Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate WP_011841060.1 RSPH17029_RS07595 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::Q97YM2 (349 letters) >NCBI__GCF_000015985.1:WP_011841060.1 Length = 364 Score = 169 bits (427), Expect = 1e-46 Identities = 116/337 (34%), Positives = 176/337 (52%), Gaps = 14/337 (4%) Query: 21 LSIEDVNIPE-PQGEEVLIRIGGAGVCRTDLR----VWKGVEAKQGFRLPIILGHENAGT 75 L IEDV P + +EV++++G AG+CRTDL VW+ + G LP I+GHENAG Sbjct: 17 LKIEDVPSPTIDRPDEVIVKVGAAGLCRTDLHIIEGVWRDIMDSHGSLLPYIMGHENAGW 76 Query: 76 IVEVGE-LAKVKKGDNVVVYATWGDLTCRYCREGKFNICKNQIIPGQTTNGGFSEYMLVK 134 + +VG + VK GD V+ + C CR G C+N + PG +GGF+EY Sbjct: 77 VEDVGSGVTSVKPGDAVICHPLRTCGICLNCRHGHDMHCQNNLFPGLGLDGGFAEYFKT- 135 Query: 135 SSRWLVKLNS-LSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIGGLAVYTIQ 193 S R L+KLN+ ++P+ AP+ADAG T+ A ++A ++ +++ G+GGL +Q Sbjct: 136 SERSLIKLNTGITPLSVAPMADAGITAYRAAKRAAKLLNPGDWALIL--GVGGLGHIALQ 193 Query: 194 ILKALMKNITIVGISRSKKHRDFALELGADYV-SEMKDAESLINKLTDGLGASIAIDLVG 252 +L M + + R + A ELGAD V S D + ++T G GA + ID VG Sbjct: 194 VLNE-MAGCRTIAVDREPGAQVLAKELGADKVLSGGPDLIEEVRQITGG-GARVVIDFVG 251 Query: 253 TEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSLNDLEDVVRLS 312 KLL G +I+VG G + + + ++ GS G +L +++ L+ Sbjct: 252 ELGIENLCWKLLKNGGDLIMVGY-GGTIEIPTLELVAREIRIGGSLVGDYTELVELMELN 310 Query: 313 ESGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVITP 349 GK+K + + L+DIN A + R GR VI P Sbjct: 311 ADGKVKMHQTEFALEDINTAIDDFKNRRFTGRGVIVP 347 Lambda K H 0.317 0.136 0.389 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: 361 Number of extensions: 17 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: 349 Length of database: 364 Length adjustment: 29 Effective length of query: 320 Effective length of database: 335 Effective search space: 107200 Effective search space used: 107200 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 (21.6 bits) S2: 49 (23.5 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