Align candidate Synpcc7942_1372 Synpcc7942_1372 (methionine synthase (B12-dependent))
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.12002.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-44 137.3 0.0 6.1e-44 136.5 0.0 1.4 1 lcl|FitnessBrowser__SynE:Synpcc7942_1372 Synpcc7942_1372 methionine synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1372 Synpcc7942_1372 methionine synthase (B12-dependent) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 136.5 0.0 6.1e-44 6.1e-44 3 256 .. 943 1189 .. 941 1190 .] 0.92 Alignments for each domain: == domain 1 score: 136.5 bits; conditional E-value: 6.1e-44 Met_synt_B12 3 eelveyidWtpff.qaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpA 68 +e+ +y+d + f W++++ ++ ++e + a+k+ q+ ++i +e+ll+ + v+g fp+ lcl|FitnessBrowser__SynE:Synpcc7942_1372 943 AEVFSYLDRQALFvGQWQFRKP-KEQSREEYDAFIAEKVEPILQQWTTRILAEDLLEPQVVYGYFPC 1008 6788899988765258999877.455555666678999999999999******************** PP Met_synt_B12 69 nsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgie 135 ++g+ +++++ ++r++ +a++ + rq + + lc+aDf ap+e g++D++ + avt+g+++ lcl|FitnessBrowser__SynE:Synpcc7942_1372 1009 VAVGNSLQLFDPNDRDRPTARFDFPRQRSLR-----RLCIADFFAPEELGIQDVFPMQAVTVGHKAT 1070 **********9999************99665.....7****************************** PP Met_synt_B12 136 elakefeaekddYsa.ilvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpA 201 e+a+++ a d+Ys+ + + la +LaeA+ae+ h+++r+e gy + e s +++++++Yqg R++ lcl|FitnessBrowser__SynE:Synpcc7942_1372 1071 EFAAQLFAG-DQYSDyLYFHGLAVQLAEALAEWTHARIRRE-LGYGSLEPESLRDILAQRYQGSRYS 1135 ****99887.99997255799*******************9.6************************ PP Met_synt_B12 202 pGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFa 256 +GYpacp+ ++ ell+a++ ig+++ es ++P++s +++ hp+a+yF+ lcl|FitnessBrowser__SynE:Synpcc7942_1372 1136 FGYPACPNVADSRIQLELLEADR-IGMSMDESEQLYPEQSTTAIVAYHPAAKYFS 1189 **********************9.******************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1190 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: 27.12 // [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