Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_110751435.1 C7477_RS09440 L-iditol 2-dehydrogenase
Query= SwissProt::Q92RN6 (256 letters) >NCBI__GCF_003217235.1:WP_110751435.1 Length = 258 Score = 131 bits (329), Expect = 2e-35 Identities = 90/258 (34%), Positives = 131/258 (50%), Gaps = 22/258 (8%) Query: 11 LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70 L + +TG GIG A EAFAR+GA VA DI L ++ AA+ G+ + +Q Sbjct: 5 LEGKSAFITGAARGIGFAFAEAFAREGATVALADI----DLDRAQESAAKIGERAYAVQI 60 Query: 71 DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMC 130 D+ ++ ++ A EAVAK G + +LVNNAA D + +T ES++ +VN+ + F Sbjct: 61 DVTDIASIERAVAEAVAKTGGIDILVNNAALFDMAPMVEITRESFERLYAVNVHGVLFTM 120 Query: 131 QAVAPHMQRQG-GGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189 QAVA M +G GG I+N +S A + Y + KA +I LT+S L I VN Sbjct: 121 QAVARAMIARGRGGKIINMASQAGRRGEALVAVYCSTKAAVISLTQSAGLDLIRHGINVN 180 Query: 190 AILPGMIVTERQRRLWLTEESIARMQERQCL--KRMLVA-----------DDLVGPCLFL 236 AI PG++ E W +++ E + L K+ LV +DL G +FL Sbjct: 181 AIAPGVVDGEH----WAGVDALFAKHENRPLGEKKRLVGEAVPFGRMGRPEDLTGMAIFL 236 Query: 237 ASDSSAAMTAQAMIIDGG 254 A S + AQ +DGG Sbjct: 237 AGPESDYVVAQTYNVDGG 254 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: 122 Number of extensions: 6 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: 256 Length of database: 258 Length adjustment: 24 Effective length of query: 232 Effective length of database: 234 Effective search space: 54288 Effective search space used: 54288 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