Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate RR42_RS31820 RR42_RS31820 short-chain dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__Cup4G11:RR42_RS31820 Length = 261 Score = 135 bits (339), Expect = 1e-36 Identities = 86/254 (33%), Positives = 141/254 (55%), Gaps = 10/254 (3%) Query: 29 FSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYK 88 F L+GKVA+ITG++ GIG A A AGA VA+ + + A + G ++ +K Sbjct: 8 FDLRGKVAAITGAARGIGAETARVLAAAGAKVAVLDLLEADGQAAVRRIEAEGGQAAFWK 67 Query: 89 CAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAY 148 V++ +V I FG++DI I NAGI P ++ +W +V+D+++ G + Sbjct: 68 LDVSSEAEVGKVFGEIAARFGRLDILINNAGIDGVNAPTHELA-LAQWQRVMDVNVTGTF 126 Query: 149 YCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAG-F 207 C K+A ++ G GS + +SM G IV P + Y+A+K AV ++++ A+ +AG Sbjct: 127 LCTKHAIAHLERAGGGSIVNVSSMYG-IVGGPDVPP-YHASKAAVRMMAKTDAMLYAGKN 184 Query: 208 ARCNTVSPGYMATEISDFIPRDTKE------KWWQLIPMGREGDPSELAGAYIYLASDAS 261 R N+V PGY+ T + + + + + PMGR G+P ++A +YL SDA+ Sbjct: 185 IRANSVHPGYIRTPMLEEVAHASGQGEGLFAYLGAQAPMGRLGEPRDIAAGILYLVSDAA 244 Query: 262 TYTTGADILVDGGY 275 Y TGA++++DGGY Sbjct: 245 RYVTGAELVIDGGY 258 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: 10 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: 261 Length adjustment: 25 Effective length of query: 253 Effective length of database: 236 Effective search space: 59708 Effective search space used: 59708 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