Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_012757079.1 RLEG_RS07465 maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >NCBI__GCF_000023185.1:WP_012757079.1 Length = 210 Score = 190 bits (482), Expect = 2e-53 Identities = 102/212 (48%), Positives = 140/212 (66%), Gaps = 9/212 (4%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKA-DYIALNPQELVPTLVV 59 ++LY YWRSSA+YRVRIALNL GV + +S++L+ HK +Y+ALNPQ LVPTLV+ Sbjct: 4 VVLYDYWRSSASYRVRIALNLLGVDYQTVSINLLEVA---HKTPEYLALNPQGLVPTLVI 60 Query: 60 DDEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQ 119 D G LTQSLAI+EYL E P+ LLP+ +R VRA+A +A +IHP+ NL V+ Sbjct: 61 D----GKTLTQSLAIVEYLAETRPECGLLPSDIADRQKVRALAYAVAMDIHPICNLHVVS 116 Query: 120 YLTQKLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQ 179 +L + +A+ W H++ G LET + + G + FG+ T+ADLCLVPQVYNA+ Sbjct: 117 HL-MSMADKADAREEWMKHFITDGLGKLETMIGKADGAFSFGNTPTMADLCLVPQVYNAR 175 Query: 180 RFNVDLTPYPNIMRVWAECNQLPAFADAAPER 211 R+ V+LT + I+ + A C LPAF A P+R Sbjct: 176 RWGVELTAFKRIVDIDAGCADLPAFQAAHPDR 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: 155 Number of extensions: 9 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_012757079.1 RLEG_RS07465 (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.45234.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-84 269.2 0.0 1.4e-84 269.0 0.0 1.0 1 NCBI__GCF_000023185.1:WP_012757079.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000023185.1:WP_012757079.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 269.0 0.0 1.4e-84 1.4e-84 2 207 .. 6 208 .. 5 210 .] 0.98 Alignments for each domain: == domain 1 score: 269.0 bits; conditional E-value: 1.4e-84 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAiieyLe 74 lY+y+rSsasyRvRiaL+L g+dy++v++nLl+ ++k++e+ alNPq+lvPtL+id g++ltqSlAi+eyL NCBI__GCF_000023185.1:WP_012757079.1 6 LYDYWRSSASYRVRIALNLLGVDYQTVSINLLE-VAHKTPEYLALNPQGLVPTLVID-GKTLTQSLAIVEYLA 76 9********************************.6**********************.6************** PP TIGR01262 75 etypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellk 147 et+pe Llp+d a+r++vrala+++a+dihP++Nl+v++ l++ + ++++++ew+kh+i++Gl lE+++ NCBI__GCF_000023185.1:WP_012757079.1 77 ETRPECGLLPSDIADRQKVRALAYAVAMDIHPICNLHVVSHLMSMA-DKADAREEWMKHFITDGLGKLETMIG 148 *******************************************776.68999********************* PP TIGR01262 148 ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenq 207 ++ gaf++G+++t+ad+cLvpqvynA+r++v+l+++ ++ i++ +a+lpafq+ahp++ NCBI__GCF_000023185.1:WP_012757079.1 149 KADGAFSFGNTPTMADLCLVPQVYNARRWGVELTAFKRIVDIDAGCADLPAFQAAHPDRV 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 12.19 // [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