Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate RR42_RS31670 RR42_RS31670 NAD-dependent dehydratase
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__Cup4G11:RR42_RS31670 Length = 254 Score = 143 bits (360), Expect = 4e-39 Identities = 90/252 (35%), Positives = 134/252 (53%), Gaps = 9/252 (3%) Query: 8 FPDLRDRG--VLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAP 65 FPD R G +VTGGGSGIG AL FA GARV +D ++ A E+VA + G Sbjct: 5 FPDFRLTGQVTVVTGGGSGIGKALAHTFAGAGARVVVLD----TNGAAAEQVANEIGSMA 60 Query: 66 HFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRH 125 AD+ N +A+ + ++ + G + VL NNA + R +T W+ ++VN+ Sbjct: 61 QHAVADVSNEDAIESVMEDVARQHGRIDVLFNNAGVNRRNTSFDLTIADWNAVVAVNMTG 120 Query: 126 LFFMCQAVAPHMQRQGGGSIVNFSSIAFLLN--MPEIPAYSTAKAGIIGLTKSLAGKLGP 183 +F +A A HM+ GGG IVN +SI + P I Y K ++ +T+S A + P Sbjct: 121 MFLCARAAARHMRDGGGGRIVNTASILGISGGWYPNI-VYQATKGAVVNMTRSWAVEWAP 179 Query: 184 DNIRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAA 243 NIRVNA+ P +I T L + +A+ + L R+ D+ GP LFLA+ +S+ Sbjct: 180 YNIRVNAVAPSIIRTPMTEALTSQPDVVAKFEALTPLGRLCEPADMTGPVLFLATAASSM 239 Query: 244 MTAQAMIIDGGV 255 +T + +DGGV Sbjct: 240 VTGHILPVDGGV 251 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: 148 Number of extensions: 12 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: 254 Length adjustment: 24 Effective length of query: 232 Effective length of database: 230 Effective search space: 53360 Effective search space used: 53360 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