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 H281DRAFT_04147 H281DRAFT_04147 L-iditol 2-dehydrogenase
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_04147 Length = 365 Score = 124 bits (310), Expect = 5e-33 Identities = 92/296 (31%), Positives = 144/296 (48%), Gaps = 31/296 (10%) Query: 27 IALRVAGVGICGSELSGYLGHNELR-------KPPLVMGHEFSGVVEEVGHGVTN---VK 76 + +R+A GIC S+ + G K P++ GHEF G V+E+G G VK Sbjct: 39 LVIRIAACGICASDCKCHSGAKMFWGGPSPWVKAPVIPGHEFFGFVQELGDGAAEHFGVK 98 Query: 77 IGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGID---FPGAYAERVLVPSNQC-YAVK 132 +GD V A +V C +C +C G+ CE I G G AE + +P + + Sbjct: 99 VGDRVIAEQIVPCAKCRYCKSGQYWMCEVHNIFGFQREVADGGMAEYMRIPPTAIVHKIP 158 Query: 133 DAI---DGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKRIAVVD 189 D I D A++EPLACA+ V +++ D V+ GAG +GLM ++ L K++ V+D Sbjct: 159 DGISLEDAAIIEPLACAIHTVNRGELQLDDVVVIAGAGPLGLMMTQVAHLKTPKKLVVID 218 Query: 190 PNDERLKISQLWGA-------TEMAPNLGALLTDNHPQSFDCVIDAVGLSTTRRDSLNAL 242 +ERL +++ +GA T+ A + LTD + D I+ G ++ + Sbjct: 219 LVEERLALAREYGADVTINPKTDDALAIIHSLTDGY--GCDVYIETTGAPIGVNQGMDLI 276 Query: 243 IRGGRAVWIGLHEALTHLDGNQI-VRDELEVRGS----FCYTDDEFIRAVSLINSQ 293 + GR V + A T LD + I R EL+VRG+ +CY + A L+ S+ Sbjct: 277 RKLGRFVEFSVFGADTTLDWSVIGDRKELDVRGAHLGPYCYPIAIDLLARGLVTSK 332 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: 328 Number of extensions: 20 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: 331 Length of database: 365 Length adjustment: 29 Effective length of query: 302 Effective length of database: 336 Effective search space: 101472 Effective search space used: 101472 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 Sep 17 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