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 SMc01214 SMc01214 zinc-containing alcohol dehydrogenase
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__Smeli:SMc01214 Length = 347 Score = 153 bits (386), Expect = 7e-42 Identities = 105/327 (32%), Positives = 165/327 (50%), Gaps = 21/327 (6%) Query: 1 MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRK-PPLVMGH 59 MK + + +S+ + P P P + ++V GICG++ +L H E PP+ +GH Sbjct: 1 MKAVRLESVGNISVRNVGIPEPGPDDLLVKVEACGICGTDR--HLLHGEFPSTPPVTLGH 58 Query: 60 EFSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGIDFPGAYAE 119 EF G+V E G V ++ G +T +P ++CGRC C G C + R IGI G +AE Sbjct: 59 EFCGIVVEAGSAVRDIAPGARITGDPNISCGRCPQCQAGRVNLCRNLRAIGIHRDGGFAE 118 Query: 120 RVLVPSNQCYAVK---DAIDGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRL 176 VLVP Q + + D + GA EPLAC + V L+ IK G T ++G G+IGL+TV+L Sbjct: 119 YVLVPRKQAFEIPLTLDPVHGAFCEPLACCLHGVDLSGIKAGSTVAILGGGVIGLLTVQL 178 Query: 177 LGLSGAKRIAVVDPNDERLKISQLWGAT-EMAPNLGALL------TDNHPQSFDCVIDAV 229 L+GA + + + ++++ GAT + P+ G ++ P D VI+ Sbjct: 179 ARLAGATTVILSTRQATKRRLAEEVGATATVDPSAGDVVEAIAGPVGLVPGGVDVVIECA 238 Query: 230 GLSTTRRDSLNALIRGGRAVWIGL--HEALTHLDGNQIVRDELEVRGSFCYTDDEFI--R 285 G++ T + S GG V +G+ ++ I+ EL V GSF + F+ R Sbjct: 239 GVAETVKQSTRLAKAGGTVVILGVLPQGEKVEIEPFDILFRELRVLGSFI---NPFVHRR 295 Query: 286 AVSLINSQKFLPVDRQWLDVRSLEEGP 312 A L+ + + +DR SL+E P Sbjct: 296 AADLV-ATGAIEIDRMISRRISLDEAP 321 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: 365 Number of extensions: 22 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: 347 Length adjustment: 28 Effective length of query: 303 Effective length of database: 319 Effective search space: 96657 Effective search space used: 96657 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