Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate 3607835 Dshi_1243 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__Dino:3607835 Length = 258 Score = 236 bits (601), Expect = 5e-67 Identities = 123/251 (49%), Positives = 162/251 (64%), Gaps = 2/251 (0%) Query: 5 SSQFPDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQA 64 ++ F DL V VTGGGSGIGAAL + F QGA+VAF I + A K+ A G+A Sbjct: 6 NATFHDLDGASVFVTGGGSGIGAALTDGFLAQGAQVAF--IGRSDASAFVAKMRAAHGRA 63 Query: 65 PHFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLR 124 P F+Q D+ + +A+RAA +A A G + LVNNAA D R + VT E WD+ ++NL+ Sbjct: 64 PLFVQGDITDTDALRAAIAQATAAHGPITALVNNAANDKRHSTAEVTPEFWDQMQAINLK 123 Query: 125 HLFFMCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPD 184 FF QAV P M GGG+IVNFSSI++++ PAY+ A AGI GLT+SLA + GPD Sbjct: 124 AYFFAAQAVTPGMAEAGGGAIVNFSSISYMMGNAGYPAYTAANAGITGLTRSLAREFGPD 183 Query: 185 NIRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAM 244 IRVNA+ PG ++T +Q +W T E +A +RQCLK L +D+V LFLAS +S M Sbjct: 184 GIRVNALAPGWVLTPKQLEMWATPEDLAAHLDRQCLKTHLAPEDIVEATLFLASGASKMM 243 Query: 245 TAQAMIIDGGV 255 T Q M++DGGV Sbjct: 244 TGQCMVVDGGV 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: 167 Number of extensions: 4 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: 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 17 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