Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_012049788.1 SWIT_RS18220 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000016765.1:WP_012049788.1 Length = 375 Score = 446 bits (1147), Expect = e-130 Identities = 233/375 (62%), Positives = 290/375 (77%) Query: 1 MLVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGS 60 M++++ Q I +AVRAFAQE+++P ++ ++ +P +E+A LGL GM+ PE GG+ Sbjct: 1 MILSETQSAIQEAVRAFAQEQIRPRSQAFEAAGGYPTGLFEELAGLGLLGMVAPEAAGGA 60 Query: 61 DTGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGA 120 YV+YA++L EIAA DGA STI+S+ NS+ +L+ G+E QK +FL L G M+GA Sbjct: 61 GADYVSYALSLIEIAAADGALSTIVSIQNSLLVGGLLKEGSEAQKARFLPELIGGRMIGA 120 Query: 121 FALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGIS 180 FALTE AGSDA++L+TRA +VLNG+KQFITSG+ AGV +VFAVTDP AGK+GIS Sbjct: 121 FALTEADAGSDAAALRTRATRAEGGWVLNGAKQFITSGKIAGVAMVFAVTDPAAGKKGIS 180 Query: 181 AFIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGG 240 AF+VPTDSPGY V +VE KLGQ ASDTC I FD++ V GAEG GY IALANLE G Sbjct: 181 AFLVPTDSPGYAVDKVEHKLGQAASDTCAIRFDDLFVEDGLLFGAEGRGYNIALANLEQG 240 Query: 241 RIGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHA 300 RIGIA+Q VGMA+AA E+A YA +R+S GKP+IEHQAV FRLAD+AT++ ARQ+VLHA Sbjct: 241 RIGIAAQCVGMAQAALEIAVAYARDRRSMGKPIIEHQAVGFRLADLATRLEAARQLVLHA 300 Query: 301 AALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 A+++DAG P L EASMAKLFASE AE + S A+QTLGGYGYL +F L +IYRDVRVCQIY Sbjct: 301 ASVKDAGLPCLKEASMAKLFASEAAEAIVSGAIQTLGGYGYLEEFGLAKIYRDVRVCQIY 360 Query: 361 EGTSDIQRMVIARNL 375 EGTSDIQRMVIAR L Sbjct: 361 EGTSDIQRMVIARAL 375 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: 447 Number of extensions: 13 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: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 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 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