Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate PfGW456L13_1427 Quinate/shikimate 5-dehydrogenase I delta (EC 1.1.1.25)
Query= BRENDA::Q6PUG0 (521 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1427 Length = 287 Score = 105 bits (263), Expect = 2e-27 Identities = 88/279 (31%), Positives = 131/279 (46%), Gaps = 40/279 (14%) Query: 244 GLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDDLK-------EFFRVYSSPDFAGFS 296 GLI + S+ P +H G +Y + +D LK + ++ G + Sbjct: 13 GLIGAGIQASRTPAMHEHEGDAQGLRYLYRLIDLDQLKLDSNALPDLLMAAERMNYTGLN 72 Query: 297 VGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNG 356 + P K+A++ DE+ P A+ IGAVNT++ + DGK IG+NTDC LK Sbjct: 73 ITFPCKQAIIPLLDELSPEARGIGAVNTVVLK--DGKRIGHNTDCLGFAEGFRRGLK--- 127 Query: 357 LTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRA-EIVIFDIDFDRAKALA----- 410 +A + V +GAGGAG A+A S ++ IFD+D RA+ LA Sbjct: 128 ----------GVAVERVVQMGAGGAGAAVAHALLSEGVQQLSIFDVDIRRAQDLADNLNQ 177 Query: 411 -----AAVSGEALPFENLASFQPEKGAILANATPIGMHPNKDRIPVSEASLKDYVVVFDA 465 AV+G LP + +A L N TP+GM +PV L+ + V + Sbjct: 178 HFGVSRAVAGYDLP-DAMAQADG-----LVNTTPMGM-KKLPGMPVPVELLRAELWVAEI 230 Query: 466 VYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFT 504 VY P +T LL++A A G T+ G M + QA+ F LF+ Sbjct: 231 VYFPLETELLRNARALGCRTLDGGNMAVFQAVKAFELFS 269 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: 268 Number of extensions: 19 Number of successful extensions: 3 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: 287 Length adjustment: 30 Effective length of query: 491 Effective length of database: 257 Effective search space: 126187 Effective search space used: 126187 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 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