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 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__SB2B:6938693 Length = 391 Score = 218 bits (554), Expect = 3e-61 Identities = 134/378 (35%), Positives = 204/378 (53%), Gaps = 8/378 (2%) Query: 1 MDFN--LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEE 58 ++FN LTE+++MI+DM E+A+ L V ++ +DR++++++GE G G PEE Sbjct: 12 LNFNSLLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGELGLLGATLPEE 71 Query: 59 YGGMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGT 118 YG + +SY L E+ +VD G +S SL PIY +GTE Q++KYL +A G Sbjct: 72 YGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQRRKYLPKLATGE 131 Query: 119 HVGAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGV 178 VG FGLTEP G+D + +T A Y + G+K++ITN AD +VV+A D + Sbjct: 132 WVGCFGLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFVVWAKLDGA--- 188 Query: 179 HGISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMET 238 I F+LEKGM G KIE K SIT E++ ++ EV ++ LL EG K Sbjct: 189 --IRGFVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEDALL-PNVEGLKGPFGC 245 Query: 239 LDGGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYL 298 L+ R G+A ALG AE AA +Y +R QF R ++ Q Q +ADM T+I + Sbjct: 246 LNKARYGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEITTGLFA 305 Query: 299 VYHAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKI 358 A L + EA ++ K + A+++ A + GG G + ++ R++ N + Sbjct: 306 CLQAGRLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRHVMNLEA 365 Query: 359 TQIYEGTNQVMRIVTSRA 376 YEGT+ + ++ RA Sbjct: 366 VNTYEGTHDIHALILGRA 383 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: 312 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: 391 Length adjustment: 30 Effective length of query: 353 Effective length of database: 361 Effective search space: 127433 Effective search space used: 127433 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 Apr 09 2024. 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