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 GFF2427 Psest_2475 Acyl-CoA dehydrogenases
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__psRCH2:GFF2427 Length = 392 Score = 241 bits (615), Expect = 3e-68 Identities = 136/375 (36%), Positives = 211/375 (56%), Gaps = 5/375 (1%) Query: 7 EDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGLDV 66 +DQ + +D F ++ +AP E+ + H R L ++GEAG G+ PE+ GG V Sbjct: 16 DDQTLFQDSVRRFLQQEVAPHYEQWEADHQLPRALWHRLGEAGLLGVDLPEQLGGCAAGV 75 Query: 67 LSYILAVEELSKVDDG---TGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAF 123 + ++ EE+S+ G +G + AN+ + I+ G Q+ +L +A G +GA Sbjct: 76 ETCLMICEEISRQGFGGLASGYNIHANIVM--PYIHHLGNPAQQACWLPRMAAGEVLGAI 133 Query: 124 GLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISA 183 +TEP AG+D +A + +A + LNGSK+FITNG AD +V A TD + G+S Sbjct: 134 AMTEPGAGSDLAAMRASAQKVPGGWKLNGSKVFITNGLLADMVIVCAKTDPNARARGVSL 193 Query: 184 FILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGR 243 F+++ +PGF GK K+G H S TAEL F+D VP++ LLG G+GF M+ L R Sbjct: 194 FLVDTTLPGFSRGKAIRKIGQHASDTAELFFDDLIVPEDALLGDAGKGFAYLMQELPRER 253 Query: 244 IGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAA 303 +GVAAQA+G +GAL + Y ++R FG+ I+ FQ +F +A++ +E R Sbjct: 254 LGVAAQAIGAIDGALQLTLDYVQQRRAFGQRIADFQNTRFTLAEVRAHLEMGRAYFEKCL 313 Query: 304 MLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYE 363 G+ S AA K S++ +Q+FGGYGYT++YP R+ +A+I IY Sbjct: 314 QRYARGEMSSTDAAALKLMLSEMQCRCVDQCLQLFGGYGYTLEYPISRFYVDARIQTIYA 373 Query: 364 GTNQVMRIVTSRALL 378 GT+++M+ V +R +L Sbjct: 374 GTSEIMKEVIARDML 388 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: 314 Number of extensions: 11 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: 383 Length of database: 392 Length adjustment: 30 Effective length of query: 353 Effective length of database: 362 Effective search space: 127786 Effective search space used: 127786 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 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