Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate GFF2043 PS417_10420 shikimate dehydrogenase
Query= BRENDA::Q88GF6 (273 letters) >FitnessBrowser__WCS417:GFF2043 Length = 272 Score = 373 bits (957), Expect = e-108 Identities = 185/271 (68%), Positives = 218/271 (80%) Query: 1 MPTTPSRDTVLCISLAGRPGTFGVRFHNHLYQQLGLDFYYKAMRTDDLPAAVAGIRALGI 60 M P++DT LC+SL+ RPG FG+RFHNHLY+QLGL+FYYKA + DLP A+ GIRALG+ Sbjct: 1 MQMHPNKDTQLCMSLSARPGNFGLRFHNHLYEQLGLNFYYKAFSSQDLPGAIGGIRALGV 60 Query: 61 RGCGVSMPYKEACMALVDEIDPSAAAIESVNTLVNCNGHLKAYNTDYLAVRQLLAQHQVD 120 RGCGVSMP+KEA +ALVDE+D S AI+S+NT+VN +GHLKAYNTDY+A+ QLL +H V Sbjct: 61 RGCGVSMPFKEAAIALVDELDDSVQAIDSLNTIVNTDGHLKAYNTDYIAIEQLLKKHAVP 120 Query: 121 PGTAFALRGSGGMAKAVASALRDAGFAEGIIVARNEQAGRQLADVCGYRWVPEPGDICPP 180 + FALRGSGGMAKAVASALRD G+A G+IVARNE AGR LA GY W E D+ P Sbjct: 121 KDSTFALRGSGGMAKAVASALRDGGYANGVIVARNEAAGRALAQNLGYAWRAELADMRPQ 180 Query: 181 MLVNVTPIGMAGGLEAEELAFPEHAIAAAERVFDVVAMPAQTPLIRRAQALGKPVITGLE 240 ML+NVTPIGM GG EA+ LAF A+ AE VFDVVA+P++TPLI R +A GK VITGLE Sbjct: 181 MLINVTPIGMTGGAEADALAFDADAVDVAETVFDVVAIPSETPLIVRGRAQGKRVITGLE 240 Query: 241 VIALQALEQFVLYTGVRPTREQVDAAVAYAR 271 VIA+QALEQFVLYTGVRPT EQ AAVA+AR Sbjct: 241 VIAIQALEQFVLYTGVRPTDEQFQAAVAFAR 271 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: 309 Number of extensions: 3 Number of successful extensions: 1 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: 272 Length adjustment: 25 Effective length of query: 248 Effective length of database: 247 Effective search space: 61256 Effective search space used: 61256 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 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