Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF245 PGA1_c02570 putative 4-carboxymuconolactone decarboxylase PcaC
Query= BRENDA::Q6SJA7 (118 letters) >FitnessBrowser__Phaeo:GFF245 Length = 141 Score = 185 bits (469), Expect = 2e-52 Identities = 93/115 (80%), Positives = 100/115 (86%) Query: 4 RRAVLGDAHVDRAEAAKTELDAPFQSLITEAAWGTVWASDKISRRERSMLTLALLAATGN 63 RR VLG AHV A+AA T LDAPFQ LITEAAWGTVWASD+ISRRERSMLTLALLAA GN Sbjct: 13 RREVLGAAHVANADAATTPLDAPFQQLITEAAWGTVWASDQISRRERSMLTLALLAALGN 72 Query: 64 FEEIPMHIRATANTGASKSDVIEAFQHVAIYAGVPKANHALKLAKQTYQEMEAVE 118 F+EIPMHIRATANTGA+ D+ E FQHVAIYAGVP+ANHALKLAK+TY EM A E Sbjct: 73 FDEIPMHIRATANTGATPQDIAETFQHVAIYAGVPRANHALKLAKKTYAEMAAEE 127 Lambda K H 0.315 0.125 0.348 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: 105 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: 118 Length of database: 141 Length adjustment: 14 Effective length of query: 104 Effective length of database: 127 Effective search space: 13208 Effective search space used: 13208 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 GFF245 PGA1_c02570 (putative 4-carboxymuconolactone decarboxylase PcaC)
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.6330.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-56 176.1 0.4 1.6e-56 175.9 0.4 1.0 1 lcl|FitnessBrowser__Phaeo:GFF245 PGA1_c02570 putative 4-carboxymu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF245 PGA1_c02570 putative 4-carboxymuconolactone decarboxylase PcaC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 175.9 0.4 1.6e-56 1.6e-56 3 122 .. 4 123 .. 2 124 .. 0.98 Alignments for each domain: == domain 1 score: 175.9 bits; conditional E-value: 1.6e-56 TIGR02425 3 eryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgreeelalhv 79 +y++G + rr vlG+ahv a aa+t +da+fq+liteaaWGtvWa+d++s+rers++t+allaalg+ +e+ +h+ lcl|FitnessBrowser__Phaeo:GFF245 4 PQYDAGQNIRREVLGAAHVANADAATTPLDAPFQQLITEAAWGTVWASDQISRRERSMLTLALLAALGNFDEIPMHI 80 68*************************************************************************** PP TIGR02425 80 raaantGvteddikevllqvaiyaGvPaankalklakevlael 122 ra+antG+t +di e +++vaiyaGvP+an+alklak+++ae+ lcl|FitnessBrowser__Phaeo:GFF245 81 RATANTGATPQDIAETFQHVAIYAGVPRANHALKLAKKTYAEM 123 *****************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (141 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: 4.63 // [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