Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_011651488.1 RL_RS09715 maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >NCBI__GCF_000009265.1:WP_011651488.1 Length = 210 Score = 194 bits (492), Expect = 1e-54 Identities = 102/211 (48%), Positives = 137/211 (64%), Gaps = 7/211 (3%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60 ++LY YWRSSA+YRVRIALNL GV + +S++L+ G DYI LNPQ LVPTLV+D Sbjct: 4 VVLYDYWRSSASYRVRIALNLLGVDYQTVSINLLE--GAHKTPDYITLNPQGLVPTLVID 61 Query: 61 DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120 G LTQSLAIIEYL EL P LLP+ +R VRA+A +A +IHP+ N+ V+ + Sbjct: 62 ----GKTLTQSLAIIEYLAELQPGCGLLPSDIADRQKVRALAYAVAMDIHPICNMHVVSH 117 Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQR 180 L +T +A+ W H+++ G LE + + G + GD T+ADLCLVPQVYNA+R Sbjct: 118 L-MSMTEKPDAREEWMKHFISDGLRKLEAMIGKADGAFSVGDTPTMADLCLVPQVYNARR 176 Query: 181 FNVDLTPYPNIMRVWAECNQLPAFADAAPER 211 + VD+T + I+ + C LPAF A P+R Sbjct: 177 WGVDMTAFKRIVDIDGRCADLPAFQAAHPDR 207 Lambda K H 0.321 0.134 0.408 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: 147 Number of extensions: 8 Number of successful extensions: 4 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: 216 Length of database: 210 Length adjustment: 22 Effective length of query: 194 Effective length of database: 188 Effective search space: 36472 Effective search space used: 36472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 45 (21.9 bits)
Align candidate WP_011651488.1 RL_RS09715 (maleylacetoacetate isomerase)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))
# 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.carbon/TIGR01262.hmm # target sequence database: /tmp/gapView.1177538.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01262 [M=211] Accession: TIGR01262 Description: maiA: maleylacetoacetate isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-86 273.7 0.0 5.7e-86 273.5 0.0 1.0 1 NCBI__GCF_000009265.1:WP_011651488.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000009265.1:WP_011651488.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 273.5 0.0 5.7e-86 5.7e-86 2 207 .. 6 208 .. 5 210 .] 0.98 Alignments for each domain: == domain 1 score: 273.5 bits; conditional E-value: 5.7e-86 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAiieyLe 74 lY+y+rSsasyRvRiaL+L g+dy++v++nLl+ G++k++++ +lNPq+lvPtL+id g++ltqSlAiieyL NCBI__GCF_000009265.1:WP_011651488.1 6 LYDYWRSSASYRVRIALNLLGVDYQTVSINLLE-GAHKTPDYITLNPQGLVPTLVID-GKTLTQSLAIIEYLA 76 9********************************.9**********************.6************** PP TIGR01262 75 etypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellk 147 e +p Llp+d a+r++vrala+++a+dihP++N++v++ l++ ++++++ew+kh+i++Gl+ lE+++ NCBI__GCF_000009265.1:WP_011651488.1 77 ELQPGCGLLPSDIADRQKVRALAYAVAMDIHPICNMHVVSHLMSM-TEKPDAREEWMKHFISDGLRKLEAMIG 148 *******************************************76.5799*********************** PP TIGR01262 148 ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenq 207 ++ gaf+vGd++t+ad+cLvpqvynA+r++vd++++ ++ i+ ++a+lpafq+ahp++ NCBI__GCF_000009265.1:WP_011651488.1 149 KADGAFSVGDTPTMADLCLVPQVYNARRWGVDMTAFKRIVDIDGRCADLPAFQAAHPDRV 208 *********************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (210 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: 00:00:00.00 # Mc/sec: 11.91 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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