Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_042443295.1 AZL_RS15340 shikimate 5-dehydrogenase
Query= BRENDA::Q88GF6 (273 letters) >NCBI__GCF_000010725.1:WP_042443295.1 Length = 278 Score = 339 bits (870), Expect = 3e-98 Identities = 178/278 (64%), Positives = 205/278 (73%), Gaps = 6/278 (2%) Query: 1 MPTTPSRDTVLCISLAGRPGTFGVRFHNHLYQQLGLDFYYKAMRTDDLPAAVAGIRALGI 60 MP RDT LCISL+GRP G RFHNHLY+ L L++ YKA TD+LP A+ GIRALGI Sbjct: 1 MPHKIDRDTRLCISLSGRPSNIGTRFHNHLYEALRLNYAYKAFTTDNLPGAITGIRALGI 60 Query: 61 RGCGVSMPYKEACMALVDEIDPSAAAIESVNTLVN-----CNGHLKAYNTDYLAVRQLLA 115 RGCGVSMP+KEAC+ +DE+DPSAA + SVNT+VN L+ YNTDYLAVR LL Sbjct: 61 RGCGVSMPFKEACIPFLDELDPSAAGLRSVNTIVNDRDDAGGSRLRGYNTDYLAVRTLLD 120 Query: 116 QHQVDPGTAFALRGSGGMAKAVASALRDAGFAEGIIVARNEQAGRQLADVCGYRWVPEPG 175 +H V PG FALRGSGGMA+AV ALRD+GF G ++ARNE+ GR+LA W P+ Sbjct: 121 RHDVSPGLPFALRGSGGMARAVLCALRDSGFTNGRLIARNEETGRRLAAEYSLPWQPDTT 180 Query: 176 DICP-PMLVNVTPIGMAGGLEAEELAFPEHAIAAAERVFDVVAMPAQTPLIRRAQALGKP 234 I +LVNVTP+GMAGG EA LAF IAAA VFDVVAMPA+TPLIR A+ GKP Sbjct: 181 GIAEGSLLVNVTPLGMAGGPEAGTLAFEPGLIAAAAHVFDVVAMPAETPLIRAAREAGKP 240 Query: 235 VITGLEVIALQALEQFVLYTGVRPTREQVDAAVAYARA 272 VITG EVIALQALEQFVLYTGVRPT EQ AA AY++A Sbjct: 241 VITGAEVIALQALEQFVLYTGVRPTEEQAAAAAAYSQA 278 Lambda K H 0.322 0.136 0.406 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: 318 Number of extensions: 11 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: 273 Length of database: 278 Length adjustment: 25 Effective length of query: 248 Effective length of database: 253 Effective search space: 62744 Effective search space used: 62744 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 (21.9 bits) S2: 47 (22.7 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