Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_066048523.1 C0029_RS02325 crotonase/enoyl-CoA hydratase family protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_002869505.1:WP_066048523.1 Length = 256 Score = 166 bits (421), Expect = 3e-46 Identities = 98/251 (39%), Positives = 143/251 (56%), Gaps = 3/251 (1%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65 +LV+ V +TLNR KA NA+N A+ + + AA+ E D++D I ++TG++ F AG Sbjct: 7 VLVDVTDGVMTITLNRGKAKNAVNKAMAEGVAAAMDELDSNDDIRVAIITGADNTFCAGM 66 Query: 66 DIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADT 125 D+ T M + G E +KP+IAAV GFAL GG E+ + CD++ AD Sbjct: 67 DLKAFVTGE-MPMLPGRGFAGFVEAPP--KKPLIAAVEGFALAGGLEVMIACDLVVVADN 123 Query: 126 AKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAAS 185 AKFG PE+K G+ AGG RLP+ + AM++ LT F+DA +A GLV+R++PA S Sbjct: 124 AKFGIPEVKRGLAAAAGGLVRLPKQIPPRVAMEMALTGDFIDATKAADVGLVNRIVPAGS 183 Query: 186 LVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMA 245 ++ A AATI AV + K+ + + + T AE + + +F +ED EG Sbjct: 184 ALEGAKELAATIVANGPLAVRLSKQVIAESGDWTAAEMWDKQNEIVMPVFTSEDAIEGAT 243 Query: 246 AFVEKRKPVFK 256 AF EKR P +K Sbjct: 244 AFAEKRAPNWK 254 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: 172 Number of extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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