Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate GFF3761 Psest_3830 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__psRCH2:GFF3761 Length = 393 Score = 181 bits (459), Expect = 3e-50 Identities = 123/380 (32%), Positives = 192/380 (50%), Gaps = 10/380 (2%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 +D +LT E ++ + +FA D +AP++ + + + I REMG GL G PE YG Sbjct: 15 LDQQLTEEERMVQGSAAQFAADKLAPRVLEAFRHEQTDPAIFREMGETGLLGATIPEAYG 74 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 G G +Y+ G+ E+ R+DS + SL +PI+ FG +A + ++LP+L SGE + Sbjct: 75 GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPIYEFGNEATRQKYLPKLASGEYI 134 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 G FGLTEP+ GSD G+ T A+ + + ++G+K +ITNS + V V + Sbjct: 135 GCFGLTEPNHGSDPGSMVTRAK--KVDGGYRLSGSKMWITNS-----PIADVFVVWAKDD 187 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 G+ I ++ G G + + KVG AS T E+ +V P N + RG Sbjct: 188 AGE--IRGFVLEKGWEGLSAPTIHGKVGLRASITGEIVMDNVFCPEENAFPDV-RGLKGP 244 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 L+ R IS A G A+ C + +Y +R FGR + A Q IQ K+ADM+ + +A Sbjct: 245 FTCLNSARYGISWGALGAAEFCWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLA 304 Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360 G G + +I K S A+D AR A + GG G +E+ VAR + Sbjct: 305 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVN 364 Query: 361 SKILEIGEGTSEVQRMLIAR 380 +++ EGT +V +++ R Sbjct: 365 LEVVNTYEGTHDVHALILGR 384 Lambda K H 0.318 0.136 0.402 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: 417 Number of extensions: 25 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: 386 Length of database: 393 Length adjustment: 30 Effective length of query: 356 Effective length of database: 363 Effective search space: 129228 Effective search space used: 129228 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