Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__SB2B:6938693 Length = 391 Score = 194 bits (493), Expect = 3e-54 Identities = 123/372 (33%), Positives = 185/372 (49%), Gaps = 6/372 (1%) Query: 2 LVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61 L+ +E++ I D V +AQ++L ++D F +E ++E+ ELGL G +PE++G ++ Sbjct: 17 LLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGELGLLGATLPEEYGCAN 76 Query: 62 TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121 YV+Y + EI D + MSV +S+ PI +G E Q+ ++L LATG +G F Sbjct: 77 ANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQRRKYLPKLATGEWVGCF 136 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181 LTEP GSD + +KTRA Y + G+K +IT+ A V +V+A D I Sbjct: 137 GLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFVVWAKLD-----GAIRG 191 Query: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 F++ G ++E K AS T +IV DNV+V + L EG K L R Sbjct: 192 FVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVG-EDALLPNVEGLKGPFGCLNKAR 250 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 GIA A+G A + AR Y +R F +PL +Q +LADM T+I+ L A Sbjct: 251 YGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEITTGLFACLQAG 310 Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 L D + S+ K + A + A GG G +F + R ++ YE Sbjct: 311 RLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRHVMNLEAVNTYE 370 Query: 362 GTSDIQRMVIAR 373 GT DI +++ R Sbjct: 371 GTHDIHALILGR 382 Lambda K H 0.319 0.134 0.382 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: 320 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: 391 Length adjustment: 30 Effective length of query: 345 Effective length of database: 361 Effective search space: 124545 Effective search space used: 124545 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