Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_092481562.1 BM299_RS00820 enoyl-CoA hydratase-related protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_900115975.1:WP_092481562.1 Length = 260 Score = 204 bits (519), Expect = 1e-57 Identities = 111/258 (43%), Positives = 161/258 (62%), Gaps = 2/258 (0%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59 M ++NI++E + ++T+NRPK LNALN + ELG A+ + + ++ I I++TG+ EK Sbjct: 1 MDWKNIIIEKEDNIAIITINRPKVLNALNYETVMELGNAISQLENENGIKVIILTGAGEK 60 Query: 60 AFAAGADIGMMSTYTYMDVYK-GDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCD 118 +F AGADI M T ++ K Y + + KP+IAA+ G+ALGGGCELAM CD Sbjct: 61 SFVAGADIAYMQNLTPLEAKKFARYGQSVLSKIENFPKPVIAAINGYALGGGCELAMACD 120 Query: 119 IIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVS 178 I A+ AKFGQPE+ LG++ G GGTQRL R V+ A ++ LTA DA A + GLV+ Sbjct: 121 IRIASSNAKFGQPEVNLGLIAGFGGTQRLTRLVNPGLAKEILLTANVYDAEAACKFGLVN 180 Query: 179 RVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATE 238 V+ L++ A+ IA AV + KE++N E L + + E LF +FAT+ Sbjct: 181 HVVEPGELMNYCKKMASVIASRGPIAVQLTKEAINDGLEMDLEKALAHEADLFAIVFATK 240 Query: 239 DQKEGMAAFVEKRKPVFK 256 D++EG++AF+ KRKP FK Sbjct: 241 DKEEGISAFLSKRKPEFK 258 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: 165 Number of extensions: 4 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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 Apr 09 2024. 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