Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_007729089.1 C1M55_RS30565 SDR family oxidoreductase
Query= SwissProt::Q92RN6 (256 letters) >NCBI__GCF_002893965.1:WP_007729089.1 Length = 257 Score = 129 bits (325), Expect = 5e-35 Identities = 86/243 (35%), Positives = 135/243 (55%), Gaps = 5/243 (2%) Query: 17 LVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQADLRNVE 76 L+TG GSGIG + A GARVA VD+ ES+ + +Q G A ++AD+R+ Sbjct: 11 LITGAGSGIGRGIALRLASDGARVAVVDLHIESAKETVALIESQYGTAALALEADVRDRA 70 Query: 77 AVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMCQAVAPH 136 AV AA + VA+ G LVNNA +LE +T+E WD L VNL+ +F + Q P+ Sbjct: 71 AVSAAFEATVAEWGRFDYLVNNAGLITMSSLENLTDEEWDLVLDVNLKGMFIVTQIATPY 130 Query: 137 MQRQGGGSIVNFSSI-AFLLNMPEIPA---YSTAKAGIIGLTKSLAGKLGPDNIRVNAIL 192 + G++VN S++ A ++ + A Y+ +K G+ LTK+LA +L N+RVNAI Sbjct: 131 FRDGNSGAVVNLSTVEADVVVSSQGFAQVHYNASKGGVKMLTKALAVELSRYNVRVNAIA 190 Query: 193 PGMIVTERQRRLWLTE-ESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAMII 251 PG + T + ++ E + M+ R + R+ +D+ G FL SD ++ ++ + + Sbjct: 191 PGPVPTAFLPGIDVSSGEVLDFMKSRLLVPRVGRPEDMGGAVSFLLSDDASYISGVQLPV 250 Query: 252 DGG 254 DGG Sbjct: 251 DGG 253 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: 120 Number of extensions: 5 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 232 Effective length of database: 233 Effective search space: 54056 Effective search space used: 54056 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