Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate HSERO_RS14055 HSERO_RS14055 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__HerbieS:HSERO_RS14055 Length = 388 Score = 187 bits (476), Expect = 3e-52 Identities = 121/355 (34%), Positives = 189/355 (53%), Gaps = 7/355 (1%) Query: 10 IRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGANLDYLTLAL 69 +RDAVRD +T + + D+ +P+ L G +P+E+GG+ L ++ Sbjct: 13 LRDAVRDLCKTFPPEYWRKIDEARGYPEQFVDALTKAGWLAALIPQEYGGSGLGLTEASV 72 Query: 70 VLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEM-LGAFCLTEPHV 128 ++EEI GG S A + +L R+G+ +QK +L +A GE+ L + +TEP Sbjct: 73 IMEEINR-TGGNSGACHGQMYNMGTLL-RHGSPEQKERYLPRIASGELRLQSMAVTEPTT 130 Query: 129 GSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDK----GAGKKGMSAFLV 184 G+D + ++T AVK+GD YVING K +I+ ++ + I++A T +GMS FLV Sbjct: 131 GTDTTRIKTVAVKKGDRYVINGQKVWISRVQHSDLMILLARTTPLEQVSRKSEGMSIFLV 190 Query: 185 PTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGGRIGI 244 + L + +T ++ FDN IPAENLIG EG G++ L L R I Sbjct: 191 DLKEAIGHGMEVRPILNMVNHETNELFFDNLEIPAENLIGEEGRGFRYILDGLNAERTLI 250 Query: 245 AAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIWHAAALR 304 AA+ +G D A Y++ER F I +Q V F LA+ ++EAA + + A AL Sbjct: 251 AAECIGDGYWFIDKATQYARERVVFDRPIGMNQGVQFPLAEAYIEVEAANLMRYQACALF 310 Query: 305 DAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQI 359 DA + C +A MAK A++ A + +QT GG+G ++ VER +R+ R+ Q+ Sbjct: 311 DAQQSCGAQANMAKYLAAKAAWEAANVCLQTHGGFGFACEYDVERKFRETRLYQV 365 Lambda K H 0.319 0.134 0.396 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: 325 Number of extensions: 23 Number of successful extensions: 4 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: 376 Length of database: 388 Length adjustment: 30 Effective length of query: 346 Effective length of database: 358 Effective search space: 123868 Effective search space used: 123868 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