Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_067472746.1 BJL86_RS11635 mycofactocin-coupled SDR family oxidoreductase
Query= metacyc::MONOMER-13092 (266 letters) >NCBI__GCF_001659785.1:WP_067472746.1 Length = 271 Score = 67.8 bits (164), Expect = 2e-16 Identities = 76/283 (26%), Positives = 120/283 (42%), Gaps = 44/283 (15%) Query: 9 GKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGE--------------KHENL--- 51 GK V +TG + G G+ + K+ D+ D + E L Sbjct: 6 GKVVYITGIARGQGRKYATRFAAEGAKIIGCDIADKASAWTRYPASTPEDMAETEKLVAE 65 Query: 52 ----LFQKV-DVTSREQVEASVAAVVEHFG-TVDAVVNNAGI-NIPRLLVDPKDPHGQYE 104 LF +V DV + VA V HFG +D VV NAGI N +L +E Sbjct: 66 AGGELFARVGDVRDLAFQQQLVADGVAHFGGRLDIVVANAGICNWGKL----------WE 115 Query: 105 LDDATFEKITMINQKGLYLVSQA-VGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKA 163 +D+ + IN G + +A + +L A G I ++S AGL+ Q+AY+ +K Sbjct: 116 MDEEQWNDTIDINLTGYWKTLKASIPHMLEAGNGGAITLLSSVAGLKSMPMQAAYSASKH 175 Query: 164 AVYSYTRSWAKELGKYGVRVVGIAP-GIMEATGLRTLAYEEALGYTRGKTVEEIRAGYAS 222 V ++ AKELG++G+RV + P G++ G + E + E + Sbjct: 176 GVVGLAQTAAKELGRHGIRVNTVHPYGVLTPMGGKDEGAHEVF-----NDMPEFLPHFEP 230 Query: 223 TTTTPLGRSGKLSEVADLVAYYISDRSSYITGITTNVAGGKTR 265 + K ++AD V + S+++ ITG T V G T+ Sbjct: 231 ILGMGM---AKTDDIADSVLFLSSEQARTITGTTFTVDMGATK 270 Lambda K H 0.313 0.131 0.361 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: 188 Number of extensions: 7 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: 266 Length of database: 271 Length adjustment: 25 Effective length of query: 241 Effective length of database: 246 Effective search space: 59286 Effective search space used: 59286 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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