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 BPHYT_RS20780 BPHYT_RS20780 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS20780 Length = 381 Score = 299 bits (766), Expect = 8e-86 Identities = 161/383 (42%), Positives = 236/383 (61%), Gaps = 21/383 (5%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64 S +Q ++E FA+ ++P+ ELD +ERFP E +M + G+ GI P+ +GG G D Sbjct: 4 SDTHQQIRETTRRFAQEVIRPITEELDRDERFPAEIYTQMGELGLFGITVPEAFGGAGLD 63 Query: 65 TVGYIMAVEELSR-------VCGT---TGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLA 114 Y + +EELSR CG G +LS H G + Q+ K+++PL Sbjct: 64 VTAYALVMEELSRGYASVADQCGLLELVGTLLSVH-----------GTDSQRAKYMQPLL 112 Query: 115 SGEKLGAFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKS 174 + A+ +TE +AGTD SG +TTA+ D + L+G+K++I NA D+ V+A TD + Sbjct: 113 RAKLRPAYCITEADAGTDVSGIRTTAMRTPDGWELSGAKLWIHNAPVADVAFVLARTDPA 172 Query: 175 KGNKGISAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIA 234 G +G+S FIV+ G S G KE KMG R S EL F+ ++P++ LLG+EG+GF I Sbjct: 173 AGRRGMSIFIVDCALAGVSKGAKEHKMGQRASQVGELHFDRVKLPQDALLGQEGRGFHIM 232 Query: 235 MSTLDGGRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAA 294 MS LD GR+GIAA A+G+AQ L+ + Y + R QFG +++FQ Q+ LADM +QAA Sbjct: 233 MSVLDKGRVGIAALAVGIAQAGLEAALDYAQTRKQFGSHIAEFQGIQWMLADMATDIQAA 292 Query: 295 RHLVYQAAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRD 354 R LV+ AA + G+ + +MAK FA +TA++ + AVQ+ GG GY R Y VER+ RD Sbjct: 293 RLLVHDAAERLEAGERASIACSMAKCFAGDTAVKHSANAVQIFGGSGYIRGYEVERLYRD 352 Query: 355 AKITEIYEGTSEVQRMVISGKLL 377 AKIT+IYEGT+++QR +++ L+ Sbjct: 353 AKITQIYEGTNQIQRTIVARDLI 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: 305 Number of extensions: 18 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: 378 Length of database: 381 Length adjustment: 30 Effective length of query: 348 Effective length of database: 351 Effective search space: 122148 Effective search space used: 122148 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