Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_047094365.1 AAV99_RS12275 enoyl-CoA hydratase/isomerase family protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_001013305.1:WP_047094365.1 Length = 252 Score = 94.0 bits (232), Expect = 3e-24 Identities = 80/262 (30%), Positives = 118/262 (45%), Gaps = 24/262 (9%) Query: 5 NILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA--FA 62 N+ +E G V + ++R NA N A+ + + L + AD A+ +V+ ++ F Sbjct: 2 NLRLEFDGPVAHLLIDRLDKRNAFNMAMWEAMPGLLEQARADPAVRTLVIRSAQPGGVFC 61 Query: 63 AGADIGMMSTYTYMDVYKGDYITRNWETVRSIRK-------PIIAAVAGFALGGGCELAM 115 AGADI M + G ++ N + ++ P +A V G +GGGC +A+ Sbjct: 62 AGADIKEMLLHKD----DGAWLAANQAAINRVQHDLARLTLPTVAFVEGDCVGGGCGIAI 117 Query: 116 MCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAG 175 CD+ A D A+FG KLGI+ + L V +A + T +DAAEA+R G Sbjct: 118 ACDLRVATDKARFGITPGKLGIVYPLHDVKLLTDLVGPGQAKRMLFTGGLLDAAEAQRIG 177 Query: 176 LVSRVI--PAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHS 233 LV + P L D A+ +I E V V + + TLA +F Sbjct: 178 LVEMIADSPRGLLNDILSASPHSIREI-KMFVRRVLDGQTGDDDQTLA--------IFTD 228 Query: 234 LFATEDQKEGMAAFVEKRKPVF 255 F D EG AAF KRKP F Sbjct: 229 AFMRGDFAEGAAAFAGKRKPDF 250 Lambda K H 0.321 0.134 0.380 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: 137 Number of extensions: 7 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: 258 Length of database: 252 Length adjustment: 24 Effective length of query: 234 Effective length of database: 228 Effective search space: 53352 Effective search space used: 53352 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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