Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 7024269 Shewana3_1461 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__ANA3:7024269 Length = 709 Score = 111 bits (278), Expect = 4e-29 Identities = 75/244 (30%), Positives = 129/244 (52%), Gaps = 11/244 (4%) Query: 1 MPHTLSVDAPEQGVRLITLQRP-EALNALNTQLLDELAAELALAEQDAETRAVVL-TGSR 58 M T ++ E G+ ++ + P E +N L + E++ L+ ++D+ R +VL +G + Sbjct: 1 MEKTFNLTRREDGIAILMMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKK 60 Query: 59 KAFAAGADIKEMAERDLVG---ILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMH 115 +F AGADI + G L + + A + P++AA++G CLGGG ELA+ Sbjct: 61 DSFVAGADISMLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALA 120 Query: 116 ADILIAGEDAR--FGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRA 173 + +D + G PE+ LG++PG GGTQRL R VG + A+ M+L+G+ I + A + Sbjct: 121 CHQRVCSDDGKTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKM 180 Query: 174 GLVSEVTLPELTIERALAIARVIAQKA-PLAVRLAKEALLKAEDTDLASGLRFERHAFTV 232 GLV++V + ++ A+ +A + A P+ L + L E T + F++ A V Sbjct: 181 GLVNDVVPQTILLQTAVEMALAGKRTAKPVKKSLVNQLL---EGTGFGRNIIFDQAAKQV 237 Query: 233 LAGT 236 + T Sbjct: 238 VKKT 241 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: 346 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 257 Length of database: 709 Length adjustment: 32 Effective length of query: 225 Effective length of database: 677 Effective search space: 152325 Effective search space used: 152325 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: 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