Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate AO353_06175 AO353_06175 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >FitnessBrowser__pseudo3_N2E3:AO353_06175 Length = 284 Score = 112 bits (280), Expect = 2e-29 Identities = 90/279 (32%), Positives = 133/279 (47%), Gaps = 30/279 (10%) Query: 239 DTKVFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDDLK-------EFFRVYSSPD 291 +T + GLI + S+ P LH G +Y + +D LK + + Sbjct: 5 NTVLAGLIGAGIQASRTPALHEREGDAQGLRYLYRLIDLDQLKLDSGALPDLLMSAERMN 64 Query: 292 FAGFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDA 351 F G ++ P K+A++ DE+ P A+ IGAVNT++ + DGK IG+NTDC Sbjct: 65 FTGLNITFPCKQAIIPLLDELSPEARGIGAVNTVVLK--DGKRIGHNTDCLGFAEGFRRG 122 Query: 352 LKVNGLTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRA-EIVIFDIDFDRAKALA 410 LK A + V +GAGGAG A+A S ++ IFD+D RA++LA Sbjct: 123 LK-------------DAARERVVQMGAGGAGAAVAHALLSEGVQQLSIFDVDVSRAQSLA 169 Query: 411 AAV-----SGEALPFENLASFQPEKGAILANATPIGMHPNKDRIPVSEASLKDYVVVFDA 465 + SG A +L S + L N TP+GM +PV L+ + V + Sbjct: 170 NNLNQHFGSGRACAGSDLPSALAQADG-LVNTTPMGM-AKLPGMPVPVELLRAELWVAEI 227 Query: 466 VYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFT 504 VY P +T LL++A A G T+ G M + QA+ F LF+ Sbjct: 228 VYFPLETELLRNARALGCRTLDGGNMAVFQAVKAFELFS 266 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: 274 Number of extensions: 19 Number of successful extensions: 4 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: 284 Length adjustment: 30 Effective length of query: 491 Effective length of database: 254 Effective search space: 124714 Effective search space used: 124714 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