Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate WP_012645274.1 GEOB_RS00845 thiolase family protein
Query= SwissProt::P76503 (436 letters) >NCBI__GCF_000022265.1:WP_012645274.1 Length = 396 Score = 99.8 bits (247), Expect = 1e-25 Identities = 82/259 (31%), Positives = 124/259 (47%), Gaps = 24/259 (9%) Query: 181 GLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWS-DGKLKEEVMTAF---IPPYKQ 236 G M TAE +AK +GITREQ D L R +++ QA + D + ++ M I K Sbjct: 155 GEAMIRTAENVAKEFGITREQCDELTLRRYEQYQQALAGDREFQKRYMFPVEVQISKKKT 214 Query: 237 PLVEDNNIRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLV 296 +E + ++ A L+P G +T T DG + + T +AKEL Sbjct: 215 ITLEADEGVMATTKEGLAGLKPVLP--DGVLTFGAQTFPADGNCGISVTTREKAKELSAN 272 Query: 297 PLGYLRSYAFT-AIDVWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQ 355 P ++ +F A M A S +AL++AG+ +SD+ + H FAA LA + Sbjct: 273 PSLEIQIVSFGFARTKKAHMAAAVAPSAQMALDKAGIKVSDIKAVKTHNPFAANDLAMAK 332 Query: 356 LLGSERFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGG 415 LG +D + N G S+ YGHP A TGAR++ + + EL +GGG Sbjct: 333 ELG-----------------MDVNTMNNYGSSLIYGHPQAPTGARLMIEGIEELAVKGGG 375 Query: 416 FGLVTACAAGGLGAAMVLE 434 + L + CAAG A++VL+ Sbjct: 376 YLLFSGCAAGDTAASVVLK 394 Lambda K H 0.319 0.133 0.377 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: 351 Number of extensions: 13 Number of successful extensions: 4 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: 436 Length of database: 396 Length adjustment: 31 Effective length of query: 405 Effective length of database: 365 Effective search space: 147825 Effective search space used: 147825 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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