Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate 350921 BT1393 4-carboxymuconolactone decarboxylase (NCBI ptt file)
Query= BRENDA::A2FEX8 (233 letters) >FitnessBrowser__Btheta:350921 Length = 401 Score = 150 bits (379), Expect = 4e-41 Identities = 79/229 (34%), Positives = 129/229 (56%), Gaps = 5/229 (2%) Query: 10 IEQNDPEYTAFFKRFELMVKNESKIDDKSRYLGILGALIGAKAIDYFPIILEMSLDNILT 69 + DPE A F F V+ +D K+R + L + I ++A + ++LE +L+ +T Sbjct: 173 LSATDPELDAIFGNFTKEVQQYGNLDTKTRLMVTLASNIASQAQTEYRMMLESALNAGIT 232 Query: 70 PNEVKEVLYEAAYILGIANVFPFLKLTNDIFKAKNINLPLENQSKVAPGEGLQKGIEKQA 129 P E+KE+LY+A G+A V F+ +TN+ A + LPLE Q+ V+ KG+ Q Sbjct: 233 PIEIKEILYQAVAYAGMAKVMDFVGITNEALLAHGVRLPLEGQAVVSAETRFDKGLALQK 292 Query: 130 EAFGPGMEKFHTMGP-----MAKWVVSFMYGEFYTREVLTVKERELVLSCIFIGHGDAAP 184 FG +++ H P + +++ + +G++ TR L VK REL+ I + G Sbjct: 293 SIFGERIDQMHKNAPENQKHIQRYLSANCFGDYQTRGGLDVKTRELLTFSILVSLGGCES 352 Query: 185 QFNQHIKANIHVGNNKKFLIQMILSLVPYLGYPRTFNALKVLNDAIPDE 233 Q HI+ N++VGNNK L+ ++ L+PY+GYPRT NA+ LN+ IP++ Sbjct: 353 QVKGHIQGNVNVGNNKDTLLAVVTQLLPYIGYPRTLNAIACLNEVIPEK 401 Lambda K H 0.320 0.139 0.404 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: 213 Number of extensions: 6 Number of successful extensions: 2 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: 233 Length of database: 401 Length adjustment: 27 Effective length of query: 206 Effective length of database: 374 Effective search space: 77044 Effective search space used: 77044 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: 48 (23.1 bits)
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