Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_02129 CCNA_02129 acyl-CoA dehydrogenase, short-chain specific
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Caulo:CCNA_02129 Length = 377 Score = 211 bits (536), Expect = 4e-59 Identities = 134/371 (36%), Positives = 190/371 (51%), Gaps = 7/371 (1%) Query: 5 LSEEQRLLKESVEGLLKGSYDFDSRKKY--AKEKGGWSRAVWGKFAEQGLLGLPFSEEDG 62 L+EEQ +L+++ +G S + +K +K K + A W + + G G+ E Sbjct: 4 LTEEQTMLRDAAKGWASESAPVGALRKLRDSKSKQTFDPAAWAEMGQMGWAGVIVPEAYD 63 Query: 63 GFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKTFA 122 G G + +++E G +L P L T +I L+ GS AQK A LP I G Sbjct: 64 GSAFGYLGLGLILEETGRTLAASPLLSTAMIAASALQLGGSDAQKQAWLPKIATGEAVAT 123 Query: 123 FAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRTGV 182 A +++ + + +A +SG G+V++G K +VL+GEAAD LIV ART G D G+ Sbjct: 124 LA-IDEGAHHAPARTALSATQSGAGYVLNGTKTLVLDGEAADLLIVAARTSGAPGDTNGI 182 Query: 183 GVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDART 242 +FLV DA G+TR D AA I F GV+VGADA +G+ + ++E +D A Sbjct: 183 TLFLVAGDAAGVTRSHLSLIDSRGAAKIAFDGVEVGADAVLGEVDKGWAVLEPTLDRAYA 242 Query: 243 ALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFATM 302 L AE +G + T++Y+KTR QFG IG+FQ LQHRAA F E RS Sbjct: 243 GLAAEMLGSASAAFDITLDYLKTRTQFGQVIGTFQALQHRAAKWFTDLETTRSC---VEA 299 Query: 303 AAEFDDAKERAGAIA-AAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIEQ 361 A E DA + A+A AK + + + +Q+HGGIGMT G Y KR + E Sbjct: 300 ALEALDAGADSRALAFLAKAKASELVHLASNEMVQMHGGIGMTDAHDAGLYMKRARVTEA 359 Query: 362 TFGDTDHHLAR 372 FG H R Sbjct: 360 LFGGASFHRDR 370 Lambda K H 0.318 0.135 0.388 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: 363 Number of extensions: 14 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: 380 Length of database: 377 Length adjustment: 30 Effective length of query: 350 Effective length of database: 347 Effective search space: 121450 Effective search space used: 121450 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: 50 (23.9 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