Align Short-chain dehydrogenase (characterized, see rationale)
to candidate RR42_RS21135 RR42_RS21135 gluconate 5-dehydrogenase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Cup4G11:RR42_RS21135 Length = 255 Score = 108 bits (270), Expect = 1e-28 Identities = 94/258 (36%), Positives = 124/258 (48%), Gaps = 18/258 (6%) Query: 1 MDLNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARS-EPDPQFWARLTGLQPRAAL 59 + +L+ +V +VTGGA G+G AI+ LA GA +V AR+ E A L RA Sbjct: 4 LPFSLEGRVALVTGGAQGLGQAIAAGLAQAGAHVIVAARNAERVHAAVAALAADGGRAEP 63 Query: 60 FQLELQDEARCGEAVAETVRRFGRLDGLVNNAGV-NDSVGLDAGRNEFVASLERNLIHYY 118 L++ D A A A GRLD LVNNAG N S + LE NL+ Y Sbjct: 64 LVLDVTDAAAVDAAFAHIDATHGRLDILVNNAGARNRSNMAHLNAADLREMLETNLVAPY 123 Query: 119 VMAHYCVPHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVR 177 + + ++ R G I+NVSS + N Y A+KG +LTR AA L DGV Sbjct: 124 ALCRHAAQLMRRGRYGRIVNVSSIAGQVARANDVLYPATKGGLDALTRAMAADLGRDGVT 183 Query: 178 VNALIPAEVMTPLYEKWIATFENPQEKLDA-----ITSKIPLGKRFTTSEEMADMAVFLL 232 VNA+ P + AT N DA + + LG R+ EE+A VFL Sbjct: 184 VNAVAPG---------YFATEPNQPMVDDAGVAEWLRQRTALG-RWGQPEEIAGAVVFLA 233 Query: 233 SGRSSHTTGQWVFVDGGY 250 SG +S+ TG + VDGGY Sbjct: 234 SGAASYVTGHVLAVDGGY 251 Lambda K H 0.318 0.134 0.394 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: 179 Number of extensions: 10 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: 258 Length of database: 255 Length adjustment: 24 Effective length of query: 234 Effective length of database: 231 Effective search space: 54054 Effective search space used: 54054 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 (21.7 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