Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate GFF2363 PS417_12050 short-chain dehydrogenase
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__WCS417:GFF2363 Length = 251 Score = 122 bits (306), Expect = 7e-33 Identities = 83/245 (33%), Positives = 124/245 (50%), Gaps = 7/245 (2%) Query: 10 DLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQ 69 DL ++TGG +GIG A +GARVA +D A+ E VAA G I Sbjct: 10 DLTGHCAVITGGAAGIGLACASLLVERGARVALLD----RDPAVVE-VAAGLGAGHLGIA 64 Query: 70 ADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFM 129 DL + ++ D A + L+N+A V+E +WD +L +NL+ FF+ Sbjct: 65 VDLGQIGQIQHTIDTVFAHFQRLDYLINSAGVVLLDKAVDVSESAWDTTLDINLKASFFV 124 Query: 130 CQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189 QA A HM QG G IVN +S A ++ + AY +KA I+G+TK LA + P I VN Sbjct: 125 AQACARHMLAQGSGRIVNLASQAAVIGLDRHVAYCASKAAIVGMTKVLAMEWAP-QINVN 183 Query: 190 AILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAM 249 AI P ++ T ++ W E + + + R +++ G L+L SD++ +T M Sbjct: 184 AISPTIVETALGKKAWAGEVG-EKAKLQIPAGRFAQPEEIAGLALYLLSDAAQMITGANM 242 Query: 250 IIDGG 254 +IDGG Sbjct: 243 VIDGG 247 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: 101 Number of extensions: 7 Number of successful extensions: 4 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: 251 Length adjustment: 24 Effective length of query: 232 Effective length of database: 227 Effective search space: 52664 Effective search space used: 52664 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