Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate GFF4776 PS417_24435 shikimate dehydrogenase
Query= BRENDA::Q88K85 (282 letters) >FitnessBrowser__WCS417:GFF4776 Length = 282 Score = 412 bits (1060), Expect = e-120 Identities = 211/275 (76%), Positives = 232/275 (84%) Query: 6 ILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQHTGFT 65 ILAGLIG GIQ SRTPALHE EGDA+ LRYLYRLID + L LD +ALP LL+AA+ FT Sbjct: 5 ILAGLIGAGIQASRTPALHEQEGDARGLRYLYRLIDLEPLHLDTNALPHLLDAAELMHFT 64 Query: 66 GLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRGLPDV 125 GLNITYP KQAILPLLDELSDEARGIGAVNTVV KDGKR+GHNTDCLGFAEG RR L DV Sbjct: 65 GLNITYPCKQAILPLLDELSDEARGIGAVNTVVFKDGKRIGHNTDCLGFAEGFRRNLKDV 124 Query: 126 ARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAVLGTD 185 AR++VVQMGAGGAG+AVAHALL EGV++L +F+VD +RA+ LVDNL FG RA +G+ Sbjct: 125 ARQRVVQMGAGGAGAAVAHALLAEGVQQLSIFDVDISRARDLVDNLAQRFGTGRAQVGSQ 184 Query: 186 LATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARALGCR 245 L A+AEADGLVNTTP+GMAKLPGTP+P LL LWVAEI+YFPLETELLR ARALGCR Sbjct: 185 LENAMAEADGLVNTTPMGMAKLPGTPVPATLLRTELWVAEIVYFPLETELLRDARALGCR 244 Query: 246 TLDGSNMAVFQAVKAFELFSGRQADAARMQAHFAS 280 TLDG NMAVFQAVKAFELFSG DA RM AHF S Sbjct: 245 TLDGGNMAVFQAVKAFELFSGEVPDAQRMLAHFQS 279 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: 289 Number of extensions: 5 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: 282 Length adjustment: 26 Effective length of query: 256 Effective length of database: 256 Effective search space: 65536 Effective search space used: 65536 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 09 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