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 GFF3461 PS417_17720 iditol 2-dehydrogenase
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__WCS417:GFF3461 Length = 359 Score = 125 bits (314), Expect = 2e-33 Identities = 101/332 (30%), Positives = 159/332 (47%), Gaps = 38/332 (11%) Query: 27 IALRVAGVGICGSELSGYLG-------HNELRKPPLVMGHEFSGVVEEVGHGVTN---VK 76 + +R+A GIC S+ + G N K P+V GHEF G V E G G V Sbjct: 33 LVIRIAACGICASDCKCHSGAAMFWGGDNPWVKAPVVPGHEFFGYVVEAGEGAEEHFEVA 92 Query: 77 IGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGID---FPGAYAERVLVPSNQC-YAVK 132 +GD V A +V CG+C C G+ CE I G G A+ + +P + + Sbjct: 93 VGDKVIAEQIVPCGKCRFCKSGKYWMCEVHNIFGFQREVAEGGMAQYMRIPKTAIVHKIP 152 Query: 133 DAI---DGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKRIAVVD 189 +++ D ALVEP+AC++ V I++ D V+ GAG +GL V++ L K++ V+D Sbjct: 153 ESVSLEDSALVEPMACSIHTVNRGDIQLDDVVVIAGAGTLGLCMVQVAALKTPKKLVVID 212 Query: 190 PNDERLKISQLWGA-------TEMAPNLGALLTDNHPQSFDCVIDAVGLSTTRRDSLNAL 242 DERL++++ +GA + A + LTDN+ D I+ G+ L+ + Sbjct: 213 MVDERLELAKKFGADVVINPSRDNAREIINGLTDNY--GCDVYIETTGVPAGVTQGLDLI 270 Query: 243 IRGGRAVWIGLHEALTHLDGNQI-VRDELEVRGS----FCYTDDEFIRAVSLINSQKFLP 297 + GR V + A T +D + I R EL+VRG+ +CY + L+ S+ + Sbjct: 271 RKLGRFVEFSVFGAETSVDWSIIGDRKELDVRGAHLGPYCYPIAIDLFERGLVTSKGIVT 330 Query: 298 VDRQWLDVRSLEEGPAAFKELVNGSPFSKIIL 329 D L++ AF EL N + K++L Sbjct: 331 HD------FPLDDWAEAF-ELANSTKSIKVLL 355 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: 306 Number of extensions: 22 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: 359 Length adjustment: 29 Effective length of query: 302 Effective length of database: 330 Effective search space: 99660 Effective search space used: 99660 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