Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase
Query= uniprot:A0A4R8NY47 (263 letters) >NCBI__GCF_000621325.1:WP_211248857.1 Length = 255 Score = 115 bits (288), Expect = 9e-31 Identities = 79/252 (31%), Positives = 126/252 (50%), Gaps = 6/252 (2%) Query: 15 RSLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFP 74 ++LAGK VVITG SGIG A AF +G ++ E EA+ A+++ A F Sbjct: 7 QNLAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIR-ATGGEAVFV 65 Query: 75 CN--LMNLEALRATFTEIETVMGGVDILINNAANDDRHKS-EDVTPAYWDERLAVNLRHQ 131 C L + R T ++T GG+D+L NNA + + + + A +D + N+R Sbjct: 66 CTDVLQEADIARLVQTALDT-FGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSV 124 Query: 132 FFCAQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGV 191 + Q + M+ GG I+N SI H+G + LY +KA + GMT A ++ + G+ Sbjct: 125 LWGMQHAIRAMQSA-GGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGI 183 Query: 192 RVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDSGAKCTG 251 R+NA+ PG TP L +E+ +A P ++AA +FL+S + + +G Sbjct: 184 RINAVCPGITYTPMSQRLLGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNASYISG 243 Query: 252 REYYVDAGWLGA 263 + VD G+ A Sbjct: 244 QCLNVDGGYTAA 255 Lambda K H 0.322 0.137 0.417 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: 178 Number of extensions: 9 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: 263 Length of database: 255 Length adjustment: 24 Effective length of query: 239 Effective length of database: 231 Effective search space: 55209 Effective search space used: 55209 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