Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate WP_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >NCBI__GCF_002893965.1:WP_050655857.1 Length = 380 Score = 307 bits (786), Expect = 4e-88 Identities = 161/372 (43%), Positives = 236/372 (63%), Gaps = 2/372 (0%) Query: 6 TEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGLD 65 +++ + + ++ + A+K LAP V E +KA + + +G+AG + +PEE+GG Sbjct: 9 SQEARDLIELTRDVADKVLAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEEFGGGDQP 68 Query: 66 VLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFGL 125 Y+ +EE++ + +S + SL P++ FGT+EQK ++L + G +GA+ L Sbjct: 69 YEVYLQVLEEIASRWAAVAVAVSVH-SLSCFPLFTFGTDEQKNRWLPDMLGGNTIGAYSL 127 Query: 126 TEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAFI 185 +E AG+DA+A A Y +NGSK +ITNG +AD Y +FA T G G+S + Sbjct: 128 SEAQAGSDAAALSCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTS-DDGSRGVSCLL 186 Query: 186 LEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRIG 245 ++K G FGK E+KMG TA ++D +P+E L+G+ G+G IA LD GR+G Sbjct: 187 VDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIAFSALDSGRLG 246 Query: 246 VAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAML 305 +AA A+GIA+GAL AV Y+KER+ FG+ I Q L F++ADMA +++AR AA Sbjct: 247 IAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSARATYLDAARR 306 Query: 306 KNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEGT 365 ++ G PYS A++AK A+D AM+VTTDAVQ+FGGYGYT D+P ERYMR AKITQI+EGT Sbjct: 307 RDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMREAKITQIFEGT 366 Query: 366 NQVMRIVTSRAL 377 NQ+ R+V +R L Sbjct: 367 NQIQRLVIARQL 378 Lambda K H 0.318 0.134 0.379 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: 387 Number of extensions: 14 Number of successful extensions: 3 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: 383 Length of database: 380 Length adjustment: 30 Effective length of query: 353 Effective length of database: 350 Effective search space: 123550 Effective search space used: 123550 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: 41 (21.7 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