Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Btheta:354228 Length = 274 Score = 130 bits (327), Expect = 3e-35 Identities = 90/264 (34%), Positives = 136/264 (51%), Gaps = 15/264 (5%) Query: 2 EFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KA 60 E+E I + IT+NR NA E+ A+ + +I VI+ITG G KA Sbjct: 12 EYEDILFDYYNGIARITINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKA 71 Query: 61 FCAGADITQFNQLTPAEAWKFSKKG------REIMDKIEALSKPTIAMINGYALGGGLEL 114 FC+G D Q K G ++ +I ++ KP IA +NG+A+GGG L Sbjct: 72 FCSGGD-----QNVKGRGGYIGKDGVPRLSVLDVQKQIRSIPKPVIAAVNGFAIGGGHVL 126 Query: 115 ALACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEK 174 + CD+ IA+E A G +G + G L RV+G+ +A E+ + ++A Sbjct: 127 HVVCDLSIASENAIFGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALD 186 Query: 175 YGLVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL-ALESVGWG 233 GLVN+VVPL LE E + AE++ SP++L +IK +N LD +G+ L Sbjct: 187 MGLVNKVVPLEQLEDEYVQWAEEMMLLSPLALRMIKAGLNAELDGQ--AGIQELAGDATL 244 Query: 234 VVFSTEDKKEGVSAFLEKREPTFK 257 + + T++ +EG +AFLEKR+P FK Sbjct: 245 LYYLTDEAQEGKNAFLEKRKPNFK 268 Lambda K H 0.315 0.135 0.382 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: 148 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: 259 Length of database: 274 Length adjustment: 25 Effective length of query: 234 Effective length of database: 249 Effective search space: 58266 Effective search space used: 58266 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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