Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate WP_086510919.1 BZY95_RS16140 D-galactonate dehydratase family protein
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >NCBI__GCF_002151265.1:WP_086510919.1 Length = 403 Score = 192 bits (487), Expect = 2e-53 Identities = 132/412 (32%), Positives = 204/412 (49%), Gaps = 39/412 (9%) Query: 1 MKITKLETFIVPPRWCF--LKIETDEGIVGWGEPVVEGRAHTVAAAVEE-LSDYLIGKDP 57 MKI+ + P F LK+ T+ G G G+ + GR V A +EE + LIG+D Sbjct: 1 MKISDAYVIVTSPGRNFVTLKVVTESGTYGIGDATLNGREMAVVAYLEEHVIPALIGRDA 60 Query: 58 LLIEDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVY 117 IED W +YR ++R GP+TM+A++ VD ALWDIK K G+P++ LLGG+ R+++ Y Sbjct: 61 SRIEDIWHYLYRGAYWRRGPVTMAAVSAVDLALWDIKAKAAGMPLYQLLGGKSRERVMTY 120 Query: 118 SWIGGDRPSDVANNARAVVERGFKAVKMN-GSEELQIIDTFDKVQG-------------- 162 + G V+ G++AV++ G + I K +G Sbjct: 121 AHCTGKDIEGCLAEVEKHVKLGYRAVRVQAGVPGIPTIYGVAKREGERYEPADSELPAEH 180 Query: 163 ------VINNV----AAVREAVGPNIGIGVDFHGRVHKPMAKVLAKELDPYKLLFIEEPV 212 +N+V AAVRE G + + D H R+ A L K ++PY L ++E+ V Sbjct: 181 VWSTEKYLNHVPKLFAAVRERFGEELHMLHDVHHRLTPIEAARLGKAVEPYHLFWLEDCV 240 Query: 213 LSENAEALRDIVNQTNTPIALGERLYSRWDFKHILSGGYVDIIQPDASHAGGITECRKIA 272 +EN E+ R I T TP+A+GE S D++ +L ++D ++ SH GGIT R+IA Sbjct: 241 PAENQESFRLIRQHTTTPLAVGEVFNSIHDYRELLENQWIDYVRTPLSHGGGITHVRRIA 300 Query: 273 SMAEAYDVALALHCP--LGPIALATCLQIDAVSYNAFIQEQSLGIHYNQGNDLLDYIKNP 330 +A Y V H P L P+ L + D N IQE + + D + P Sbjct: 301 DLAALYHVRTGFHGPTDLSPVCLGAAVHFDTWVPNFGIQEH---MPHTPETDAV----FP 353 Query: 331 EVFKYEDGFVSIPQGPGLGIEVNEEKVREMAKVGHRWRNPVWRHEDGSVAEW 382 +++EDG + + PG G++++E ++ R PV R EDG++ W Sbjct: 354 HDYRFEDGHFLVGEAPGHGVDIDETLAKQYPY--KRASLPVNRLEDGTLWHW 403 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: 423 Number of extensions: 24 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: 403 Length adjustment: 31 Effective length of query: 351 Effective length of database: 372 Effective search space: 130572 Effective search space used: 130572 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