Align candidate WP_013088221.1 BC1002_RS01065 (methionine synthase)
to HMM PF02965 (Met_synt_B12)
# 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/PF02965.21.hmm # target sequence database: /tmp/gapView.2271.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Met_synt_B12 [M=273] Accession: PF02965.21 Description: Vitamin B12 dependent methionine synthase, activation domain 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-124 399.4 0.0 1.6e-123 397.5 0.0 1.9 2 lcl|NCBI__GCF_000092885.1:WP_013088221.1 BC1002_RS01065 methionine syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092885.1:WP_013088221.1 BC1002_RS01065 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.7 0.0 0.088 0.088 88 123 .. 563 596 .. 548 610 .. 0.73 2 ! 397.5 0.0 1.6e-123 1.6e-123 1 271 [. 615 889 .. 615 891 .. 0.98 Alignments for each domain: == domain 1 score: -1.7 bits; conditional E-value: 0.088 Met_synt_B12 88 atlhtLrqqaekeegkpnlclaDfvapkesgvkDyi 123 a ++ +r q+++++ +p ++la a+k + D+ lcl|NCBI__GCF_000092885.1:WP_013088221.1 563 ADYNRIRDQHANKKAQPMVSLAEARANK--TKIDWA 596 5567789999999999999998755553..334555 PP == domain 2 score: 397.5 bits; conditional E-value: 1.6e-123 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAn 69 dl+el++yidW pffq+W+l+g yp+il+de vge+a+++f+d+++mL+++i+ ++l+a++v+ l+pAn lcl|NCBI__GCF_000092885.1:WP_013088221.1 615 DLNELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDGKSMLARLIQGRWLQANGVITLLPAN 683 699****************************************************************** PP Met_synt_B12 70 seg.ddievyadesrseelatlhtLrqqaeke....egkpnlclaDfvapkesgvkDyiGlFavtaglg 133 +++ ddie+y+desr+e++ t++ Lrqq+ ++ +pn++laDf+apk sgv+DyiG+Favtaglg lcl|NCBI__GCF_000092885.1:WP_013088221.1 684 TVNdDDIEIYTDESRTEVALTWRNLRQQSVRPvvdgVMRPNRSLADFIAPKGSGVADYIGMFAVTAGLG 752 *96388**********************99988877889****************************** PP Met_synt_B12 134 ieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpAp 202 ++ + k+fe++ ddYsai++kaladrLaeAfae lh++vr++lWgya+ e+lsn+eli+ekY+giRpAp lcl|NCBI__GCF_000092885.1:WP_013088221.1 753 VDVKEKQFEKDLDDYSAIMLKALADRLAEAFAEALHARVRRDLWGYANSENLSNDELIAEKYRGIRPAP 821 ********************************************************************* PP Met_synt_B12 203 GYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyakr 271 GYpacpdh k+++fe+l+a+e ig+++teslam PaasvsG+y+ahp+++yF+vgki+ dq++dya+r lcl|NCBI__GCF_000092885.1:WP_013088221.1 822 GYPACPDHLVKRDMFEVLQANE-IGMSVTESLAMLPAASVSGFYLAHPDSTYFSVGKIGADQLDDYARR 889 **********************.*********************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (905 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15.51 // [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