Align D-galactonate dehydratase family member Dd703_0947; EC 4.2.1.-; D-gluconate dehydratase; EC 4.2.1.39; D-mannonate dehydratase; EC 4.2.1.8 (uncharacterized)
to candidate BPHYT_RS16405 BPHYT_RS16405 galactonate dehydratase
Query= curated2:C6CBG9 (417 letters) >FitnessBrowser__BFirm:BPHYT_RS16405 Length = 382 Score = 195 bits (496), Expect = 2e-54 Identities = 134/394 (34%), Positives = 208/394 (52%), Gaps = 48/394 (12%) Query: 4 LKITNVKTILTAPGGIDLAVVKVETNEPGLYGLGCATFTQRIFAVKSAIDEYMAPFLIGK 63 +KIT ++T + P L K+ET+E G+ G G R V +A++E ++ +LIGK Sbjct: 1 MKITKLETFIVPPRWCFL---KIETDE-GIVGWGEPVVEGRAHTVAAAVEE-LSDYLIGK 55 Query: 64 DPTRIEDIWQSAAVSGYWRNGPIMNNALSGVDMALWDIKGKLAGMPVYELLGGKCRDGIP 123 DP IED WQ SG++R GPI +A++GVD ALWDIKGK G+P++ LLGG+ RD I Sbjct: 56 DPLLIEDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIK 115 Query: 124 LYCHTDGGDEVEVEDNIRARMEEGYQYVRCQMGMYGGAGTDDLKLIATQLARAKNIQPKR 183 +Y G +V +N RA +E G++ V+ G+++L++I T Sbjct: 116 VYSWIGGDRPSDVANNARAVVERGFKAVKMN-------GSEELQIIDT------------ 156 Query: 184 SPRSKTPGIYFDP-EAYAKSVPRLFEHLRNKLGFGIEFIHDVHERVTPVTAIQLAKTLEP 242 FD + +V + E + +G G++F H RV A LAK L+P Sbjct: 157 ----------FDKVQGVINNVAAVREAVGPNIGIGVDF----HGRVHKPMAKVLAKELDP 202 Query: 243 YQLFYLEDPVAPENIDWLRMLRQQSSTPISMGELFVNINEWKPLIDNKLIDYIRCHVSTI 302 Y+L ++E+PV EN + LR + Q++TPI++GE + ++K ++ +D I+ S Sbjct: 203 YKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSRWDFKHILSGGYVDIIQPDASHA 262 Query: 303 GGITPAKKLAVYSELNGVRTAWHGPGDISPVGVCANMHLDMSSPNFGIQE------YTPM 356 GGIT +K+A +E V A H P + P+ + + +D S N IQE Y Sbjct: 263 GGITECRKIASMAEAYDVALALHCP--LGPIALATCLQIDAVSYNAFIQEQSLGIHYNQG 320 Query: 357 NDALREV-FPGCPEIDQGYAYVNDKPGLGIDINE 389 ND L + P + + G+ + PGLGI++NE Sbjct: 321 NDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNE 354 Lambda K H 0.319 0.139 0.430 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: 459 Number of extensions: 25 Number of successful extensions: 3 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: 417 Length of database: 382 Length adjustment: 31 Effective length of query: 386 Effective length of database: 351 Effective search space: 135486 Effective search space used: 135486 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