Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_007472824.1 CMTB2_RS00175 shikimate dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >NCBI__GCF_000170735.1:WP_007472824.1 Length = 255 Score = 113 bits (283), Expect = 7e-30 Identities = 80/255 (31%), Positives = 125/255 (49%), Gaps = 30/255 (11%) Query: 262 VFGIIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLVDDVASFLQTYSSTDFAGFSCTIPH 321 ++ I G PV HSKSPL++N FK +G + ++D + ++ + + G + T+PH Sbjct: 1 MYAIFGNPVSHSKSPLMHNYFFKKSGIKECYGRYKLEDGSKIIEKFKNLKLKGANVTVPH 60 Query: 322 KEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQNGNSA 381 KE A K CDEV +AK I AVN ++ + K+ GYNTD G AI++ Sbjct: 61 KEWAYKLCDEVKGIAKEIKAVNTLLLENN--KIIGYNTDAPGFKEAIKE----------- 107 Query: 382 GASPLNGKLFVVIGAGGAGKALGYGAKEKGARVVIANRT-YDRARELAETIGGDALSLAD 440 + K ++IGAGG KA+ +V+ N T +R++ E L Sbjct: 108 ----FDYKKPLIIGAGGTAKAIS---------LVLKNPTILNRSKNRFEYFEKKGLKTYT 154 Query: 441 LENFHPEDGMILANTTSIGMQPKVDETP--IPKHALKHYSLVFDAVYTPKITRLLKEAEE 498 +N + D ++ NTTS G+ +V TP I + K+ D +Y K T LKEA++ Sbjct: 155 WDNINEFDFDLIINTTSAGLSEEVLPTPKEIIEKLFKNAKFCVDVIY-GKETLFLKEAKK 213 Query: 499 CGATIVSGLEMFIGQ 513 +GL+M + Q Sbjct: 214 YNLLFKTGLDMLVYQ 228 Lambda K H 0.317 0.135 0.385 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: 308 Number of extensions: 16 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: 538 Length of database: 255 Length adjustment: 30 Effective length of query: 508 Effective length of database: 225 Effective search space: 114300 Effective search space used: 114300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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