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 H281DRAFT_06133 H281DRAFT_06133 hypothetical protein
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__Burk376:H281DRAFT_06133 Length = 377 Score = 349 bits (895), Expect = e-101 Identities = 175/373 (46%), Positives = 253/373 (67%) Query: 5 LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64 LT++ +MI++ FA + LAP + DK H + + ++GE G G+ E++GG GL Sbjct: 3 LTQEHEMIRESIRTFAAERLAPHASDWDKNHTFPAAALKELGELGALGMVVEEKWGGAGL 62 Query: 65 DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124 D +S +LA+EE++ D T +S SL +G+E+QK+++L P+A+G +G F Sbjct: 63 DYMSLVLALEEIAAGDGATSTIVSVQNSLACGITSKYGSEKQKEQWLRPLAQGQKLGCFC 122 Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184 LTEP G+DASA +TTA GD+++LNG K FIT GK AD +VFA+TDKS GIS F Sbjct: 123 LTEPHTGSDASALRTTARRDGDEWVLNGVKQFITTGKYADVAIVFAVTDKSADKKGISCF 182 Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244 ++ PG+ ++E+KMG H S TA++IFEDC V ++G+EG+G++IA+ L+ GRI Sbjct: 183 LIPTATPGYVVARLEEKMGQHASDTAQIIFEDCRVHLSAMMGQEGDGYRIALSNLEAGRI 242 Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304 G+AAQA+G+A A AAVKY+KERE FG+ + + QA+ F +ADMAT+IEAAR +V+ AA Sbjct: 243 GIAAQAVGMARAAFEAAVKYAKERETFGKLLIEHQAVTFRLADMATQIEAARMMVWRAAT 302 Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364 LK+ GK A+MAK FAS++A +V +DA+QI GG GY D+P ER R+ ++ QIYEG Sbjct: 303 LKDAGKACLTEASMAKMFASEMAEKVCSDAIQIHGGCGYVSDFPVERIYRDVRVCQIYEG 362 Query: 365 TNQVMRIVTSRAL 377 N + R+V RA+ Sbjct: 363 ANDIQRMVIGRAI 375 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: 360 Number of extensions: 15 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 353 Effective length of database: 347 Effective search space: 122491 Effective search space used: 122491 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