Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate HSERO_RS05150 HSERO_RS05150 galactonate dehydratase
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >FitnessBrowser__HerbieS:HSERO_RS05150 Length = 382 Score = 643 bits (1659), Expect = 0.0 Identities = 304/382 (79%), Positives = 340/382 (89%) Query: 1 MKITKLETFIVPPRWCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLI 60 MKITK+ TFIVPPRWCFLKIETDEG+VGWGEP+VEGRAH+VAAAVEELSDYLIGKDP I Sbjct: 1 MKITKITTFIVPPRWCFLKIETDEGVVGWGEPIVEGRAHSVAAAVEELSDYLIGKDPRNI 60 Query: 61 EDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWI 120 EDHW V+YR GFYRGG I MSA+AG+DQALWDIKGK GVP+H LLGG VR+ I+VYSWI Sbjct: 61 EDHWTVLYRGGFYRGGAIHMSALAGIDQALWDIKGKDLGVPVHQLLGGAVRNSIRVYSWI 120 Query: 121 GGDRPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGI 180 GGDRP+D A A++ V RGF AVKMNG+EELQ ID+ DK++ + NV AVREAVGPN+GI Sbjct: 121 GGDRPADTAAAAKSAVARGFTAVKMNGTEELQFIDSHDKIELTLANVQAVREAVGPNVGI 180 Query: 181 GVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSR 240 GVDFHGRVHKPMAK L KEL+PYKL+FIEEPVLSENAEAL++I + T+TPIALGERLYSR Sbjct: 181 GVDFHGRVHKPMAKALIKELEPYKLMFIEEPVLSENAEALKEIAHLTSTPIALGERLYSR 240 Query: 241 WDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQID 300 WDFK ILS GYVDIIQPD SHAGGITE RKIA MAEAYDVALALHCPLGPIALA+CLQ+D Sbjct: 241 WDFKRILSEGYVDIIQPDVSHAGGITETRKIAMMAEAYDVALALHCPLGPIALASCLQVD 300 Query: 301 AVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVREM 360 A SYNAFIQEQSLGIHYN+ NDLLDYI++ VF YEDG+V IPQGPGLGIE+NEE VR+ Sbjct: 301 AGSYNAFIQEQSLGIHYNESNDLLDYIRDKNVFAYEDGYVKIPQGPGLGIEINEEYVRQR 360 Query: 361 AKVGHRWRNPVWRHEDGSVAEW 382 A+VGHRWRNP+WRH+DGS AEW Sbjct: 361 AEVGHRWRNPIWRHKDGSFAEW 382 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: 575 Number of extensions: 14 Number of successful extensions: 1 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: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 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 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