Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate SM_b20578 SM_b20578 gamma carboxymuconolactone decarboxylase
Query= BRENDA::Q6SJC5 (136 letters) >FitnessBrowser__Smeli:SM_b20578 Length = 135 Score = 162 bits (411), Expect = 1e-45 Identities = 78/124 (62%), Positives = 95/124 (76%) Query: 11 PTDRYTTGMDTRRRVLGDAHVDRAEACKSDFDAPFQTLITEGAWGTVWASDAISPRERSM 70 P+ RY GM TRR VLGD HVDRAEA +DFD PFQ LITE AWG VW+ + RERS+ Sbjct: 7 PSGRYRQGMATRRAVLGDNHVDRAEAASTDFDRPFQELITEAAWGHVWSRAGWTKRERSI 66 Query: 71 LTLALLAATGNFEEIPMHIRATARTGASQSDVIEAFQHVAIYAGVPRANHAIRLAKETYA 130 +T+ALLAA G EE+ MH+RATA TGA++ D+ EA HVAIYAGVP ANHAI++ K+ +A Sbjct: 67 VTIALLAALGQDEEVAMHVRATANTGATREDICEALLHVAIYAGVPAANHAIKIVKQVFA 126 Query: 131 EMEA 134 EM+A Sbjct: 127 EMDA 130 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: 89 Number of extensions: 2 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: 135 Length adjustment: 15 Effective length of query: 121 Effective length of database: 120 Effective search space: 14520 Effective search space used: 14520 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 SM_b20578 SM_b20578 (gamma 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.22622.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-64 199.3 1.5 1e-63 199.2 1.5 1.0 1 lcl|FitnessBrowser__Smeli:SM_b20578 SM_b20578 gamma carboxymuconolac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b20578 SM_b20578 gamma carboxymuconolactone decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.2 1.5 1e-63 1e-63 3 122 .. 9 128 .. 7 129 .. 0.98 Alignments for each domain: == domain 1 score: 199.2 bits; conditional E-value: 1e-63 TIGR02425 3 eryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgreeela 76 ry+qG+++rravlGd+hvdra+aa+tdfd++fqeliteaaWG+vW+r g +krers+vtiallaalg++ee+a lcl|FitnessBrowser__Smeli:SM_b20578 9 GRYRQGMATRRAVLGDNHVDRAEAASTDFDRPFQELITEAAWGHVWSRAGWTKRERSIVTIALLAALGQDEEVA 82 59************************************************************************ PP TIGR02425 77 lhvraaantGvteddikevllqvaiyaGvPaankalklakevlael 122 +hvra+antG+t++di+e+ll+vaiyaGvPaan+a+k+ k+v+ae+ lcl|FitnessBrowser__Smeli:SM_b20578 83 MHVRATANTGATREDICEALLHVAIYAGVPAANHAIKIVKQVFAEM 128 ********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (135 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: 4.25 // [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