Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate WP_059149579.1 V474_RS00150 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >NCBI__GCF_001046635.1:WP_059149579.1 Length = 373 Score = 212 bits (540), Expect = 1e-59 Identities = 131/361 (36%), Positives = 185/361 (51%), Gaps = 5/361 (1%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 M+FDL+E++ +LK E + YD DSR+ + E GG+S A W E GL+ PF EE Sbjct: 1 MNFDLNEDEEMLKALTERFVTDHYDHDSRRAFLAEPGGFSGANWQLLGELGLIAAPFPEE 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 GG G A V EALG LV+EP VV+ G A + L ++ G K Sbjct: 61 LGGLGLDATGIATVFEALGRGLVVEPLAEAVVMAGRLFASTAPEALQGEWLGALMAGEKR 120 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 A A +E +R L V T+A G+ + G K G AD IV+AR G D Sbjct: 121 LALAHVEARARDGLVWVQTSATAQDGGYCLSGTKPYCAVGGGADGFIVSARLSGEPGDAD 180 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 GV +FLVPA G + + + DG A + GV + A +GD + L I + D A Sbjct: 181 GVALFLVPAGTPGASTRDWTMADGSVATSLDLEGVVLPAGNRLGD--DGLAAIASTSDLA 238 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 A AEA+G+M+ L T+ Y+KTR QFG +G+FQ +QHR + EQ+R++ A Sbjct: 239 SLARSAEALGIMERLLHETIGYLKTRDQFGSALGAFQAIQHRMVAQYAVIEQSRALLNLA 298 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 ++ E D E A A+ + I + +G + IQ HGG+G+T E IG KRL ++ Sbjct: 299 LVSWESD---EFAQAVHGVRAFIADASVELGHEMIQFHGGMGVTDELAIGGGHKRLLVLS 355 Query: 361 Q 361 + Sbjct: 356 R 356 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: 405 Number of extensions: 17 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: 373 Length adjustment: 30 Effective length of query: 350 Effective length of database: 343 Effective search space: 120050 Effective search space used: 120050 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 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