Align BadI (characterized)
to candidate 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__Btheta:354228 Length = 274 Score = 249 bits (635), Expect = 6e-71 Identities = 128/261 (49%), Positives = 174/261 (66%), Gaps = 2/261 (0%) Query: 2 QFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRA 61 ++ED++++ NG+A I INR NAF TT E+ AL + D+ IV+ GAGD+A Sbjct: 12 EYEDILFDYYNGIARITINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKA 71 Query: 62 FCTGGDQSTHD-GNYDGR-GTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICD 119 FC+GGDQ+ G Y G+ G L + ++ IR +PKPVIA V G+AIGGG+VL +CD Sbjct: 72 FCSGGDQNVKGRGGYIGKDGVPRLSVLDVQKQIRSIPKPVIAAVNGFAIGGGHVLHVVCD 131 Query: 120 LTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLAN 179 L+I SE AIFGQ GP++GS D G+G ++LARVVG+KKAREIW++C++Y+ +EA MGL N Sbjct: 132 LSIASENAIFGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALDMGLVN 191 Query: 180 LCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYDTDE 239 VP ++L+ E +W EE+ SP AL + K N + QAGI + A LYY TDE Sbjct: 192 KVVPLEQLEDEYVQWAEEMMLLSPLALRMIKAGLNAELDGQAGIQELAGDATLLYYLTDE 251 Query: 240 SREGVKALQEKRKPEFRKYIK 260 ++EG A EKRKP F+KY K Sbjct: 252 AQEGKNAFLEKRKPNFKKYPK 272 Lambda K H 0.319 0.138 0.418 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: 243 Number of extensions: 10 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: 260 Length of database: 274 Length adjustment: 25 Effective length of query: 235 Effective length of database: 249 Effective search space: 58515 Effective search space used: 58515 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 (21.7 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