Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_050463195.1 AKL27_RS12690 NAD(P)-dependent oxidoreductase
Query= SwissProt::Q92RN6 (256 letters) >NCBI__GCF_001189915.1:WP_050463195.1 Length = 249 Score = 136 bits (343), Expect = 4e-37 Identities = 90/250 (36%), Positives = 139/250 (55%), Gaps = 11/250 (4%) Query: 11 LRDRGVLVTGGGS--GIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHF- 67 L+D+ ++TG S GIG A+ FA G RVA +D+ ++ A AA+ A H Sbjct: 3 LKDKVAIITGAASARGIGKAVARLFAAHGGRVAILDLDEAAAAA-----AARDIGAGHIG 57 Query: 68 IQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLF 127 + ++ N AA E + +LG V +LVNNA + + E+++ V+LR Sbjct: 58 LACNVTNKADCERAAQEVLQRLGQVDILVNNAGITQPLKIMDIQPENYEAVTDVSLRGTL 117 Query: 128 FMCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEI--PAYSTAKAGIIGLTKSLAGKLGPDN 185 +M QA+ PHM+ + GSIV SS++ P YS AKAG++GL +++A +LGPDN Sbjct: 118 YMSQALIPHMRSRRSGSIVCLSSVSAQRGGGIFGGPHYSAAKAGVLGLARAMARELGPDN 177 Query: 186 IRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMT 245 IRVN++ PG+I T+ LT+ A + L R+ A+D+ CLFLASD S+ +T Sbjct: 178 IRVNSLTPGLIQTDITAGK-LTDAMKAEALKAIPLNRLGEANDVANSCLFLASDLSSYLT 236 Query: 246 AQAMIIDGGV 255 + ++GG+ Sbjct: 237 GVTLDVNGGM 246 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: 135 Number of extensions: 6 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: 249 Length adjustment: 24 Effective length of query: 232 Effective length of database: 225 Effective search space: 52200 Effective search space used: 52200 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: 46 (22.3 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