Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Pf6N2E2_1834 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1834 Length = 256 Score = 190 bits (482), Expect = 3e-53 Identities = 103/248 (41%), Positives = 150/248 (60%), Gaps = 1/248 (0%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65 ++VE G V ++ LNR + NAL+ ++ + +A++E + D + IV+TG + FAAGA Sbjct: 5 VVVERNGAVAILRLNRVEKRNALDLSMRVAIASAMQELERDSGVAVIVITGGDSVFAAGA 64 Query: 66 DIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADT 125 D+ ++ V + D + + W V +KP+IAAV+GFALG GCELAMMCDI+ A ++ Sbjct: 65 DLNLLVDKGAQQVAELD-LGQYWAPVAKSQKPLIAAVSGFALGAGCELAMMCDILVADNS 123 Query: 126 AKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAAS 185 A+FGQPE ++GIMPGAGGTQRL RAV K A + L + A A + GLVS ++ S Sbjct: 124 ARFGQPEARVGIMPGAGGTQRLLRAVGKPVASLMLLAGELLSAERASQLGLVSELVTEGS 183 Query: 186 LVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMA 245 + AI A A P A+ +K + + +L + E R F LF T+D+ EGM Sbjct: 184 ALARAIVLAQATATMPPKALRAIKRVLALGADQSLDLALALENREFLLLFDTQDKTEGMR 243 Query: 246 AFVEKRKP 253 AF++KR P Sbjct: 244 AFLDKRPP 251 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: 175 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 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