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 SM_b20853 SM_b20853 sugar-alcohol dehydrogenase
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__Smeli:SM_b20853 Length = 339 Score = 142 bits (359), Expect = 9e-39 Identities = 106/340 (31%), Positives = 160/340 (47%), Gaps = 16/340 (4%) Query: 1 MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRKPPLVMGHE 60 M+ + A + + + P PV PG + LRVA VG+CGS+L L K PL+ GHE Sbjct: 1 MRAIVLHAPGDIRLETRPKPVAGPGEVLLRVASVGVCGSDLPRMLVKGAW-KMPLITGHE 59 Query: 61 FSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGIDFPGAYAER 120 FSG + +G V +IG+L PL+ C +CI C G RC G GAYAE Sbjct: 60 FSGHIHALGENVEGWEIGELTAIAPLMPCNQCIECKTGNFSRCRDYDYFGSRRDGAYAEF 119 Query: 121 VLVPSNQCYAVKDAIDG---ALVEPLACAVRAVGLA-RIKVGDTAVVIGAGIIGLMTVRL 176 V VP +D A+ +P + A+ A+ A I G T V+G G IGL ++ Sbjct: 120 VAVPVENLIKTPQHVDPRAIAMTDPASIALHAIWKAGGITAGQTGAVVGCGPIGLFAIQW 179 Query: 177 LGLSGAKRIAVVDPNDERLKISQLWGATEMAPNLGALLTDNHPQSFDCVIDAVGLSTTRR 236 + + G R+ VD +E+L +++ GA L A DN ++ D VI+AVG+ +T Sbjct: 180 MRIMGTSRVIAVDVTEEKLALARQAGADLCI--LSADFADNKERA-DLVIEAVGIDSTIN 236 Query: 237 DSLNALIRGGRAVWIGL---HEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLINSQ 293 ++ GG +IG+ L++ + +R E+ + GS+ F Q Sbjct: 237 AAVMLAAPGGHVTFIGIPVPDVKLSNATFQRFLRQEVSLHGSWNSFGAPFPGPQWTTTVQ 296 Query: 294 KFLPVDRQWLDVRS----LEEGPAAFKEL-VNGSPFSKII 328 KF + +W + S L E P F+ FSK++ Sbjct: 297 KFATGELKWEFMISHDLDLAELPGIFQRFAAKDLHFSKVL 336 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: 320 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: 339 Length adjustment: 28 Effective length of query: 303 Effective length of database: 311 Effective search space: 94233 Effective search space used: 94233 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