Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011383077.1 AMB_RS03265 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000009985.1:WP_011383077.1 Length = 258 Score = 362 bits (930), Expect = e-105 Identities = 181/258 (70%), Positives = 211/258 (81%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 MA+ENI VETRG VG++ LNRPKA+NAL AL+ ELG AL F+ADD+IGA+V+TGSEKA Sbjct: 1 MAFENITVETRGNVGVIALNRPKAMNALCAALISELGQALDAFEADDSIGAVVLTGSEKA 60 Query: 61 FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120 FAAGADI M++ +YMDVY ++IT WE V RKPI+AAVAGFALGGGCE+AMMCD I Sbjct: 61 FAAGADIKEMASKSYMDVYLANFITDGWERVTKCRKPIVAAVAGFALGGGCEMAMMCDFI 120 Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180 A D AKFGQPEI +G +PGAGGTQRL RAV K+KAM++CLT R MDAAEAERAGLVSR+ Sbjct: 121 IAGDNAKFGQPEITIGTIPGAGGTQRLTRAVGKSKAMEMCLTGRMMDAAEAERAGLVSRI 180 Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240 +P A L+DEA+ AA IA P VM+ KESVN A+ETTLA+GV FERRLFHS F+TEDQ Sbjct: 181 VPVAELLDEAVKAAGKIASLSRPIVMLCKESVNAAFETTLAQGVTFERRLFHSTFSTEDQ 240 Query: 241 KEGMAAFVEKRKPVFKHR 258 KEGMAAFVEKR FK+R Sbjct: 241 KEGMAAFVEKRPAAFKNR 258 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: 241 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: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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