Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate PP_3725 PP_3725 putative Acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >FitnessBrowser__Putida:PP_3725 Length = 386 Score = 248 bits (633), Expect = 2e-70 Identities = 149/384 (38%), Positives = 220/384 (57%), Gaps = 13/384 (3%) Query: 3 DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMG----ELGLLGMVVPE 58 + +L+++Q M+ + R F +E+ PH +A ++A + L AQ+ G +PE Sbjct: 2 NFQLTQEQEMLVEAVRSFVAKELLPHEEAVDRADAVSPELAAQIRGKAIAAGFYAFNMPE 61 Query: 59 EWGGSYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASG 118 E GG +DY++ AL E+S A ++ + + L Q +++L G Sbjct: 62 EVGGGGLDYLSQALIERELSKVSWALHVFVARPSKI-----LMACKDEQINDYLLPCVQG 116 Query: 119 RAIGCFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDP--E 176 + CFALTEP AGS+A+ ++TRA +V+NGSK F S+A + AIVFAVTD Sbjct: 117 EKVDCFALTEPGAGSDANAIKTRAVRQGDDFVINGSKHFISHAGHADFAIVFAVTDTYEH 176 Query: 177 LGKK--GLSAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLA 234 G+K ++A LV TPG + R + R T + DCR+P + +LGE GKG Sbjct: 177 NGRKRNAVTALLVDRGTPGMTIRRGPKCVSNRGYHTYELFFDDCRVPASKVLGEVGKGWE 236 Query: 235 IALSNLEGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLN 294 +A + L GR+ + A +G A+ A + +L +A +R QFG+ I +Q ++ LADM TQ+ Sbjct: 237 VANAWLTAGRVMVAANCVGQAQRALDLSLQWAADRKQFGQAIGSYQGVSFKLADMATQIR 296 Query: 295 AARLLILHAARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYY 354 AA +L LH A G EA AKLFASE+ KV +AVQI GG G +++ PVER + Sbjct: 297 AAEMLTLHTAWKMDQGNMTDGEAGMAKLFASEVLGKVADEAVQIFGGMGLMDEGPVERIW 356 Query: 355 RDARITQIYEGSSEIQRLLIAREL 378 R+ARI +I+EG+SEIQR +IAREL Sbjct: 357 RNARIERIWEGTSEIQRHIIAREL 380 Lambda K H 0.318 0.133 0.390 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: 343 Number of extensions: 18 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