Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate GFF1748 HP15_1707 short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__Marino:GFF1748 Length = 256 Score = 139 bits (350), Expect = 6e-38 Identities = 92/261 (35%), Positives = 147/261 (56%), Gaps = 19/261 (7%) Query: 26 MERFSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTY---GV 82 MER LKGKVA ITG S GIG A A A+ GA VAI D + E L+K G+ Sbjct: 1 MER--LKGKVAVITGGSVGIGAATALRMAEEGAAVAIL---DCQDSEGEALAKQLEGRGL 55 Query: 83 RSKAYKCAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDL 142 ++ + C V+ ++V+ + + FG + + NAGI P ++ EEWD V D+ Sbjct: 56 KAGYWHCDVSKEQEVKQVLDAVANTFGTPTVLVNNAGIAGANKPTHEL-TEEEWDHVQDV 114 Query: 143 DLNGAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAV 202 ++ G ++C K+A KK G GS I +S+ G +V+ P + Y+A+K AV +S++ A+ Sbjct: 115 NVKGVFFCTKHAIPHMKKAGVGSIINLSSIYG-LVSAPDIPP-YHASKGAVRLMSKTDAL 172 Query: 203 EWAGF-ARCNTVSPGYMATEISDFI-------PRDTKEKWWQLIPMGREGDPSELAGAYI 254 +A RCN++ PG++ T + + P + K+ + P+G G+P ++A + Sbjct: 173 LYATENIRCNSIHPGFIWTPLVEAHLKTTGQDPEEAKKATAAMHPVGHMGEPDDIAWGAV 232 Query: 255 YLASDASTYTTGADILVDGGY 275 YLASD S + TG+++++DGGY Sbjct: 233 YLASDESKFVTGSELVIDGGY 253 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: 168 Number of extensions: 9 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: 256 Length adjustment: 25 Effective length of query: 253 Effective length of database: 231 Effective search space: 58443 Effective search space used: 58443 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