Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate WP_011427916.1 RHE_RS24315 4-carboxymuconolactone decarboxylase
Query= BRENDA::Q6SJC5 (136 letters) >NCBI__GCF_000092045.1:WP_011427916.1 Length = 134 Score = 165 bits (418), Expect = 2e-46 Identities = 78/126 (61%), Positives = 100/126 (79%) Query: 10 TPTDRYTTGMDTRRRVLGDAHVDRAEACKSDFDAPFQTLITEGAWGTVWASDAISPRERS 69 +P++RY GM TRR VLGDAHVDRA A ++ FD PFQ LITE AWG VW+ ++ RERS Sbjct: 6 SPSERYRQGMATRRAVLGDAHVDRAAAGETGFDRPFQELITEAAWGHVWSRPTLTKRERS 65 Query: 70 MLTLALLAATGNFEEIPMHIRATARTGASQSDVIEAFQHVAIYAGVPRANHAIRLAKETY 129 ++T+ALLAA G EE+ MH+RATA TGA++ D+ EA HVAIYAGVP ANHAI++AK+ + Sbjct: 66 IVTIALLAALGQDEEVAMHVRATANTGATRDDICEALLHVAIYAGVPAANHAIKIAKQAF 125 Query: 130 AEMEAE 135 A+M+AE Sbjct: 126 AQMDAE 131 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: 91 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: 134 Length adjustment: 15 Effective length of query: 121 Effective length of database: 119 Effective search space: 14399 Effective search space used: 14399 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 WP_011427916.1 RHE_RS24315 (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.1821811.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-65 203.0 1.2 7.7e-65 202.8 1.2 1.0 1 NCBI__GCF_000092045.1:WP_011427916.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000092045.1:WP_011427916.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.8 1.2 7.7e-65 7.7e-65 2 122 .. 8 128 .. 7 129 .. 0.98 Alignments for each domain: == domain 1 score: 202.8 bits; conditional E-value: 7.7e-65 TIGR02425 2 keryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgreee 74 +ery+qG+++rravlGdahvdra a++t fd++fqeliteaaWG+vW+r+ l+krers+vtiallaalg++ee NCBI__GCF_000092045.1:WP_011427916.1 8 SERYRQGMATRRAVLGDAHVDRAAAGETGFDRPFQELITEAAWGHVWSRPTLTKRERSIVTIALLAALGQDEE 80 68*********************************************************************** PP TIGR02425 75 lalhvraaantGvteddikevllqvaiyaGvPaankalklakevlael 122 +a+hvra+antG+t+ddi+e+ll+vaiyaGvPaan+a+k+ak+++a++ NCBI__GCF_000092045.1:WP_011427916.1 81 VAMHVRATANTGATRDDICEALLHVAIYAGVPAANHAIKIAKQAFAQM 128 *********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (134 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: 11.79 // [ok]
This GapMind analysis is from Apr 09 2024. 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