Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Ac3H11_2717 Acyl-CoA dehydrogenase, long-chain specific, mitochondrial precursor (EC 1.3.99.13)
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2717 Length = 329 Score = 169 bits (427), Expect = 1e-46 Identities = 119/345 (34%), Positives = 176/345 (51%), Gaps = 29/345 (8%) Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVS-MVGPVIYTFGSEEQKKRFLPRIAN 119 P +YGG S Y+ EEL AA AP + GP+I +G+E Q++++LP I Sbjct: 4 PHQYGGHDASPWARYVVIEELLAAGAPVSAHWIADRQSGPLILRYGTEAQRQKYLPGICK 63 Query: 120 VDDWWCQGFSEPGSGSDLASLKTKA---EKKGD-KWIINGQKTWTTLAQHADWIFCLCRT 175 + ++C G SEP SGSDLAS++++A E GD W ++GQK WTT A HA ++ L RT Sbjct: 64 GEVYFCIGMSEPNSGSDLASIRSRAVRDEAAGDGSWRLSGQKVWTTNAHHAQYMIALVRT 123 Query: 176 DPA----AKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQEN 231 A A + EG+S ++D+K G+TVRPI+ + GG NEV+ DDV + + L+G E Sbjct: 124 GAATGEKAARHEGMSQFIIDLKAAGVTVRPIRDLAGGEHFNEVYLDDVRLDADALIGTEG 183 Query: 232 KGWDYAKFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIE 291 +GW+ L ER+G R S + + G +P +L+A + Sbjct: 184 QGWEQVTAELAFERSGPERFLSSMALLHTLIDAV-----GAQPDALQAHAVGRLSARLVV 238 Query: 292 LKALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHG 351 L+ + L +A G P A+S LK G+ +Q EL +V+ A V G Sbjct: 239 LRQMSLAVTAELA-----AGGNPAWAASCLKDLGAAFEQEIPELAQQVLDVAPA---VGG 290 Query: 352 DDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 D + + Q+AP + S+ GG+ EI R II + LGL Sbjct: 291 GSDHAQVLAALMQMAPSF------SLRGGTREILRGIIARG-LGL 328 Lambda K H 0.317 0.135 0.411 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: 296 Number of extensions: 12 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: 396 Length of database: 329 Length adjustment: 29 Effective length of query: 367 Effective length of database: 300 Effective search space: 110100 Effective search space used: 110100 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 (21.6 bits) S2: 49 (23.5 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