Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate AZOBR_RS09410 AZOBR_RS09410 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__azobra:AZOBR_RS09410 Length = 253 Score = 132 bits (331), Expect = 1e-35 Identities = 84/255 (32%), Positives = 138/255 (54%), Gaps = 17/255 (6%) Query: 29 FSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYK 88 F L + A +TG+S+G+G A A AGA VA+ + S + A + G ++ A Sbjct: 3 FPLTNRTALVTGASAGLGRHFAGVLAAAGARVALAARRRESLDAAVAEIEAAGGQAIAVP 62 Query: 89 CAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAY 148 VT+A V ++ G +DI + NAG A P +D EEWD+V+D +L GA+ Sbjct: 63 LDVTDAASVRNGVREAAGALGGLDILVNNAGAT-VAKPALDYA-EEEWDRVIDTNLKGAF 120 Query: 149 YCAKYAGQIFKKQGYGSFIFTAS------MSGHIVNIPQMQACYNAAKCAVLHLSRSLAV 202 A+ ++ ++QG G I + ++GH+V Y A+K ++ +++++A+ Sbjct: 121 LTAQETARVMREQGRGGSIVNIASILGLRVAGHVV-------AYTASKAGLVQMTQAVAL 173 Query: 203 EWAGFA-RCNTVSPGYMATEIS-DFIPRDTKEKWWQLIPMGREGDPSELAGAYIYLASDA 260 EWA + R N ++PGYM T+++ DF+ D + + +P R G ++L G + L SDA Sbjct: 174 EWARYGIRVNALAPGYMETDLNRDFLATDAGQALIRRVPQRRLGRLADLDGPLLLLCSDA 233 Query: 261 STYTTGADILVDGGY 275 S Y TGA + VDGG+ Sbjct: 234 SAYMTGAVVPVDGGH 248 Lambda K H 0.317 0.132 0.409 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: 161 Number of extensions: 7 Number of successful extensions: 5 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: 278 Length of database: 253 Length adjustment: 25 Effective length of query: 253 Effective length of database: 228 Effective search space: 57684 Effective search space used: 57684 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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