Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_043920527.1 jaqu_RS18685 SDR family oxidoreductase
Query= SwissProt::Q92RN6 (256 letters) >NCBI__GCF_000877395.1:WP_043920527.1 Length = 256 Score = 221 bits (562), Expect = 2e-62 Identities = 119/251 (47%), Positives = 155/251 (61%), Gaps = 3/251 (1%) Query: 6 SQFPDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAP 65 + FPDLRD + +TGGGSGIGAAL E F RQGARVAF I + A +++ TG P Sbjct: 4 ASFPDLRDASIFITGGGSGIGAALTEGFLRQGARVAF--IGRSDASAFVDEMEEATGNRP 61 Query: 66 HFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRH 125 FIQ D+ ++ A D+A G + LVNNAA D R A V E WD S+S+NL+ Sbjct: 62 LFIQGDVTENASLFRAMDQAAEAHGPITRLVNNAANDQRHATLDVDEAFWDWSISINLKA 121 Query: 126 LFFMCQAVAPHMQRQG-GGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPD 184 F CQ M G G IVNFSSI++++ Y+ A +GI GLT+SLA + GPD Sbjct: 122 YLFACQHAIRGMTAAGLPGHIVNFSSISYMMGNAGYAIYTAANSGINGLTRSLAREFGPD 181 Query: 185 NIRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAM 244 IRVNA+ PG ++T++Q LW +S+ +RQC+ L DD+VGP LFLASD S M Sbjct: 182 GIRVNALAPGWVLTQKQLDLWADPDSLKAHLDRQCIPEHLAPDDIVGPTLFLASDISKMM 241 Query: 245 TAQAMIIDGGV 255 T QA+++DGGV Sbjct: 242 TGQALVVDGGV 252 Lambda K H 0.321 0.133 0.377 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: 8 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: 256 Length of database: 256 Length adjustment: 24 Effective length of query: 232 Effective length of database: 232 Effective search space: 53824 Effective search space used: 53824 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 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