Align enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) (characterized)
to candidate 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)
Query= BRENDA::P14604 (290 letters) >FitnessBrowser__Btheta:354228 Length = 274 Score = 132 bits (332), Expect = 9e-36 Identities = 92/255 (36%), Positives = 134/255 (52%), Gaps = 15/255 (5%) Query: 45 SSVGLIQLNRPKALNALCNGLIEELNQALETFEEDPAVGAIVLTG-GEKAFAAGADIKEM 103 + + I +NR + NA E++ AL E+ + IV+TG G+KAF +G D Sbjct: 22 NGIARITINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKAFCSGGD---- 77 Query: 104 QNRTFQDCYSGK-------FLSHWDHITRIKKPVIAAVNGYALGGGCELAMMCDIIYAGE 156 QN + Y GK L I I KPVIAAVNG+A+GGG L ++CD+ A E Sbjct: 78 QNVKGRGGYIGKDGVPRLSVLDVQKQIRSIPKPVIAAVNGFAIGGGHVLHVVCDLSIASE 137 Query: 157 KAQFGQPEILLGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGLVSKIFPVE 216 A FGQ +G+ G L R VG+ A E+ + +AQ+A GLV+K+ P+E Sbjct: 138 NAIFGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALDMGLVNKVVPLE 197 Query: 217 TLVEEAIQCAEKIANNSKIIVAMAKESVNAAFEMTLTEG-NKLEKKLFYSTFATDDRREG 275 L +E +Q AE++ S + + M K +NA E+ G +L + TD+ +EG Sbjct: 198 QLEDEYVQWAEEMMLLSPLALRMIKAGLNA--ELDGQAGIQELAGDATLLYYLTDEAQEG 255 Query: 276 MSAFVEKRKANFKDH 290 +AF+EKRK NFK + Sbjct: 256 KNAFLEKRKPNFKKY 270 Lambda K H 0.319 0.133 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: 188 Number of extensions: 12 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: 290 Length of database: 274 Length adjustment: 26 Effective length of query: 264 Effective length of database: 248 Effective search space: 65472 Effective search space used: 65472 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 (21.8 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