Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate CA265_RS13715 CA265_RS13715 glucose dehydrogenase
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__Pedo557:CA265_RS13715 Length = 248 Score = 107 bits (267), Expect = 2e-28 Identities = 80/243 (32%), Positives = 127/243 (52%), Gaps = 12/243 (4%) Query: 16 VLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALC-EKVAAQTGQAPHFIQADLRN 74 +++TG +GIG A+ F +QG V ++ A ES+L ++ AQ A + D+ Sbjct: 6 IIITGASTGIGRAIAALFLKQGHNVV-INSANESNLIRAFNELGAQHQLA--MVAGDISK 62 Query: 75 VEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMCQAVA 134 + + AVA+ G+V VLVNNA + +A V E D L++NL+ FF QA Sbjct: 63 ATTGQLLVETAVARFGTVDVLVNNAGIFEPKAFLEVDEAHLDSFLNINLKGTFFTSQAAI 122 Query: 135 PHMQRQGGGSIVNFSSIAFLLNMPEIPAYS--TAKAGIIGLTKSLAGKLGPDNIRVNAIL 192 M +Q GGSI+N ++ + PA + ++K GI LTK LA + G +NIRVN I Sbjct: 123 AQMLKQDGGSIINIGTVLVDHAIGGFPATAPISSKGGIHALTKQLAAEFGKNNIRVNGIA 182 Query: 193 PGMIVTERQRRLWLTE-ESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAMII 251 PG+I + Q + ++ + +A + L R+ D+ L+LA S +T + + + Sbjct: 183 PGIIRSPLQEKNGISNADDLAGL---HLLNRIGETQDVAQLALYLA--ESNFVTGEIINL 237 Query: 252 DGG 254 DGG Sbjct: 238 DGG 240 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: 118 Number of extensions: 6 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: 248 Length adjustment: 24 Effective length of query: 232 Effective length of database: 224 Effective search space: 51968 Effective search space used: 51968 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