Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate GFF42 HP15_42 short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__Marino:GFF42 Length = 266 Score = 119 bits (297), Expect = 8e-32 Identities = 84/247 (34%), Positives = 128/247 (51%), Gaps = 3/247 (1%) Query: 11 LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70 L ++ L+TG G GIG + F +QGA V +++ + A+ + AQ G+A F Sbjct: 4 LENKVALITGAGGGIGEGVARYFVKQGAAVIIAELSEQLGEAVAADLRAQGGKA-LFCHT 62 Query: 71 DLRNVEAVRAAADEAVAKLGSVRVLVNNA-ARDDRQALEAVTEESWDESLSVNLRHLFFM 129 D+ N ++ A AV GS+ VLVNNA A LE T+E ++L+ + ++ Sbjct: 63 DVSNKSSIENAVATAVDHFGSIDVLVNNAFAPTPNVKLEEKTDEMLTQTLNTTVWAAWWA 122 Query: 130 CQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189 +A PHM +GGGSIVNF SI + Y+TAK+ I+GLT+S A + G NIR N Sbjct: 123 MKAAFPHMCERGGGSIVNFYSIDTEIGAWLHGDYNTAKSAILGLTRSAAAEWGRFNIRAN 182 Query: 190 AILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCL-FLASDSSAAMTAQA 248 AI P + + R + L R + +GP + FLAS+ S +T ++ Sbjct: 183 AIAPTAMGATFHKLAAENPGFEERSAAMRPLGRCGEPEADIGPVVAFLASEMSRFVTGES 242 Query: 249 MIIDGGV 255 + +DGG+ Sbjct: 243 IHVDGGL 249 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: 127 Number of extensions: 8 Number of successful extensions: 5 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: 266 Length adjustment: 25 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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