Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate AO353_24520 AO353_24520 short-chain dehydrogenase
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24520 Length = 249 Score = 125 bits (315), Expect = 6e-34 Identities = 86/249 (34%), Positives = 133/249 (53%), Gaps = 9/249 (3%) Query: 11 LRDRGVLVTGGGS--GIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFI 68 L+ + ++TG S GIG A FA+QGARV +D+ ++ AA G+ I Sbjct: 3 LQGKVAIITGAASARGIGRATATTFAQQGARVVILDLDESAA----RDAAASLGEGHLGI 58 Query: 69 QADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFF 128 A++ + VR A + + G + +L+NNA + +D+ L V+LR Sbjct: 59 GANVADELQVRQAVAKIIEHFGRIDILINNAGITQPLKTLDIRPSDYDKVLDVSLRGTLL 118 Query: 129 MCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEI--PAYSTAKAGIIGLTKSLAGKLGPDNI 186 M QAV P M++Q GSIV SS++ P YS AKAG++GL K++A +LGPD + Sbjct: 119 MSQAVIPTMRQQSSGSIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLAKAMARELGPDKV 178 Query: 187 RVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTA 246 RVN+I PG+I T+ L + +E + + L R+ A D+ LFLASD S+ +T Sbjct: 179 RVNSIAPGLIHTDITGGL-MQDERRHAIIDGIPLGRLGEAQDVANAALFLASDLSSYLTG 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: 128 Number of extensions: 5 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: 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