Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate WP_011842510.1 RSPH17029_RS18320 galactonate dehydratase
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >NCBI__GCF_000015985.1:WP_011842510.1 Length = 382 Score = 596 bits (1537), Expect = e-175 Identities = 277/382 (72%), Positives = 322/382 (84%) Query: 1 MKITKLETFIVPPRWCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLI 60 MKIT L+TFIVPPRW FLKIETDEGIVGWGEPVVEG+A TV AAV E++DYLIG+DPL I Sbjct: 1 MKITALKTFIVPPRWLFLKIETDEGIVGWGEPVVEGKALTVEAAVHEMADYLIGQDPLRI 60 Query: 61 EDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWI 120 EDHWQV+YR GFYRGGP+ MSA+AG+DQALWDIKG+ G+P+H +LGG RD+I+VYSWI Sbjct: 61 EDHWQVLYRGGFYRGGPVLMSALAGIDQALWDIKGRAAGLPVHQMLGGACRDRIRVYSWI 120 Query: 121 GGDRPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGI 180 GGDRP DVA AR V RGF A+K+NG+EELQI+D DK+ ++ + AVR+AVGP++GI Sbjct: 121 GGDRPEDVAQGAREAVARGFTAIKLNGAEELQIVDGHDKIDRIVETIGAVRDAVGPHVGI 180 Query: 181 GVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSR 240 GVDFHGRV KPMAKVL LDP++L+FIEEPVLSEN EAL +I T+TPIALGERLYSR Sbjct: 181 GVDFHGRVQKPMAKVLIHALDPFRLMFIEEPVLSENLEALPEITRGTSTPIALGERLYSR 240 Query: 241 WDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQID 300 WDFK + VDIIQPD SHAGGITECRKIA+MAEAYD+ +A HCPLGPIALA CLQ+D Sbjct: 241 WDFKRVFETRCVDIIQPDLSHAGGITECRKIAAMAEAYDIGVAFHCPLGPIALAACLQVD 300 Query: 301 AVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVREM 360 AVS+NAFIQEQSLGIHYN G+DLLDY+ +P VF+YE G V IP GPGLGIE++E V Sbjct: 301 AVSHNAFIQEQSLGIHYNAGSDLLDYLVDPSVFRYEAGAVEIPTGPGLGIEIDEGAVLRA 360 Query: 361 AKVGHRWRNPVWRHEDGSVAEW 382 A+ GHRWRNP+WRH DGSVAEW Sbjct: 361 AETGHRWRNPLWRHADGSVAEW 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: 568 Number of extensions: 19 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 24 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