Align shikimate dehydrogenase (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Pf6N2E2_5061 Quinate/shikimate 5-dehydrogenase I delta (EC 1.1.1.25)
Query= BRENDA::Q6PUG0 (521 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5061 Length = 285 Score = 111 bits (277), Expect = 4e-29 Identities = 89/282 (31%), Positives = 134/282 (47%), Gaps = 30/282 (10%) Query: 236 MDTDTKVFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDDLK-------EFFRVYS 288 M T + GLI + S+ P LH G +Y + +D LK + + Sbjct: 3 MSNITVLAGLIGAGIQASRTPALHEHEGDAQGMRYLYRLIDLDALKLDSGALPDLLKAAE 62 Query: 289 SPDFAGFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAI 348 F G ++ P K+A++ DE+ P A+ IGAVNT++ + DGK IG+NTDC Sbjct: 63 RMSFTGLNITFPCKQAIIPLLDELSPEARGIGAVNTVVLK--DGKRIGHNTDC------- 113 Query: 349 EDALKVNGLTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRAE-IVIFDIDFDRAK 407 G G +A + V +GAGGAG A+A + + + IFD++ RA+ Sbjct: 114 ------LGFAEGFRRGLGDVARRRVVQMGAGGAGAAVAHALLAEGVQTLSIFDVEVSRAE 167 Query: 408 ALAAAVS-----GEALPFENLASFQPEKGAILANATPIGMHPNKDRIPVSEASLKDYVVV 462 ALA ++ G A +L++ E L N TP+GM +PV L + V Sbjct: 168 ALANNLNQHFGVGRARAGHDLSAAMAEADG-LVNTTPMGM-AKLPGMPVPVELLHGQLWV 225 Query: 463 FDAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFT 504 + VY P +T LL++A A G T+ G M + QA+ F LF+ Sbjct: 226 AEIVYFPLETELLRNARALGCRTLDGGNMAVFQAVKAFELFS 267 Lambda K H 0.320 0.138 0.405 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: 270 Number of extensions: 18 Number of successful extensions: 5 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: 521 Length of database: 285 Length adjustment: 30 Effective length of query: 491 Effective length of database: 255 Effective search space: 125205 Effective search space used: 125205 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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