Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_043828506.1 RSPH17029_RS18305 L-idonate 5-dehydrogenase
Query= SwissProt::P0DOW0 (331 letters) >NCBI__GCF_000015985.1:WP_043828506.1 Length = 348 Score = 110 bits (275), Expect = 5e-29 Identities = 104/332 (31%), Positives = 150/332 (45%), Gaps = 22/332 (6%) Query: 17 APAPVPEPGWIALRVAGVGICGSELSGY----LGHNELRKPPLVMGHEFSGVVEEVGHGV 72 A A P PG + + V+ GICGS+L Y G LR+P + +GHE SG+V +G GV Sbjct: 19 AAAADPGPGEVRVAVSHGGICGSDLHYYHHGGFGTVRLREP-MALGHEVSGIVTALGAGV 77 Query: 73 TNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIG--IDFP---GAYAERVLVPSNQ 127 T+++ GD V NP CGRC +C RG C R G + FP G + V +P+ Q Sbjct: 78 TDLREGDRVAVNPSRPCGRCDYCRRGLAHHCLDMRFNGSAMRFPHEQGLFRAAVTLPAAQ 137 Query: 128 CY---AVKDAIDGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKR 184 A D A+ EPLA + AV A +G +V G G IG +T+ +GA+ Sbjct: 138 AVRLPAETDLALAAMSEPLAVCLHAVAGAGSLIGKRVLVSGCGPIGCLTILAARAAGAEE 197 Query: 185 IAVVDPNDERLKISQLWGATEMAPNLGALLTDNHPQS-----FDCVIDAVGLSTTRRDSL 239 I D L ++ GA + +L A P + D V++ G +L Sbjct: 198 IVASDIAAPALAAARAVGADRVL-DLAAESEALEPFAEGKGRIDVVLECSGAPPALLAAL 256 Query: 240 NALIRGGRAVWIGLHEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLINSQKFLPVD 299 L G V +GL + L +V E+ ++GSF + D EF A I S + + V Sbjct: 257 RVLRPQGLLVAVGLGPEVA-LPVTALVAREIRLQGSFRF-DAEFATAARAIASGR-IDVS 313 Query: 300 RQWLDVRSLEEGPAAFKELVNGSPFSKIILTF 331 V + E AF + S K+ + F Sbjct: 314 PLLTRVLPVTEAADAFALASDKSRAMKVQIAF 345 Lambda K H 0.322 0.139 0.424 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: 290 Number of extensions: 18 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: 331 Length of database: 348 Length adjustment: 28 Effective length of query: 303 Effective length of database: 320 Effective search space: 96960 Effective search space used: 96960 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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