Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_011445240.1 SARO_RS07970 shikimate dehydrogenase
Query= BRENDA::Q88K85 (282 letters) >NCBI__GCF_000013325.1:WP_011445240.1 Length = 276 Score = 262 bits (669), Expect = 7e-75 Identities = 136/271 (50%), Positives = 175/271 (64%) Query: 6 ILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQHTGFT 65 I +GL+GR I SR+P LH+ EG A L Y L D L DSAL ++ + GF Sbjct: 3 IRSGLVGRSILASRSPDLHQGEGRALGLEVSYELFDFTARDLPDSALAEVIGTLRDDGFA 62 Query: 66 GLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRGLPDV 125 G N+TYPFKQAI+PLLDEL + A +GAVNTV +++G+ +G+NTD +GF + +GLP Sbjct: 63 GFNVTYPFKQAIVPLLDELDESALAVGAVNTVAIREGRLIGYNTDMIGFRLSMEQGLPGA 122 Query: 126 ARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAVLGTD 185 +VVQ+GAGGAG+AVA+ALL GV RLVL +VD RA+ L L F + G Sbjct: 123 RLERVVQLGAGGAGAAVANALLSLGVRRLVLVDVDPARAEQLRSELAARFPGQDVECGAP 182 Query: 186 LATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARALGCR 245 ADG+VN TP+GM PG PLP E + R WVA+IIYFP ETELLR A++ GC Sbjct: 183 GTLDTTGADGIVNATPIGMNGKPGMPLPPEKIAARQWVADIIYFPRETELLRVAKSKGCA 242 Query: 246 TLDGSNMAVFQAVKAFELFSGRQADAARMQA 276 T++G M V QA +AFE+ +G ADA RM+A Sbjct: 243 TINGVGMVVGQAARAFEIITGHAADARRMRA 273 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: 219 Number of extensions: 8 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: 276 Length adjustment: 26 Effective length of query: 256 Effective length of database: 250 Effective search space: 64000 Effective search space used: 64000 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