Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate PfGW456L13_1427 Quinate/shikimate 5-dehydrogenase I delta (EC 1.1.1.25)
Query= BRENDA::Q88K85 (282 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1427 Length = 287 Score = 417 bits (1072), Expect = e-121 Identities = 212/275 (77%), Positives = 231/275 (84%) Query: 6 ILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQHTGFT 65 ILAGLIG GIQ SRTPA+HEHEGDAQ LRYLYRLID DQL+LD +ALP LL AA+ +T Sbjct: 10 ILAGLIGAGIQASRTPAMHEHEGDAQGLRYLYRLIDLDQLKLDSNALPDLLMAAERMNYT 69 Query: 66 GLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRGLPDV 125 GLNIT+P KQAI+PLLDELS EARGIGAVNTVVLKDGKR+GHNTDCLGFAEG RRGL V Sbjct: 70 GLNITFPCKQAIIPLLDELSPEARGIGAVNTVVLKDGKRIGHNTDCLGFAEGFRRGLKGV 129 Query: 126 ARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAVLGTD 185 A +VVQMGAGGAG+AVAHALL EGV++L +F+VD RAQ L DNLN HFG RAV G D Sbjct: 130 AVERVVQMGAGGAGAAVAHALLSEGVQQLSIFDVDIRRAQDLADNLNQHFGVSRAVAGYD 189 Query: 186 LATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARALGCR 245 L A+A+ADGLVNTTP+GM KLPG P+PVELL LWVAEI+YFPLETELLR ARALGCR Sbjct: 190 LPDAMAQADGLVNTTPMGMKKLPGMPVPVELLRAELWVAEIVYFPLETELLRNARALGCR 249 Query: 246 TLDGSNMAVFQAVKAFELFSGRQADAARMQAHFAS 280 TLDG NMAVFQAVKAFELFSG DA RM HF S Sbjct: 250 TLDGGNMAVFQAVKAFELFSGVVPDAQRMLEHFQS 284 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: 280 Number of extensions: 3 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: 287 Length adjustment: 26 Effective length of query: 256 Effective length of database: 261 Effective search space: 66816 Effective search space used: 66816 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