Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate AZOBR_RS01765 AZOBR_RS01765 shikimate 5-dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >FitnessBrowser__azobra:AZOBR_RS01765 Length = 279 Score = 131 bits (329), Expect = 4e-35 Identities = 98/267 (36%), Positives = 142/267 (53%), Gaps = 21/267 (7%) Query: 264 GIIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLV--DDVASFLQTYSSTDFAGFSCTIPH 321 G++G P+GHS+SP L+ + G DG ++ L V D + ++ + F G + T+PH Sbjct: 11 GVMGWPIGHSRSPRLHGYWLEQYGIDGAYVPLAVPPDRIEQAIRALPALGFRGCNVTVPH 70 Query: 322 KEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQNGNSA 381 KEAA + D +D AK +GAVN I+ + + L G NTD G I + LR G A Sbjct: 71 KEAACRTVDRLDATAKRMGAVNTIVVGE-NGSLEGRNTDGFGFI----ENLRSGAPGWKA 125 Query: 382 GASPLNGKLFVVIGAGGAGKALGYGAKEKGA-RVVIANRTYDRARELAETIGGDALSLAD 440 P +VIGAGGA +A+ ++GA RV + NRT RA ELA IGG A+ AD Sbjct: 126 ADGPA-----LVIGAGGAARAVVASLLDEGAPRVWLVNRTRARADELAADIGG-AIETAD 179 Query: 441 LENFHP--EDGMILANTTSIGM--QPKVDETPIPKHALKHYSLVFDAVYTPKITRLLKEA 496 + E ++ NTT+ GM QP ++ + AL ++V D VYTP +T LL A Sbjct: 180 WVSRETLLEGAALVVNTTTQGMAGQPPLE---LNLRALPGSAVVTDIVYTPLMTPLLTAA 236 Query: 497 EECGATIVSGLEMFIGQAYGQYERYTG 523 + G +V G+ M + QA + + G Sbjct: 237 QARGNRVVDGVGMLLHQARPGFAAWFG 263 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: 300 Number of extensions: 12 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: 538 Length of database: 279 Length adjustment: 30 Effective length of query: 508 Effective length of database: 249 Effective search space: 126492 Effective search space used: 126492 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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