Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BWI76_RS01365 BWI76_RS01365 multifunctional fatty acid oxidation complex subunit alpha
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__Koxy:BWI76_RS01365 Length = 729 Score = 115 bits (287), Expect = 3e-30 Identities = 68/199 (34%), Positives = 104/199 (52%), Gaps = 11/199 (5%) Query: 4 TLSVDAPEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAA 63 TL +D E G+ + P ++N L+T + L L + E+ + + ++L + AF Sbjct: 7 TLYLDWREDGIAELVFDAPGSVNKLDTATVASLGEALDVLEKQKDLKGLLLRSEKAAFIV 66 Query: 64 GADIKEMAERDLVGILEDPRVAHW--------QRIAAFSKPLIAAVNGFCLGGGCELAMH 115 GADI E LV + +++ W R+ P I+AVNG+ LGGGCE + Sbjct: 67 GADITEFLSLFLV---PEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCECVLA 123 Query: 116 ADILIAGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGL 175 D +A D R G PE LGIMPG GG+ R+ R +G A++++ +G+ + A A + GL Sbjct: 124 TDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDLGAEQALKIGL 183 Query: 176 VSEVTLPELTIERALAIAR 194 V V E I+ A+AI R Sbjct: 184 VDGVVKHEKLIDGAVAILR 202 Lambda K H 0.320 0.134 0.374 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: 350 Number of extensions: 10 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: 257 Length of database: 729 Length adjustment: 32 Effective length of query: 225 Effective length of database: 697 Effective search space: 156825 Effective search space used: 156825 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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