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_011840752.1 RSPH17029_RS05225 glucose 1-dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >NCBI__GCF_000015985.1:WP_011840752.1 Length = 254 Score = 141 bits (355), Expect = 2e-38 Identities = 94/252 (37%), Positives = 140/252 (55%), Gaps = 12/252 (4%) Query: 29 FSLKGKVASITGSSSGIGFAVAEAFAQAGAD-VAIWYNSKPSDEKAEYLSKTYGVRSKAY 87 F L G A++TGS SGIG + AFA +GA + I S D AE L R A Sbjct: 7 FRLDGACAAVTGSGSGIGLEICRAFAASGARLILIDRESAALDRAAEELGAAVAARIVA- 65 Query: 88 KCAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGA 147 VT+A+ + E + I + +AGI + ++ W +V+ ++++G Sbjct: 66 --DVTDAEAMTAAAAEAEA-VAPVSILVNSAGIARLHDAL--ETDDATWRQVMAVNVDGM 120 Query: 148 YYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAG- 206 ++ ++ G+ +G G+ + SMSG IVN PQ + Y A+K AV L+R+LA EWAG Sbjct: 121 FWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGR 180 Query: 207 FARCNTVSPGYMATEISDFIPRDTKE---KWWQLIPMGREGDPSELAGAYIYLASDASTY 263 R N ++PGY+ATE++ R+ E W + PMGR G+PSE+A A ++LAS A++Y Sbjct: 181 GVRVNALAPGYVATEMT-LKMRERPELFGTWLDMTPMGRCGEPSEIAAAALFLASPAASY 239 Query: 264 TTGADILVDGGY 275 TGA + VDGGY Sbjct: 240 VTGAILAVDGGY 251 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: 155 Number of extensions: 10 Number of successful extensions: 4 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: 254 Length adjustment: 25 Effective length of query: 253 Effective length of database: 229 Effective search space: 57937 Effective search space used: 57937 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 Apr 10 2024. 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