Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate AZOBR_RS04900 AZOBR_RS04900 dehydratase
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >FitnessBrowser__azobra:AZOBR_RS04900 Length = 386 Score = 169 bits (427), Expect = 2e-46 Identities = 116/381 (30%), Positives = 181/381 (47%), Gaps = 24/381 (6%) Query: 1 MKITKLETFIVPPRWC---FLKIETDEGIVGWGEPVVE---GRAHTVAAAVEELSDYLIG 54 MKITK +++ +K++TDEGI G GE GR + + ++IG Sbjct: 1 MKITKATIYVINSEGLKPVIVKLDTDEGISGLGEVATAYGCGRTGAAGMIQDLCARFVIG 60 Query: 55 KDPLLIEDHWQVMYRSGFYRGGP--ITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRD 112 DP I MY F+ P I + ++ ++QALWDI+ + VP+H L GG++RD Sbjct: 61 ADPTRINSLVGEMYDQSFWLKNPGGIAGAGLSAIEQALWDIRARALNVPVHELFGGRMRD 120 Query: 113 KIKVYS---WIGGDRPSDVANNARAVVERGFKAVKMNGSEELQ-----------IIDTFD 158 + Y+ + G +D+ A A V+ G KA+KM +Q D D Sbjct: 121 TLAYYANGWYFGATSVADLLRQAEAAVKDGHKALKMYPLARIQPNGTLRHTVNRYADDRD 180 Query: 159 KVQGVINNVAAVREAVGPNIGIGVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAE 218 V ++ VA VR VG ++ + +D G L+ + FIEE + Sbjct: 181 AVNAALDIVAQVRRTVGADVTLMLDLAGGFSVSDTIRFVHGLEDLDIAFIEEICDPGDLG 240 Query: 219 ALRDIVNQTNTPIALGERLYSRWDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAY 278 AL + +TN PIA GER Y R+ F+ +L V I+QPD + GG E KIA+MA+AY Sbjct: 241 ALEQVAAKTNIPIATGERQYLRYGFRDLLERRAVGILQPDIGNTGGFAETHKIAAMADAY 300 Query: 279 DVALALHCPLGPIALATCLQIDAVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDG 338 V + H +A + + AV N ++QE ++ + ++ P + ++G Sbjct: 301 GVKVQPHVCGSSVAASIATHLSAVIPNFYVQEHF--PYWARIPGWIEVATEPFESRLKNG 358 Query: 339 FVSIPQGPGLGIEVNEEKVRE 359 + IP GPG G+ + + VRE Sbjct: 359 ALQIPDGPGYGVTLKDAVVRE 379 Lambda K H 0.319 0.139 0.428 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: 374 Number of extensions: 17 Number of successful extensions: 4 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: 382 Length of database: 386 Length adjustment: 30 Effective length of query: 352 Effective length of database: 356 Effective search space: 125312 Effective search space used: 125312 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: 50 (23.9 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