Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate BWI76_RS16120 BWI76_RS16120 4-carboxymuconolactone decarboxylase
Query= BRENDA::Q6SJB9 (125 letters) >FitnessBrowser__Koxy:BWI76_RS16120 Length = 127 Score = 113 bits (283), Expect = 8e-31 Identities = 53/122 (43%), Positives = 74/122 (60%) Query: 3 ERYDNGMKVRRRVLGDAYVDRAEAGKTAFEAPFQTLITEGAWGTVWASDGISDRERSMLT 62 +RY GM+VRR+VLGDA+VD+ T FQ IT AWG W G+ RSM+T Sbjct: 5 QRYQRGMEVRRKVLGDAHVDKTLQKLTPLNEEFQDFITRYAWGETWTRPGLDHHTRSMIT 64 Query: 63 LALLAALGNFDEIPMHIRATARTGASKQDVLEAFQHVAIYAGVPRANQALKLARQTYDEM 122 +A+L AL E+ MH+RA G ++ ++ E H A+Y G+P AN + LA+Q +DEM Sbjct: 65 IAMLIALNREAELKMHLRAAFNNGVTRDELKELIMHSALYCGLPAANATMHLAQQVFDEM 124 Query: 123 EA 124 +A Sbjct: 125 DA 126 Lambda K H 0.318 0.131 0.376 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: 54 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: 125 Length of database: 127 Length adjustment: 14 Effective length of query: 111 Effective length of database: 113 Effective search space: 12543 Effective search space used: 12543 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 (21.8 bits) S2: 41 (20.4 bits)
Align candidate BWI76_RS16120 BWI76_RS16120 (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.8635.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-59 183.7 0.2 7e-59 183.5 0.2 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS16120 BWI76_RS16120 4-carboxymuconolac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS16120 BWI76_RS16120 4-carboxymuconolactone decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 183.5 0.2 7e-59 7e-59 2 122 .. 4 124 .. 3 125 .. 0.99 Alignments for each domain: == domain 1 score: 183.5 bits; conditional E-value: 7e-59 TIGR02425 2 keryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgre 72 k+ry++G++vrr+vlGdahvd++l++ t +++efq++it++aWG+ W+r+gl++++rs++tia+l+al+re lcl|FitnessBrowser__Koxy:BWI76_RS16120 4 KQRYQRGMEVRRKVLGDAHVDKTLQKLTPLNEEFQDFITRYAWGETWTRPGLDHHTRSMITIAMLIALNRE 74 79********************************************************************* PP TIGR02425 73 eelalhvraaantGvteddikevllqvaiyaGvPaankalklakevlael 122 +el++h+raa n+Gvt+d++ke ++++a+y+G+Paan++++la++v++e+ lcl|FitnessBrowser__Koxy:BWI76_RS16120 75 AELKMHLRAAFNNGVTRDELKELIMHSALYCGLPAANATMHLAQQVFDEM 124 ************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (127 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: 5.08 // [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