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 PP_3725 PP_3725 putative Acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__Putida:PP_3725 Length = 386 Score = 254 bits (650), Expect = 2e-72 Identities = 150/387 (38%), Positives = 222/387 (57%), Gaps = 13/387 (3%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLI----DKMGEAGFCGICFP 56 M+F LT++Q+M+ + F K L P E D+A +L K AGF P Sbjct: 1 MNFQLTQEQEMLVEAVRSFVAKELLPHEEAVDRADAVSPELAAQIRGKAIAAGFYAFNMP 60 Query: 57 EEYGGMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAE 116 EE GG GLD LS L ELSKV + ++ + I M +EQ YL P + Sbjct: 61 EEVGGGGLDYLSQALIERELSKVSWALHVFVAR-----PSKILMACKDEQINDYLLPCVQ 115 Query: 117 GTHVGAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTD--- 173 G V F LTEP AG+DA+A +T AV +GD +++NGSK FI++ AD +VFA+TD Sbjct: 116 GEKVDCFALTEPGAGSDANAIKTRAVRQGDDFVINGSKHFISHAGHADFAIVFAVTDTYE 175 Query: 174 -KSQGVHGISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGF 232 + + ++A ++++G PG + + T EL F+DC VP +LG+ G+G+ Sbjct: 176 HNGRKRNAVTALLVDRGTPGMTIRRGPKCVSNRGYHTYELFFDDCRVPASKVLGEVGKGW 235 Query: 233 KIAMETLDGGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKI 292 ++A L GR+ VAA +G A+ AL +++++ +R+QFG++I +Q + F +ADMAT+I Sbjct: 236 EVANAWLTAGRVMVAANCVGQAQRALDLSLQWAADRKQFGQAIGSYQGVSFKLADMATQI 295 Query: 293 EAARYLVYHAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERY 352 AA L H A ++G A MAK FAS+V +V +AVQIFGG G + P ER Sbjct: 296 RAAEMLTLHTAWKMDQGNMTDGEAGMAKLFASEVLGKVADEAVQIFGGMGLMDEGPVERI 355 Query: 353 MRNAKITQIYEGTNQVMRIVTSRALLR 379 RNA+I +I+EGT+++ R + +R LLR Sbjct: 356 WRNARIERIWEGTSEIQRHIIARELLR 382 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: 19 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: 383 Length of database: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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