Align candidate N515DRAFT_0495 N515DRAFT_0495 (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.21870.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-132 425.7 0.1 6.4e-132 425.1 0.1 1.3 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0495 N515DRAFT_0495 methionine syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0495 N515DRAFT_0495 methionine synthase (B12-dependent) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.1 0.1 6.4e-132 6.4e-132 1 273 [] 606 876 .. 606 876 .. 0.98 Alignments for each domain: == domain 1 score: 425.1 bits; conditional E-value: 6.4e-132 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglf 66 dl+el+eyidWtpffqaWel+g+yp+il+de vg++a++lf+dAqamL++i++e++l+a+av+g++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0495 606 DLAELREYIDWTPFFQAWELAGRYPAILKDEIVGTQASELFRDAQAMLDRIVAERWLTARAVIGFW 671 699*************************************************************** PP Met_synt_B12 67 pAnsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtagl 132 +A ++gdd evy ++ ++la+l++Lrqqa+k++++p ++l Df+apke+g++D++G+Favtag+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0495 672 RAAQVGDDTEVYGEDG--RKLAVLRHLRQQADKPADRPDFSLGDFIAPKEAGKQDWVGAFAVTAGI 735 ***********96666..4589******************************************** PP Met_synt_B12 133 gieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgi 198 giee++++fea++ddYs+il+kaladrLaeAfae++h++vr+e+Wgya+de+l+ne+li+ekY+gi lcl|FitnessBrowser__Dyella79:N515DRAFT_0495 736 GIEEHVARFEAAHDDYSSILLKALADRLAEAFAERMHQRVRREFWGYAPDEALDNEALIDEKYRGI 801 ****************************************************************** PP Met_synt_B12 199 RpApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdq 264 RpApGYpacpdhtek+tlf+llda++++gieLte +am+P+a+vsG+yf+hp+++yF vg+++++q lcl|FitnessBrowser__Dyella79:N515DRAFT_0495 802 RPAPGYPACPDHTEKSTLFKLLDATANAGIELTEGYAMYPTAAVSGWYFSHPDSQYFVVGRLTREQ 867 ****************************************************************** PP Met_synt_B12 265 vedyakrkg 273 vedyakrkg lcl|FitnessBrowser__Dyella79:N515DRAFT_0495 868 VEDYAKRKG 876 *******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (895 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 19.10 // [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