Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate Pf6N2E2_5061 Quinate/shikimate 5-dehydrogenase I delta (EC 1.1.1.25)
Query= BRENDA::Q88K85 (282 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5061 Length = 285 Score = 427 bits (1098), Expect = e-124 Identities = 215/278 (77%), Positives = 238/278 (85%) Query: 1 MSQQAILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQ 60 MS +LAGLIG GIQ SRTPALHEHEGDAQ +RYLYRLID D L+LD ALP LL+AA+ Sbjct: 3 MSNITVLAGLIGAGIQASRTPALHEHEGDAQGMRYLYRLIDLDALKLDSGALPDLLKAAE 62 Query: 61 HTGFTGLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRR 120 FTGLNIT+P KQAI+PLLDELS EARGIGAVNTVVLKDGKR+GHNTDCLGFAEG RR Sbjct: 63 RMSFTGLNITFPCKQAIIPLLDELSPEARGIGAVNTVVLKDGKRIGHNTDCLGFAEGFRR 122 Query: 121 GLPDVARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERA 180 GL DVARR+VVQMGAGGAG+AVAHALL EGV+ L +F+V+ +RA+AL +NLN HFG RA Sbjct: 123 GLGDVARRRVVQMGAGGAGAAVAHALLAEGVQTLSIFDVEVSRAEALANNLNQHFGVGRA 182 Query: 181 VLGTDLATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAAR 240 G DL+ A+AEADGLVNTTP+GMAKLPG P+PVELLH +LWVAEI+YFPLETELLR AR Sbjct: 183 RAGHDLSAAMAEADGLVNTTPMGMAKLPGMPVPVELLHGQLWVAEIVYFPLETELLRNAR 242 Query: 241 ALGCRTLDGSNMAVFQAVKAFELFSGRQADAARMQAHF 278 ALGCRTLDG NMAVFQAVKAFELFSG DA RM HF Sbjct: 243 ALGCRTLDGGNMAVFQAVKAFELFSGVAPDAQRMLEHF 280 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: 288 Number of extensions: 1 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: 285 Length adjustment: 26 Effective length of query: 256 Effective length of database: 259 Effective search space: 66304 Effective search space used: 66304 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