Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate PP_2216 PP_2216 short-chain acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__Putida:PP_2216 Length = 375 Score = 271 bits (694), Expect = 2e-77 Identities = 153/375 (40%), Positives = 235/375 (62%), Gaps = 5/375 (1%) Query: 8 ELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGDYL 67 E +++ V FA + + P + + H FP E + EM +GLFG+ PE++GG Y+ Sbjct: 6 EQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGYV 65 Query: 68 ALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGLTE 127 A +ALEE+A D + + + S+G +PI FG + QK ++L L +G +LGAF LTE Sbjct: 66 AYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALTE 125 Query: 128 PDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKPLIS 187 P GSDA + +T ARL+ + +V+NG+K FIT+ G+V V AVT + GK IS Sbjct: 126 PQAGSDASSLKTRARLEG--DHYVLNGSKQFITSGQN--AGVVIVFAVTDPEA-GKRGIS 180 Query: 188 SIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILDEG 247 + IVP+ +PG+ VA K+G +ASDT ++ F +V+VP AN LG +G GY L L+ G Sbjct: 181 AFIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGG 240 Query: 248 RIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWRDA 307 RI I++ A G+A+ + + YA ER +FG+ + +QA+ F++ADM K +AR A Sbjct: 241 RIGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHA 300 Query: 308 ASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILEIG 367 A+ AG P EA++AKL++S +A +A Q GGYG+++++P+ R++RD ++ +I Sbjct: 301 AALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 Query: 368 EGTSEVQRMLIAREL 382 EGTS++QRM+IAR L Sbjct: 361 EGTSDIQRMVIARNL 375 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: 383 Number of extensions: 18 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: 386 Length of database: 375 Length adjustment: 30 Effective length of query: 356 Effective length of database: 345 Effective search space: 122820 Effective search space used: 122820 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