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 351334 BT1806 acyl-CoA dehydrogenase (NCBI ptt file)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__Btheta:351334 Length = 568 Score = 178 bits (451), Expect = 4e-49 Identities = 117/362 (32%), Positives = 190/362 (52%), Gaps = 35/362 (9%) Query: 42 IDKMGEAGFCGICFPEEYGGMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMF 101 +D M +AG G+ P +GG+ + Y + E ++ D G G S + C +Y F Sbjct: 95 LDAMVKAGLNGMTMPRRFGGLNFPITPYTMCAEIVAAADAGFGNIWS--LQDCIETLYEF 152 Query: 102 GTEEQKQKYLAPIAEGTHVGAFGLTEPSAGTDASAQQTTAVL--KGDKYILNGSKIFITN 159 G +Q +++ + +G + + LTEP AG+D A A K ++LNG K FITN Sbjct: 153 GNADQHSRFIPRVCQGETM-SMDLTEPDAGSDLQAVMLKATYSEKDGCWLLNGVKRFITN 211 Query: 160 GKEADTYVVFAMTDK-SQGVHGISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCE 218 G +AD ++V A +++ ++ G+S FI +K G +IE K+G H S T EL++++ Sbjct: 212 G-DADIHLVLARSEEGTRDGRGLSMFIYDKRQGGVDVRRIEHKLGIHGSPTCELVYKNA- 269 Query: 219 VPKENLLGKEGEGF-KIAMETLDGGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISK 277 K L G G K M ++G R+G+AAQ++G+++ A + Y+K+R+QFG++I Sbjct: 270 --KAELCGDRKLGLIKYVMALMNGARLGIAAQSVGLSQAAYNEGLAYAKDRKQFGKAIID 327 Query: 278 FQALQFMMADMATKIEAARYLVYHAAML--------------------KNEGKPYSEAA- 316 F A+ M+A M K++A R L+Y A + E K Y++ A Sbjct: 328 FPAVYDMLAIMKGKLDAGRALLYQTARYVDIYKALDDISRERKLTPEERLEQKKYAKLAD 387 Query: 317 ---AMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEGTNQVMRIVT 373 +AK S+ A + D +QI GG G+ ++Y +R R+A+IT IYEGT Q+ + Sbjct: 388 SFTPLAKGMNSEYANQNAYDCIQIHGGSGFMMEYACQRIYRDARITSIYEGTTQLQTVAA 447 Query: 374 SR 375 R Sbjct: 448 IR 449 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: 505 Number of extensions: 23 Number of successful extensions: 5 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: 568 Length adjustment: 33 Effective length of query: 350 Effective length of database: 535 Effective search space: 187250 Effective search space used: 187250 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: 51 (24.3 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