS16550 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= CharProtDB::CH_124367 (764 letters) >NCBI__GCF_001730305.1:WP_069664705.1 Length = 754 Score = 648 bits (1672), Expect = 0.0 Identities = 351/767 (45%), Positives = 498/767 (64%), Gaps = 24/767 (3%) Query: 2 VKSAVLGFPRIGKNRELKKATEAYWSGKTSAEELLATAKQLRLEHWKLQKAQGVDIIPSN 61 +K++++GFPR+G+ RELK ATE Y+ + +A+EL AT LR +HW+L Q +D IPS Sbjct: 1 MKTSIIGFPRVGELRELKFATEKYFRKEITADELEATGYALRKKHWQLLVNQELDFIPSG 60 Query: 62 DFSLYDQIMDHSFSFNVIPPRYRLSGLSSLDTYFAMGRGMQRAATADKAAVDVPAGEMVK 121 DFS +D +D + S N++P +Y+ LS L+TYFA+ RG Q A DV A M K Sbjct: 61 DFSFFDTTLDTAVSLNLVPKKYQDLHLSPLETYFALARGYQGEAG------DVTALAMKK 114 Query: 122 WFDSNYHFLRPEVSEETDFKLSSTKALDEFLEAKEAGIITRPVLVGPVTYLFIAKAAKGS 181 WF++NYH++ PE+ +ET+ +L ++ F EA AG+ TRP ++GP T L +A Sbjct: 115 WFNTNYHYMVPEIDDETNLELVGHTLVETFKEAAAAGVKTRPTILGPFTLLKLATYHGEK 174 Query: 182 SIKPIELLPKLLPVYVELIKKLTEAGAEYIQIDEPILTLDLPQEILASYKEAYETL---- 237 + + + Y +L +L+EAG E++QIDEP L LDL Q+ + ++ Y++L Sbjct: 175 QAE--DFYQAAISAYSQLFTELSEAGCEWLQIDEPALVLDLSQKEIQQFEALYQSLLSEK 232 Query: 238 GKIGKLILTTYFGSLQSNADVLKGLPIAGVHVDVVRAPENLDRALAV-LGENQIISVGVV 296 G + K+++ TYFG ++ L LP G+ +D V + D +++I+ G+V Sbjct: 233 GTL-KILVQTYFGDVRDVYQELIRLPFDGIGLDFVEGRKTRDLIEQYGFPKDKILFAGIV 291 Query: 297 SGRNIWKTDFQKATAIIEKAISAVGSERVQVASSSSILHIPHSLSGEDQINPEIKRWFAF 356 +G+NIW D+Q++ ++E S V + +S S+LH+P +L+ E + E+K +FAF Sbjct: 292 NGKNIWINDYQQSLNLLENLGSVA---EVVLNTSCSLLHVPFTLTNETSLTSEVKDYFAF 348 Query: 357 AVEKCAELAILTKAANDGPASVRAELEANAADCKARAESPITNVEAVRERQSKVTPQMHE 416 AVEK AEL L K + D AS +A +E N A K + T E ++++ K+T Sbjct: 349 AVEKLAELNDLKKISEDKVAS-QAIVEKNRALFK---KERFTKNERLKQQLEKLTDADFI 404 Query: 417 RKSPFETRYAKQQASLKLPLFPTTTIGSFPQTKEIRVTRNRFAKGLISQEEYDAFIRKEI 476 R R A Q+ LKLPL PTTTIGSFPQTKE++ R +F +G IS+ EY F + +I Sbjct: 405 RLPVLTQRTAIQKEKLKLPLLPTTTIGSFPQTKEVKQNRAKFKRGEISEAEYTVFNQAKI 464 Query: 477 SDVVKFQEEVGLDVLVHGEPERNDMVQYFGERMEGFVFTVNGWVQSYGSRCVRPPIIVGD 536 ++ V FQEE+GLDVLVHGE ERNDMV+YFGE ++G++FT WVQSYG+RCV+PPII GD Sbjct: 465 AECVAFQEEIGLDVLVHGEFERNDMVEYFGESLDGYLFTEKAWVQSYGTRCVKPPIIWGD 524 Query: 537 VYRPAPMTVKESQYAQSITSKPMKGMLTAPITILRWSFPRDDVHDSVQAQQIALGLRDEV 596 V R P+TV S YAQS+T KPMKGMLT P+TIL WSFPR+D+ Q+AL +++EV Sbjct: 525 VSRSKPITVAYSTYAQSLTDKPMKGMLTGPVTILNWSFPREDISLRESTLQLALAIQEEV 584 Query: 597 LDLEKAGIKVIQCDEPALREGLPLRRAEW-DEYLKWAIDAFRLATAAVQDDTQIHSHFCY 655 LDLE GI++IQ DE ALRE LPLR+++W EYL WAI AFRL + VQ TQIH+H CY Sbjct: 585 LDLEANGIEIIQIDEAALREKLPLRQSDWHSEYLDWAIPAFRLVHSKVQPTTQIHTHMCY 644 Query: 656 SDFNDIFDAIQRLDADVVSIENSKSDMKLLNVLSR--YTSCIGPGLFDIHSPRVPPVSEF 713 S+F DI I +DADV+S E S+S + +L+ L+R + + +GPG++DIHSPRVP V E Sbjct: 645 