Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate BPHYT_RS21435 BPHYT_RS21435 4-carboxymuconolactone decarboxylase
Query= BRENDA::Q6SJC5 (136 letters) >FitnessBrowser__BFirm:BPHYT_RS21435 Length = 131 Score = 109 bits (273), Expect = 1e-29 Identities = 52/124 (41%), Positives = 72/124 (58%) Query: 13 DRYTTGMDTRRRVLGDAHVDRAEACKSDFDAPFQTLITEGAWGTVWASDAISPRERSMLT 72 DRY G+D RR VLG AHVDR+ A +++ FQ IT AWG +W D + RS+LT Sbjct: 5 DRYEAGLDVRRAVLGSAHVDRSLANRNELTEEFQNFITRYAWGEIWTRDGLPRHTRSLLT 64 Query: 73 LALLAATGNFEEIPMHIRATARTGASQSDVIEAFQHVAIYAGVPRANHAIRLAKETYAEM 132 +A++ A EE+ +H+RA G ++ + E AIY GVP AN A LA + + E Sbjct: 65 IAMMVALNRSEELALHLRAAKNNGVTREQIKEVLLQTAIYCGVPAANSAFHLADKLFRED 124 Query: 133 EAEA 136 +A A Sbjct: 125 DAAA 128 Lambda K H 0.317 0.128 0.374 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: 52 Number of extensions: 1 Number of successful extensions: 1 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: 136 Length of database: 131 Length adjustment: 15 Effective length of query: 121 Effective length of database: 116 Effective search space: 14036 Effective search space used: 14036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 42 (20.8 bits)
Align candidate BPHYT_RS21435 BPHYT_RS21435 (4-carboxymuconolactone decarboxylase)
to HMM TIGR02425 (pcaC: 4-carboxymuconolactone decarboxylase (EC 4.1.1.44))
# 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/TIGR02425.hmm # target sequence database: /tmp/gapView.27200.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02425 [M=123] Accession: TIGR02425 Description: decarb_PcaC: 4-carboxymuconolactone decarboxylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-60 189.1 0.2 1.5e-60 188.9 0.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS21435 BPHYT_RS21435 4-carboxymuconolac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS21435 BPHYT_RS21435 4-carboxymuconolactone decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 188.9 0.2 1.5e-60 1.5e-60 2 121 .. 4 123 .. 3 125 .. 0.98 Alignments for each domain: == domain 1 score: 188.9 bits; conditional E-value: 1.5e-60 TIGR02425 2 keryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgr 71 ++rye+Gl+vrravlG ahvdr+la+++++++efq++it++aWG++W+rdgl++++rsl+tia+++al+r lcl|FitnessBrowser__BFirm:BPHYT_RS21435 4 EDRYEAGLDVRRAVLGSAHVDRSLANRNELTEEFQNFITRYAWGEIWTRDGLPRHTRSLLTIAMMVALNR 73 68******************************************************************** PP TIGR02425 72 eeelalhvraaantGvteddikevllqvaiyaGvPaankalklakevlae 121 +eelalh+raa+n+Gvt+++ikevllq+aiy+GvPaan+a++la +++ e lcl|FitnessBrowser__BFirm:BPHYT_RS21435 74 SEELALHLRAAKNNGVTREQIKEVLLQTAIYCGVPAANSAFHLADKLFRE 123 *********************************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (131 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: 5.04 // [ok]
This GapMind analysis is from Sep 17 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