Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate CCNA_03491 CCNA_03491 gluconate 5-dehydrogenase (Ga5DH)-related protein
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__Caulo:CCNA_03491 Length = 260 Score = 105 bits (261), Expect = 1e-27 Identities = 79/255 (30%), Positives = 132/255 (51%), Gaps = 17/255 (6%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPA---AIDRARTA-HPQLHAGVADVS 67 G L++G GIG +A+A GA++ I +P A ++ TA ++ A DVS Sbjct: 10 GKVALVTGGNRGIGLGMAKAMAQAGADIVIWGSNPERNLAAEQTLTALGVRVKAQTVDVS 69 Query: 68 DCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRK 127 D AQV +++A + +G +D + NAGI + + D+ + + + NL+ F+ LR+ Sbjct: 70 DEAQVREGMEEAVAAMGRVDSVFANAGIGYGSPSFVDMSTEVYRKVLAVNLDGVFFTLRE 129 Query: 128 AVPLLKETS--ANPG--IIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVR 183 A + E + +PG ++ +AS+A G A YAA+K A++ M+KS+A+E VR Sbjct: 130 ACRHMVERAKAGDPGGSLVGVASLAAIEGAARNEAYAATKGAVISMIKSVAVEHARYGVR 189 Query: 184 VNAILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLAS 243 NAILPG + + ++A A+ G + + ++ RR D MA++LAS Sbjct: 190 ANAILPGWIATD-----MTAGAQ----GNAAFAEKVIPRVPARRWGEPEDFGGMAVYLAS 240 Query: 244 PAGQNISGQAISVDG 258 A SG + +DG Sbjct: 241 DASSYHSGTTLVIDG 255 Lambda K H 0.320 0.136 0.391 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: 135 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: 263 Length of database: 260 Length adjustment: 25 Effective length of query: 238 Effective length of database: 235 Effective search space: 55930 Effective search space used: 55930 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 (21.8 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