Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_034999703.1 DL88_RS19030 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000745425.1:WP_034999703.1 Length = 280 Score = 130 bits (326), Expect = 8e-35 Identities = 98/281 (34%), Positives = 144/281 (51%), Gaps = 21/281 (7%) Query: 245 LISKPVGHSKGPILHNPTFRHVGYNGIYVPMFV--DDLKEFFRVYSSPDFAGFSVGIPYK 302 +I P+ HS+ P++HN + G +G Y V ++L EF R + F G +V +P+K Sbjct: 11 VIGYPIKHSRSPLIHNFWLKRYGISGTYEKREVAPEELAEFLRDLENNGFVGANVTLPHK 70 Query: 303 EAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNGLTNGAA 362 E+ CDEV A+ +GAVNT+ QR DG+LIG+NTD E + A++ AA Sbjct: 71 ESAFGLCDEVSDEARQLGAVNTLYQR--DGRLIGHNTDGEGFLAALDQE---------AA 119 Query: 363 FLPSPLAGKLFVLVGAGGAGRALAFGAKSRRA-EIVIFDIDFDRAKALAAAVSGEALPFE 421 +PL + V++GAGGA RAL F R A E+ I + R++ +AA G + Sbjct: 120 GWDAPL--RRAVVIGAGGAARALVFALLRRGAEEVAIVNRTLARSQEIAAQ-GGPRVTCH 176 Query: 422 NLASFQP--EKGAILANATPIGMHPNKDRIPVSEASLKDYVVVFDAVYTPRKTTLLKDAE 479 +L + +L NAT +GM + + + A L VV D VY P +T LL+ A Sbjct: 177 SLEDLPELLKTTDLLVNATSLGM-VGQAPLVIDLAPLPPNAVVDDIVYVPLETDLLRQAR 235 Query: 480 AAGAITVSGVEMFLRQAIGQFHL-FTRTKAPEEFMRDIVMA 519 G V G+ M L QA+ F L F RT +R ++ A Sbjct: 236 ERGLRCVGGLGMLLYQAVPGFRLWFGRTPEVTPELRALIEA 276 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: 307 Number of extensions: 18 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: 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