Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate Ac3H11_2074 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2074 Length = 249 Score = 135 bits (340), Expect = 8e-37 Identities = 88/249 (35%), Positives = 136/249 (54%), Gaps = 9/249 (3%) Query: 11 LRDRGVLVTGGG--SGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFI 68 L+++ ++TGG +G+G A A QGA+VA +D+ AA+ G+ + Sbjct: 3 LKNQVAIITGGAGINGLGFATARLMAEQGAKVAILDLEGADPAG----AAARLGEGHLGL 58 Query: 69 QADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFF 128 AD+ + + AAA + A G + LVNNA +T +D L+V+LR + Sbjct: 59 VADVTDKASCEAAAAQVHAHFGRIDTLVNNAGITQPVKTLEITGADYDRILNVSLRGTLY 118 Query: 129 MCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEI--PAYSTAKAGIIGLTKSLAGKLGPDNI 186 M QAV P ++ Q GSI+ SS++ + P YS AKAG++GL +++A + GP+NI Sbjct: 119 MSQAVLPTLRAQQSGSIICISSVSAQRGGGILGGPHYSAAKAGVLGLARAMAREFGPENI 178 Query: 187 RVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTA 246 R+N I PG+I T+ + LTEE A + E L R+ ADD+ G C+FLAS S T Sbjct: 179 RINCITPGLIGTDIIKGK-LTEEKKAEIAETIPLARLGRADDIAGACVFLASPLSTYCTG 237 Query: 247 QAMIIDGGV 255 + ++GG+ Sbjct: 238 ITLDVNGGM 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: 144 Number of extensions: 8 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 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