Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000009985.1:WP_011385957.1 Length = 378 Score = 357 bits (916), Expect = e-103 Identities = 178/372 (47%), Positives = 248/372 (66%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64 +++ Q+++++ SFA ++ P A D E FP + + +M + G +G+ P E+ G G D Sbjct: 4 TEEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGAGTD 63 Query: 65 TVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGL 124 V Y MAV E++ CG I+S H S+G PI YG E QK +FLRP+A GEKLG F L Sbjct: 64 YVSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGCFCL 123 Query: 125 TEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184 TEP AG+DA+ +T A DGD Y+L+G+K FI+ A G + +V A+TD G +GISAF+ Sbjct: 124 TEPEAGSDAASIRTRARRDGDHYVLSGAKQFISTAKNGQVAIVFAVTDPQAGKRGISAFV 183 Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244 V TPGF+ E K+G S T +L FED R+P LG+EG G KIA++ L+GGR+G Sbjct: 184 VPTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLEGGRLG 243 Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304 IAAQ++G+A+ ALD + Y KER QFG+P+ + Q F+LADM +V+ A +V AA Sbjct: 244 IAAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVLHAASL 303 Query: 305 KDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGT 364 +D G P EA+MAKLFA+E A V + A+Q+HGGYGY D+PVER+ RD ++ +IYEGT Sbjct: 304 RDAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQIYEGT 363 Query: 365 SEVQRMVISGKL 376 S++QR+VIS L Sbjct: 364 SDIQRLVISRAL 375 Lambda K H 0.315 0.133 0.373 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: 347 Number of extensions: 10 Number of successful extensions: 1 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: 378 Length of database: 378 Length adjustment: 30 Effective length of query: 348 Effective length of database: 348 Effective search space: 121104 Effective search space used: 121104 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: 42 (22.0 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