Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_012673490.1 SULAZ_RS07145 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000021545.1:WP_012673490.1 Length = 280 Score = 113 bits (282), Expect = 1e-29 Identities = 89/291 (30%), Positives = 135/291 (46%), Gaps = 31/291 (10%) Query: 236 MDTDTKVFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFV--DDLKEFFRVYSSPDFA 293 +D TKV+G+ PV HSK P F H+G N +YVP V +DL++ A Sbjct: 3 LDGQTKVYGIFGYPVKHSKSPTFQTAAFLHLGINAVYVPFEVNPNDLEKAVESLKVLKIA 62 Query: 294 GFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALK 353 G ++ IP+KE V+++ +E+ K I A NTI + DG LI YNTD Sbjct: 63 GVNITIPHKENVINYVNELSEEVKIIKAANTI--KNIDGYLIAYNTDW------------ 108 Query: 354 VNGLTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRAE-IVIFDIDFDRAKALAAA 412 G G L L K +++GAGG+ RA+ +G + I + + + L Sbjct: 109 -IGFVEGLKELEPNLEDKRVLVIGAGGSSRAVVYGLLRENVDKIYLANRTLPKVYNLIQE 167 Query: 413 VSGEALPFENL---ASFQPEKG-----AILANATPIGMHPNKDRIPVSEAS-LKDYVVVF 463 + + S Q +G I+ N T +G+ N + P+ + S LKD +V Sbjct: 168 YKSHFRIIDKIITPISLQDIEGFLNNVDIIVNTTSVGL--NDEDFPLFDYSLLKDSHIVV 225 Query: 464 DAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFTRTKAPEEFMR 514 D +Y ++T LLK A+ G +G M + Q F ++T KAP E M+ Sbjct: 226 DIIY--KETKLLKVAKEKGCKHQNGFPMLIYQGAKSFEIWTGQKAPVEIMK 274 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: 356 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 280 Length adjustment: 30 Effective length of query: 491 Effective length of database: 250 Effective search space: 122750 Effective search space used: 122750 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 10 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