Align candidate CCNA_02221 CCNA_02221 (methionine synthase I metH)
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.2185.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-124 400.9 0.0 2.6e-124 400.1 0.0 1.4 1 lcl|FitnessBrowser__Caulo:CCNA_02221 CCNA_02221 methionine synthase I Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02221 CCNA_02221 methionine synthase I metH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 400.1 0.0 2.6e-124 2.6e-124 2 273 .] 597 872 .. 596 872 .. 0.98 Alignments for each domain: == domain 1 score: 400.1 bits; conditional E-value: 2.6e-124 Met_synt_B12 2 leelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAnsegdd 74 l+elv++idW+pff++Wel g++p+iled++vg++a++l++dA+amL+k++eek++ ak+v+g++pA+++gdd lcl|FitnessBrowser__Caulo:CCNA_02221 597 LAELVPFIDWSPFFASWELIGRFPQILEDDVVGQAATDLYRDARAMLDKVVEEKWFGAKGVIGFWPAQAQGDD 669 89*********************************************************************** PP Met_synt_B12 75 ievyadesrseelatlhtLrqqaeke.....egkpnlclaDfvapkesgvkDyiGlFavtaglgieelakefe 142 i++y+de+r +e +lhtLrqq++k e k+n++l+Dfvap +g +Dy+G+Favtag+g +e++++f+ lcl|FitnessBrowser__Caulo:CCNA_02221 670 IVLYTDETRVAEFSRLHTLRQQMDKGadksgEAKANVALSDFVAPIGQG-ADYVGGFAVTAGHGEDEIVAKFK 741 **********************99886666777899*********9998.7********************** PP Met_synt_B12 143 aekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApGYpacpdhtekkt 215 a+ ddY+ai++ aladrLaeAfae+lh k r elWgya+de+ ++e+li+ekYqgiRpApGYpa+pdhtek t lcl|FitnessBrowser__Caulo:CCNA_02221 742 AAGDDYNAIMASALADRLAEAFAEWLHYKARVELWGYAADEDADVERLIAEKYQGIRPAPGYPAQPDHTEKGT 814 ************************************************************************* PP Met_synt_B12 216 lfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyakrkg 273 lf+lldae+++g++Ltes+amtP a+vsGl+f+h +a+yF+vgki+ dqvedya+rkg lcl|FitnessBrowser__Caulo:CCNA_02221 815 LFKLLDAEAATGLQLTESYAMTPGAAVSGLFFSHRQAHYFGVGKIDADQVEDYARRKG 872 ********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (899 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: 00:00:00.00 # Mc/sec: 27.50 // [ok]
This GapMind analysis is from Apr 09 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