Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate WP_097068497.1 CRO22_RS02400 beta-ketoacyl-ACP reductase
Query= SwissProt::Q6CEE9 (278 letters) >NCBI__GCF_900217815.1:WP_097068497.1 Length = 240 Score = 119 bits (298), Expect = 6e-32 Identities = 79/242 (32%), Positives = 126/242 (52%), Gaps = 9/242 (3%) Query: 34 KVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYKCAVTN 93 +VA +TG + GIG A++ A +AG V Y +DE A + G+ K K +V + Sbjct: 3 RVALVTGGTRGIGAAISMALKEAGYTVVANYAG--NDEAAREFTHVTGI--KTVKWSVAD 58 Query: 94 AKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAYYCAKY 153 E I+ IE + G ID+ + NAGI T + E+WD+V+ +LNG + Sbjct: 59 YTGCEDGIRQIEDEVGPIDVLVNNAGI--TRDAPFHKMSREQWDQVIGTNLNGLFNMTHP 116 Query: 154 AGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAGFA-RCNT 212 +++ +G I +S++G Q+ Y+AAK + +++LA E A N Sbjct: 117 LWNGMRERKFGRIINISSINGQKGQFGQVN--YSAAKAGDIGFTKALAQEGARSGITVNA 174 Query: 213 VSPGYMATEISDFIPRDTKEKWWQLIPMGREGDPSELAGAYIYLASDASTYTTGADILVD 272 + PGY+ATE+ +P +E IP+GR G+P E+A ++LASD + + TGA V+ Sbjct: 175 ICPGYIATEMVMAVPEKVRESIIATIPVGRLGEPDEIARTVVFLASDQAGFITGATFTVN 234 Query: 273 GG 274 GG Sbjct: 235 GG 236 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: 171 Number of extensions: 7 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: 278 Length of database: 240 Length adjustment: 24 Effective length of query: 254 Effective length of database: 216 Effective search space: 54864 Effective search space used: 54864 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 24 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