Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate WP_085125981.1 B9O00_RS27750 mandelate racemase/muconate lactonizing enzyme family protein
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >NCBI__GCF_900177295.1:WP_085125981.1 Length = 400 Score = 183 bits (465), Expect = 6e-51 Identities = 122/378 (32%), Positives = 197/378 (52%), Gaps = 30/378 (7%) Query: 1 MKITKLETFIV---PPRW-----CFLKIETDEGIVGWGEPV-VEGRAHTVAAAVEELSD- 50 MKIT + TF+V PP + F+K+ TD G+ G GE + V A +E+L+ Sbjct: 1 MKITDVRTFVVGNPPPSFGGRYFVFVKLVTDGGVEGLGEVYCLPFHPRVVVAMIEDLAGR 60 Query: 51 YLIGKDPLLIEDHWQVMYRSGFYRGGPITMSAI-AGVDQALWDIKGKHHGVPIHALLGGQ 109 YL+G+DP IE W+ +Y +G+ + ++++ I +G++ A WDI GK G P+HALLGG+ Sbjct: 61 YLVGQDPTRIESLWRRVYSAGYGQRPDLSVAGILSGLEMACWDILGKETGKPVHALLGGR 120 Query: 110 VRDKIKVYSWI--GGDRPSDVANNARAVVER-------GFKAVKMNGSEELQIIDTFDKV 160 V ++++ Y+++ G +D ++A ER GF A+K + + D Sbjct: 121 VHERLRSYTYLYPGEGETADFYHDAERSAERAAEYVRQGFTAIKFDPAGPYSAFDPRMPD 180 Query: 161 QGVINN----VAAVREAVGPNIGIGVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSEN 216 Q + +R AVG + HG+ A LA+ L+PY L++EEP E Sbjct: 181 QESLARSEQFCRLIRAAVGGGADLLFGTHGQFTPAGALRLARRLEPYDPLWLEEPTPPEM 240 Query: 217 AEALRDIVNQTNTPIALGERLYSRWDFKHILSGGYVDIIQPDASHAGGITECRKIASMAE 276 E + + T P+A GERL ++++F +L G I+QP+ GG+ E +KIA +AE Sbjct: 241 PEQMALVARGTTIPVAAGERLATKYEFARLLDAGAAAILQPNLGRVGGLLEAKKIAGLAE 300 Query: 277 AYDVALALHCPLGPIALATCLQIDAVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYE 336 A +A H GP+ A +Q+ A N I E G + +K P +++ Sbjct: 301 ARYAQVAPHLYCGPVVGAANIQLAATLPNFLILESI----QTWGGFHAELLKTP--IRWQ 354 Query: 337 DGFVSIPQGPGLGIEVNE 354 +G+V +P PGLG+E++E Sbjct: 355 EGYVLVPDAPGLGVELDE 372 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: 443 Number of extensions: 15 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: 400 Length adjustment: 31 Effective length of query: 351 Effective length of database: 369 Effective search space: 129519 Effective search space used: 129519 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