Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_078717840.1 B5D49_RS11430 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_900167125.1:WP_078717840.1 Length = 268 Score = 112 bits (281), Expect = 1e-29 Identities = 88/268 (32%), Positives = 128/268 (47%), Gaps = 27/268 (10%) Query: 243 FGLISKPVGHSKGPILHNPTFRHVGYNGIY----VPMFVDDLKEFFRVYSSPDFAGFSVG 298 +G+I P+GHS P LHN F + +Y P D L F + + G SV Sbjct: 4 YGIIGHPLGHSLSPALHNWGFARWSMDAVYDFWDTPP--DSLAAFVDRVRAENIRGVSVT 61 Query: 299 IPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNGLT 358 IP+K ++ D V A++IGAVNTI G+L G NTD + + + Sbjct: 62 IPHKRTIMPLLDRVSTTARAIGAVNTICWDE-HGRLRGTNTDVAGCLEPLRRVI------ 114 Query: 359 NGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRAEIV-IFDIDFDRAKALAAAVSGEA 417 P P K +++GAGGA RA E V + + + ++A ALA S A Sbjct: 115 ------PKP---KTALVLGAGGAARAAIAALNQLGVEWVGVSNRNPEKADALALEFSIHA 165 Query: 418 LPFENLASFQPEKGAILANATPIGMH-PNKDRIPVSEASLKDYVVVFDAVYTPRKTTLLK 476 + ++ + +L NATP+GM P + + P +L VFD VY P +T LL Sbjct: 166 VRWDERHKNPCD---VLVNATPLGMSGPYQGQNPWPMKALPQDTTVFDLVYNPLETPLLA 222 Query: 477 DAEAAGAITVSGVEMFLRQAIGQFHLFT 504 A+ G +SG+EMFL Q + QFH++T Sbjct: 223 LAKTCGCGRISGLEMFLHQGLKQFHIWT 250 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: 303 Number of extensions: 17 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: 268 Length adjustment: 30 Effective length of query: 491 Effective length of database: 238 Effective search space: 116858 Effective search space used: 116858 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: 49 (23.5 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