Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >NCBI__GCF_000621325.1:WP_211248857.1 Length = 255 Score = 139 bits (350), Expect = 6e-38 Identities = 94/257 (36%), Positives = 136/257 (52%), Gaps = 19/257 (7%) Query: 5 LQDKVAILTGAASGIGEAVARRYLDEGARCVLVD--VKPADSFGDSLRATYGDRVLTVSA 62 L KV ++TGA+SGIGEA A + EG + VL + ++ ++RAT G+ V V Sbjct: 9 LAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIRATGGEAVF-VCT 67 Query: 63 DVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPIL-EESWDVFDRLFAVNVKGMFFL 121 DV + DI R+V + L+ FG +D+LFNNA + E+S +D NV+ + + Sbjct: 68 DVLQEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSVLWG 127 Query: 122 MQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKINV 181 MQ + M Q GG IIN +S G A + Y A+KAAV+ T+ AA+ I + Sbjct: 128 MQHAIRAM--QSAGGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGIRI 185 Query: 182 NGIAPGVVDTPMWNEVDALFARYENRPLG--EKKRLVGEAVPLGRMGVPDDLTGAALFLA 239 N + PG+ TPM R LG +++ P GR G P+++ A +FLA Sbjct: 186 NAVCPGITYTPM-----------SQRLLGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLA 234 Query: 240 SADADYITAQTLNVDGG 256 S +A YI+ Q LNVDGG Sbjct: 235 SGNASYISGQCLNVDGG 251 Lambda K H 0.321 0.135 0.393 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: 167 Number of extensions: 13 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: 260 Length of database: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 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