Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate WP_012113724.1 XAUT_RS08530 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-20677 (380 letters) >NCBI__GCF_000017645.1:WP_012113724.1 Length = 354 Score = 150 bits (380), Expect = 4e-41 Identities = 119/367 (32%), Positives = 162/367 (44%), Gaps = 27/367 (7%) Query: 7 EEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEEDGGFGA 66 EE LL++S L+ +Y ++ + +A W AE G L E GG G Sbjct: 9 EEDALLRDSARRFLEDTY------AWSPTRACDPKARWRAMAELGWFALGLPEALGGIGG 62 Query: 67 GAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAG-SAAQKAAHLPGIIDGSKTFAFAQ 125 A + M+++E G L P L ++++ L AQ A G+ GS A+ Sbjct: 63 DAAQCMVILEEAGRVLDEAPLLASLLLAAPVLAALPLEVAQPLAD--GLQAGSVRLAYVP 120 Query: 126 LEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRTGVGVF 185 D G + G ++ G + L + A IV G G V Sbjct: 121 -------DAG-----LRLGEGGTLLSGRSRLALGIDLATHWIVPV----GSGSANGAAVL 164 Query: 186 LVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDARTALC 245 L+PA A + DG AA ++F + V DA + E A EL + D A Sbjct: 165 LLPASAAAALDRTL-LMDGRTAAVLSFANLPVAPDAIVARGEAAFELAALLADAAAVGAS 223 Query: 246 AEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFATMAAE 305 AEA+G D L TV Y+K R QFG P+ SFQ +QH A+ F Q RS+ M+A A Sbjct: 224 AEALGAADAGLALTVSYLKDRTQFGAPLASFQAVQHMMAESFCEIAQMRSLLMWAADALA 283 Query: 306 FDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIEQTFGD 365 A ERA A +A K G G + IQ+ GGIG+T E +IGH +KRL FG Sbjct: 284 -GPAGERARAASALKAYAGMQGLKAVARCIQVSGGIGVTQEYRIGHVYKRLQTHAALFGS 342 Query: 366 TDHHLAR 372 T HLAR Sbjct: 343 TQEHLAR 349 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: 279 Number of extensions: 9 Number of successful extensions: 3 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: 354 Length adjustment: 30 Effective length of query: 350 Effective length of database: 324 Effective search space: 113400 Effective search space used: 113400 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: 49 (23.5 bits)
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