Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011802737.1 PNAP_RS16825 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000015505.1:WP_011802737.1 Length = 262 Score = 377 bits (969), Expect = e-109 Identities = 188/262 (71%), Positives = 218/262 (83%), Gaps = 4/262 (1%) Query: 1 MAYENILVETRG----RVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTG 56 M YE I+ T G +VG+VTLNRPK LNALN+ LMDELG+AL+ FDADD+IG I++TG Sbjct: 1 MTYELIVTSTEGPDSRQVGIVTLNRPKQLNALNNELMDELGSALKAFDADDSIGCIILTG 60 Query: 57 SEKAFAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMM 116 SEKAFAAGADIG M+ Y++ DVY DYITRNWE +RSIRKP+IAAV+GFALGGGCELAMM Sbjct: 61 SEKAFAAGADIGAMANYSFADVYNNDYITRNWEQIRSIRKPVIAAVSGFALGGGCELAMM 120 Query: 117 CDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGL 176 CD I AAD A+FGQPEIKLGI+PGAGGTQRLPRAV KAKAMDL LT R MDA EAERAGL Sbjct: 121 CDFIIAADNARFGQPEIKLGIIPGAGGTQRLPRAVGKAKAMDLALTGRMMDAVEAERAGL 180 Query: 177 VSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFA 236 VSRV+P L+DEA+ AA I + P+V KE+VNRA+E++L++GV FERRLFH+LFA Sbjct: 181 VSRVVPLDKLMDEALGAALMICSYGQPSVFAAKEAVNRAFESSLSDGVMFERRLFHALFA 240 Query: 237 TEDQKEGMAAFVEKRKPVFKHR 258 TEDQKEGM AFV KRKP FK+R Sbjct: 241 TEDQKEGMDAFVNKRKPEFKNR 262 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: 274 Number of extensions: 8 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: 258 Length of database: 262 Length adjustment: 24 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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