Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_010442982.1 G7G_RS0118680 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000192475.1:WP_010442982.1 Length = 277 Score = 100 bits (250), Expect = 5e-26 Identities = 84/262 (32%), Positives = 119/262 (45%), Gaps = 19/262 (7%) Query: 244 GLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVD--DLKEFFRVYSSPDFAGFSVGIPY 301 G+I PV HS+ P LH + G G Y+PM V DL+ F G +V +P+ Sbjct: 10 GVIGHPVAHSRSPKLHGHWLKTYGLAGHYIPMDVAPADLETVLHTLPKAGFVGANVTVPH 69 Query: 302 KEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNGLTNGA 361 KEA + D V A IGA NT++ R DG + NTD + + +G Sbjct: 70 KEAALRLADHVSDRASVIGAANTLVFRE-DGSIHADNTDGYGFMANLRAGAPDWNPADGP 128 Query: 362 AFLPSPLAGKLFVLVGAGGAGRALAFG-AKSRRAEIVIFDIDFDRAKALAAAVSGEALPF 420 A V+ GAGGA RA+ A++ EI++ + RA L Sbjct: 129 A-----------VVFGAGGAARAVLQALAEAGVPEILLTNRTRTRADHLKEEFGQRITVV 177 Query: 421 ENL-ASFQPEKGAILANATPIGMHPNKD-RIPVSEASLKDYVVVFDAVYTPRKTTLLKDA 478 + + A E ++ N T +GM + R+P+ L+ VV D VY P +T LL+ A Sbjct: 178 DWVQAGNVIENAELVVNTTSLGMQGQPELRVPLD--GLQPGAVVTDLVYAPLQTRLLQQA 235 Query: 479 EAAGAITVSGVEMFLRQAIGQF 500 E AG TV G+ M L QA+ F Sbjct: 236 EEAGCTTVDGLGMLLHQAVPGF 257 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: 325 Number of extensions: 18 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: 277 Length adjustment: 30 Effective length of query: 491 Effective length of database: 247 Effective search space: 121277 Effective search space used: 121277 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 Jul 26 2024. The underlying query database was built on Jul 25 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