Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate YP_001314391.1 Smed_5746 enoyl-CoA hydratase/isomerase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000017145.1:YP_001314391.1 Length = 256 Score = 159 bits (402), Expect = 5e-44 Identities = 98/258 (37%), Positives = 143/258 (55%), Gaps = 7/258 (2%) Query: 4 ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFA 62 ++IL + G + +TLNRP+ LNA+ + D + AA+ E + D+I +++TG+ E++F Sbjct: 3 QDILFKVDGAIATITLNRPQKLNAVTPEMADAIVAAVDECNDSDSIRCVILTGAGERSFC 62 Query: 63 AGADIGMMSTYTYMDVYKG--DYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120 AG+DI + TY ++ DY + R++ KP I AV G+ALGGG E AM CDI Sbjct: 63 AGSDIKELDTYKTPWQFRNRPDYC----DAFRALLKPTICAVNGYALGGGLETAMSCDIR 118 Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180 A+D A+F PEIKLG + G G L ++ + A + +T + A +A GL+S V Sbjct: 119 IASDNAQFAAPEIKLGWIGGGGMAAHLMHSIGASNAALMLMTGDPITAEKALAWGLISEV 178 Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240 +P L+ A A A IA A K ++ A L + + +ER L FAT D Sbjct: 179 VPQTELLARARAIADAIAARAPIAAETAKANLKAAVSMPLDKAIEYERDLQTICFATADA 238 Query: 241 KEGMAAFVEKRKPVFKHR 258 EG AAF EKR+PVF R Sbjct: 239 AEGRAAFKEKRQPVFNRR 256 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: 182 Number of extensions: 9 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: 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