SEFADIIRDIDNMDADVISFEASRSSLTILDALNRIDFQTQVGPGVYDIHSPRVPLVGEI 704 Query: 714 KERIDAIVKHVPKDHLWLNPDCGLKTRGWPETTADLKNMIAAAREAR 760 + I I+ + + +W+NPDCGLKTRG PET A LKN++ AA++ R Sbjct: 705 ETTIHNILNKLSIEKVWINPDCGLKTRGVPETEASLKNLVLAAKKVR 751 Lambda K H 0.318 0.134 0.389 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: 1260 Number of extensions: 64 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: 764 Length of database: 754 Length adjustment: 40 Effective length of query: 724 Effective length of database: 714 Effective search space: 516936 Effective search space used: 516936 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: 55 (25.8 bits)
Align candidate WP_069664705.1 BCR25_RS16550 (5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase)
to HMM TIGR01371 (metE: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (EC 2.1.1.14))
# 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/TIGR01371.hmm # target sequence database: /tmp/gapView.2187022.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01371 [M=754] Accession: TIGR01371 Description: met_syn_B12ind: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 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 1052.5 0.1 0 1052.4 0.1 1.0 1 NCBI__GCF_001730305.1:WP_069664705.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069664705.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1052.4 0.1 0 0 1 752 [. 6 751 .. 6 753 .. 0.97 Alignments for each domain: == domain 1 score: 1052.4 bits; conditional E-value: 0 TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgai 73 +gfPr+ge Relk+a+eky++++i+++el+++ lrkk+++ + ++++d+ip++dfs++D+ Ldtav l+ + NCBI__GCF_001730305.1:WP_069664705.1 6 IGFPRVGELRELKFATEKYFRKEITADELEATGYALRKKHWQLLVNQELDFIPSGDFSFFDTTLDTAVSLNLV 78 69*********************************************************************** PP TIGR01371 74 perfkeladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeake 144 p+++++l + s l+tyFa+aRG++ dv+al+m+kwfntnYhY+vPe+++e++++l + l+e +kea + NCBI__GCF_001730305.1:WP_069664705.1 79 PKKYQDL--HLSPLETYFALARGYQGeaGDVTALAMKKWFNTNYHYMVPEIDDETNLELVGHTLVETFKEAAA 149 ******9..5557***********987789******************************************* PP TIGR01371 145 lgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaa 217 +gv+t+P +lGp+t+lkLa + ek++++ ++ +++Y++++++l+eag+ew+qideP+lvldls++e+++ NCBI__GCF_001730305.1:WP_069664705.1 150 AGVKTRPTILGPFTLLKLATYHG--EKQAEDFYQAAISAYSQLFTELSEAGCEWLQIDEPALVLDLSQKEIQQ 220 *******************6664..57899******************************************* PP TIGR01371 218 vkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee.lelakakfeedkvLvaGvidG 289 ++++y++l +++ +lk+l+qtYf++v++ +++l++lp++++glD+ve++++ +++++f++dk+L+aG+++G