Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate AO356_17045 AO356_17045 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17045 Length = 378 Score = 259 bits (663), Expect = 7e-74 Identities = 140/379 (36%), Positives = 220/379 (58%), Gaps = 5/379 (1%) Query: 1 MIP----NDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQ 56 MIP + + + RD R F ++ P+ ++W+++ ++ + G +PE Sbjct: 1 MIPRTLFSPEHELFRDSVRTFLEKEAVPYHSQWEKQGHVDRQLWNKAGEAGMLCSHLPEA 60 Query: 57 WGGCDTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGA 116 +GG D +L + +EEI G S+H+ + IL+YG++ K ++L L SG Sbjct: 61 YGGLDADFLYSTVVIEEIGRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKLVSGE 119 Query: 117 MLGAFALTEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGK 176 M+ A A+TEP AGSD G+KT A L+GD YV+NG K FIT+G A +VIV A TDP AG Sbjct: 120 MVTAIAMTEPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGFLADLVIVVAKTDPKAGA 179 Query: 177 RGISAFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALAN 236 +G S F+V +PG++ + +K+G A DT ++ F+DV+VP N LG+ G G+ + Sbjct: 180 KGTSLFLVEAGTPGFEKGKRLEKVGMKAQDTSELFFQDVRVPKDNLLGQAGMGFAYLMQE 239 Query: 237 LEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQM 296 L R+ +A + A AA + DY RER++FGK I + Q F+LA+MAT+I + R Sbjct: 240 LPQERLTVAIGGLASAEAALQWTLDYTRERKAFGKTIADFQNTRFKLAEMATEIQIGRVF 299 Query: 297 VHYAAALRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRV 356 V L GK + A+MAK + +++ KV +Q GGYG++ ++P+ R + D RV Sbjct: 300 VDRCLELHLQGKLDVPTAAMAKYWGTDLQCKVLDECVQLHGGYGFMWEYPIARAWADARV 359 Query: 357 CQIYEGTSDIQRMVISRNL 375 +IY GT++I + +I+R+L Sbjct: 360 QRIYAGTNEIMKEIIARSL 378 Lambda K H 0.320 0.135 0.394 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: 337 Number of extensions: 15 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: 375 Length of database: 378 Length adjustment: 30 Effective length of query: 345 Effective length of database: 348 Effective search space: 120060 Effective search space used: 120060 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 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