Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Btheta:354228 Length = 274 Score = 122 bits (307), Expect = 6e-33 Identities = 85/258 (32%), Positives = 133/258 (51%), Gaps = 6/258 (2%) Query: 3 YENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAF 61 YE+IL + + +T+NR + NA E+ ALR + I IV+TG+ +KAF Sbjct: 13 YEDILFDYYNGIARITINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKAF 72 Query: 62 AAGADIGMMSTYTYM--DVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDI 119 +G D + Y+ D + + +RSI KP+IAAV GFA+GGG L ++CD+ Sbjct: 73 CSGGDQNVKGRGGYIGKDGVPRLSVLDVQKQIRSIPKPVIAAVNGFAIGGGHVLHVVCDL 132 Query: 120 IFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSR 179 A++ A FGQ ++G G L R V + KA ++ R +A EA GLV++ Sbjct: 133 SIASENAIFGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALDMGLVNK 192 Query: 180 VIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLA-EGVHFERRLFHSLFATE 238 V+P L DE + A + A+ M+K +N + + + + L + + T+ Sbjct: 193 VVPLEQLEDEYVQWAEEMMLLSPLALRMIKAGLNAELDGQAGIQELAGDATLLY--YLTD 250 Query: 239 DQKEGMAAFVEKRKPVFK 256 + +EG AF+EKRKP FK Sbjct: 251 EAQEGKNAFLEKRKPNFK 268 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: 154 Number of extensions: 7 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: 274 Length adjustment: 25 Effective length of query: 233 Effective length of database: 249 Effective search space: 58017 Effective search space used: 58017 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