Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF1326 PS417_06740 4-carboxymuconolactone decarboxylase
Query= BRENDA::Q9L5B1 (130 letters) >FitnessBrowser__WCS417:GFF1326 Length = 132 Score = 106 bits (265), Expect = 1e-28 Identities = 48/119 (40%), Positives = 73/119 (61%) Query: 4 RYETGMKVRRRILGDAHVDRAEAAKTPFDTPFQEMIAETAWGNVWASDRITDRERSMLTL 63 RY G++VRR +LGDAHVDR+ A T F++ FQEMI AWG++W + RS++T+ Sbjct: 6 RYAEGLQVRREVLGDAHVDRSLNALTEFNSEFQEMITRHAWGDIWTRPGLPRHTRSLITI 65 Query: 64 AVLAATGSFDEIPMHIRATARTGASKEDVAEAFQHVAIYAGVPKANHALKLAKQTYAEM 122 A+L +E+ +H+RA A G ++ ++ E AIY G+P AN LA+ + E+ Sbjct: 66 AMLIGMNRSEELKLHLRAAASNGVTRAEIKEVLMQSAIYCGIPAANATFHLAESVWDEL 124 Lambda K H 0.317 0.128 0.371 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: 60 Number of extensions: 3 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: 130 Length of database: 132 Length adjustment: 14 Effective length of query: 116 Effective length of database: 118 Effective search space: 13688 Effective search space used: 13688 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: 41 (20.4 bits)
Align candidate GFF1326 PS417_06740 (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.16499.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-62 193.4 0.1 7e-62 193.2 0.1 1.0 1 lcl|FitnessBrowser__WCS417:GFF1326 PS417_06740 4-carboxymuconolacto Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF1326 PS417_06740 4-carboxymuconolactone decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 193.2 0.1 7e-62 7e-62 1 122 [. 3 124 .. 3 125 .. 0.98 Alignments for each domain: == domain 1 score: 193.2 bits; conditional E-value: 7e-62 TIGR02425 1 ekeryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgreeel 75 ek+ry++Gl+vrr vlGdahvdr+l+a t+f++efqe+it++aWG++W+r+gl++++rsl+tia+l++++r+eel lcl|FitnessBrowser__WCS417:GFF1326 3 EKQRYAEGLQVRREVLGDAHVDRSLNALTEFNSEFQEMITRHAWGDIWTRPGLPRHTRSLITIAMLIGMNRSEEL 77 589************************************************************************ PP TIGR02425 76 alhvraaantGvteddikevllqvaiyaGvPaankalklakevlael 122 +lh+raaa +Gvt+++ikevl+q+aiy+G+Paan++++la++v++el lcl|FitnessBrowser__WCS417:GFF1326 78 KLHLRAAASNGVTRAEIKEVLMQSAIYCGIPAANATFHLAESVWDEL 124 ********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (132 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: 5.88 // [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