Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_028310872.1 H566_RS0106940 shikimate dehydrogenase
Query= BRENDA::Q88K85 (282 letters) >NCBI__GCF_000482785.1:WP_028310872.1 Length = 288 Score = 320 bits (821), Expect = 2e-92 Identities = 164/272 (60%), Positives = 199/272 (73%) Query: 7 LAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQHTGFTG 66 LAGLIG GIQ S +P +HE EG AQ L Y YR++D +QL L LP LLEAA+ GF G Sbjct: 10 LAGLIGAGIQRSLSPTMHEREGQAQGLNYQYRILDIEQLGLTPVDLPRLLEAAKLMGFGG 69 Query: 67 LNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRGLPDVA 126 LN+T+P KQAI+P LDELS +A+ +GAVNTVV++DG+ +GHNTD GFAEG +RGLP V Sbjct: 70 LNVTHPCKQAIIPHLDELSPDAKALGAVNTVVIRDGRTIGHNTDWWGFAEGFKRGLPGVK 129 Query: 127 RRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAVLGTDL 186 + VQ+GAGGAG+AVAHALL GV RL +F++D TRA L + L FGA RAV G+ L Sbjct: 130 LDRAVQLGAGGAGAAVAHALLTMGVGRLAIFDMDPTRAARLAEELCERFGAGRAVGGSSL 189 Query: 187 ATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARALGCRT 246 +A DGLV+ TP GMA PG PL LL P +WV+EI+YFPLETELL AR LGC+ Sbjct: 190 EDEMAATDGLVHCTPTGMAAHPGLPLDAALLRPAIWVSEIVYFPLETELLATARKLGCKV 249 Query: 247 LDGSNMAVFQAVKAFELFSGRQADAARMQAHF 278 + G MAVFQAV AF+ F+G +ADAARM AHF Sbjct: 250 VSGGGMAVFQAVGAFQHFTGLEADAARMLAHF 281 Lambda K H 0.321 0.137 0.395 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: 242 Number of extensions: 4 Number of successful extensions: 1 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: 282 Length of database: 288 Length adjustment: 26 Effective length of query: 256 Effective length of database: 262 Effective search space: 67072 Effective search space used: 67072 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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