Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011157317.1 TX73_RS09240 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000195775.1:WP_011157317.1 Length = 259 Score = 305 bits (781), Expect = 6e-88 Identities = 155/256 (60%), Positives = 192/256 (75%) Query: 3 YENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFA 62 +E I+VE + VG++ LNRPK LNAL+ + E+GAA+ + +ADDAIG I++TGSEKAFA Sbjct: 4 FEFIIVERQNAVGIIKLNRPKMLNALSFGVFREIGAAVEDLEADDAIGCILITGSEKAFA 63 Query: 63 AGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122 AGADI M ++D++ D+ + + + RKP +AAVAG+ALGGGCELAMMCDII A Sbjct: 64 AGADIKEMQPKGFIDMFNEDFTSIGGDRLARCRKPTVAAVAGYALGGGCELAMMCDIIIA 123 Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182 ADTAKFGQPEI LG +PG GGTQRL RA+ K KAMDLCLT R MDA EAER+GLVSR++P Sbjct: 124 ADTAKFGQPEITLGTIPGIGGTQRLTRAIGKYKAMDLCLTGRMMDAQEAERSGLVSRIVP 183 Query: 183 AASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKE 242 A L++EA+ AA IA P M K +VNRA ETTLAEG+ ER LF S FA ED+ E Sbjct: 184 ADKLMEEALGAAEKIATMSRPTAAMAKSAVNRALETTLAEGLAVERDLFRSTFALEDRAE 243 Query: 243 GMAAFVEKRKPVFKHR 258 GMAAF+EKRKP ++R Sbjct: 244 GMAAFIEKRKPNNQNR 259 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: 218 Number of extensions: 3 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: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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