Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate 14185 b0039 crotonobetaine reductase subunit II, FAD-binding (NCBI)
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Keio:14185 Length = 380 Score = 185 bits (469), Expect = 2e-51 Identities = 116/372 (31%), Positives = 183/372 (49%), Gaps = 4/372 (1%) Query: 3 VNDEQQQIADAVRAF-AQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61 +NDEQ+ +R A E + + + D+D +P+ + +A++G+ +L+PE+ GG D Sbjct: 5 LNDEQELFVAGIRELMASENWEAYFAECDRDSVYPERFVKALADMGIDSLLIPEEHGGLD 64 Query: 62 TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121 G+V A E+ G T + G LR G ++Q ++ + TG + Sbjct: 65 AGFVTLAAVWMEL--GRLGAPTYVLYQLPGGFNTFLREGTQEQIDKIMAFRGTGKQMWNS 122 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181 A+TEP AGSD SLKT LNGSK FITS ++V A K + Sbjct: 123 AITEPGAGSDVGSLKTTYTRRNGKIYLNGSKCFITSSAYTPYIVVMARDGASPDKPVYTE 182 Query: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 + V PG +V ++E KLG C+I FD+V++ + G EG G+ + R Sbjct: 183 WFVDMSKPGIKVTKLE-KLGLRMDSCCEITFDDVELDEKDMFGREGNGFNRVKEEFDHER 241 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 +A G A AFE A YAN+R FG+ + Q + + A MA K++ + M+ AA Sbjct: 242 FLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRFQLIQEKFAHMAIKLNSMKNMLYEAA 301 Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 D G +A+M K F + A +V A+Q LGG G + + R +RD+RV ++ Sbjct: 302 WKADNGTITSGDAAMCKYFCANAAFEVVDSAMQVLGGVGIAGNHRISRFWRDLRVDRVSG 361 Query: 362 GTSDIQRMVIAR 373 G+ ++Q + + R Sbjct: 362 GSDEMQILTLGR 373 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: 292 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 380 Length adjustment: 30 Effective length of query: 345 Effective length of database: 350 Effective search space: 120750 Effective search space used: 120750 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 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