Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011952613.1 SWIT_RS08955 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000016765.1:WP_011952613.1 Length = 256 Score = 280 bits (715), Expect = 3e-80 Identities = 150/258 (58%), Positives = 182/258 (70%), Gaps = 2/258 (0%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 MA+E ILVET G V ++ LNRP+ALNA++ ++ +L A R FDAD ++TGSEKA Sbjct: 1 MAFETILVETEGPVTVIRLNRPQALNAIDTQVLADLIVAFRAFDADPEQRCAILTGSEKA 60 Query: 61 FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120 FAAG DI M Y +++ D W V RKP IAAVAGFALGGGCELAMM DI+ Sbjct: 61 FAAGGDIKQMREKGYAEMFGED--VDGWSRVTGTRKPWIAAVAGFALGGGCELAMMADIM 118 Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180 AAD A+FGQPEIKLG+ PG GG+QRL RAV K+KAMD+CLT R MDA EAERA L S+V Sbjct: 119 IAADNARFGQPEIKLGVCPGMGGSQRLTRAVGKSKAMDMCLTGRMMDATEAERANLCSKV 178 Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240 +P A L+DEA+ A IA P A + KE+VN A+ET L G+ FERR F+ L AT+D+ Sbjct: 179 VPLADLMDEAMKMAQAIAAMPPLAAIANKEAVNAAFETGLHHGLLFERRSFNGLCATDDK 238 Query: 241 KEGMAAFVEKRKPVFKHR 258 EGMAAFVEKR V+K R Sbjct: 239 AEGMAAFVEKRPGVWKGR 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: 217 Number of extensions: 5 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