NCBI__GCF_001730305.1:WP_069664705.1 221 FEALYQSLLSEKGTLKILVQTYFGDVRDVYQELIRLPFDGIGLDFVEGRKTrDLIEQYGFPKDKILFAGIVNG 293 ************************************************9995667899*************** PP TIGR01371 290 rniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkeale 362 +niw +d+++sl+ll++l + a ++v++tscsllhvp++l++e++l +e+k+++afa+ekl+el+ lk++ e NCBI__GCF_001730305.1:WP_069664705.1 294 KNIWINDYQQSLNLLENLGSVA--EVVLNTSCSLLHVPFTLTNETSLTSEVKDYFAFAVEKLAELNDLKKISE 364 *******************887..8*********************************************999 PP TIGR01371 363 geaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfP 435 ++ a + a+ ++++a+ +kk++++++e+ k++le+l+++++ r +++R+++q++kl+lPllPtttiGsfP NCBI__GCF_001730305.1:WP_069664705.1 365 DKVASQ-AIVEKNRAL--FKKERFTKNERLKQQLEKLTDADFIRLPVLTQRTAIQKEKLKLPLLPTTTIGSFP 434 855554.454544555..8999999************************************************ PP TIGR01371 436 qtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngW 508 qtkev+++Rakf++geise+eY+ f +++i++++++qee+glDvLvhGefeRnDmveyFge l+G++ft+++W NCBI__GCF_001730305.1:WP_069664705.1 435 QTKEVKQNRAKFKRGEISEAEYTVFNQAKIAECVAFQEEIGLDVLVHGEFERNDMVEYFGESLDGYLFTEKAW 507 ************************************************************************* PP TIGR01371 509 vqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialal 581 vqsYG+RcvkPpii+gdvsr kp+tv+ s+yaqslt+kp+kGmLtGPvtilnWsf+ReD++++e++ q+ala+ NCBI__GCF_001730305.1:WP_069664705.1 508 VQSYGTRCVKPPIIWGDVSRSKPITVAYSTYAQSLTDKPMKGMLTGPVTILNWSFPREDISLRESTLQLALAI 580 ************************************************************************* PP TIGR01371 582 rdevkdLeeagikiiqiDepalReglPlrksdk.eeYldwaveaFrlaasgvkdetqihthmCYsefneiiea 653 ++ev dLe++gi+iiqiDe+alRe+lPlr+sd+ +eYldwa+ aFrl++s+v+++tqihthmCYsef +ii+ NCBI__GCF_001730305.1:WP_069664705.1 581 QEEVLDLEANGIEIIQIDEAALREKLPLRQSDWhSEYLDWAIPAFRLVHSKVQPTTQIHTHMCYSEFADIIRD 653 ********************************9789************************************* PP TIGR01371 654 iaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPD 726 i+++daDvis+easrs +ldal+ +++++++G+GvyDihsprvP + e++++++++l+kl e++W+nPD NCBI__GCF_001730305.1:WP_069664705.1 654 IDNMDADVISFEASRSSLTILDALNR-IDFQTQVGPGVYDIHSPRVPLVGEIETTIHNILNKLSIEKVWINPD 725 **************************.66******************************************** PP TIGR01371 727 CGLktRkweevkaalknlveaakelR 752 CGLktR ++e++a+lknlv aak++R NCBI__GCF_001730305.1:WP_069664705.1 726 CGLKTRGVPETEASLKNLVLAAKKVR 751 ************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (754 nodes) Target sequences: 1 (754 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 31.00 // [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