Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_041456249.1 AVA_RS15705 shikimate dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >NCBI__GCF_000204075.1:WP_041456249.1 Length = 293 Score = 134 bits (336), Expect = 6e-36 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 28/268 (10%) Query: 260 TKVFGIIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLV--DDVASFLQTYSSTDFAGFSC 317 TK+ G+IG PV HS SP+++N A G D V+L + D++ + + ++ GFS Sbjct: 10 TKLLGVIGHPVEHSLSPVMHNAAIAQLGLDYVYLPFPIAPDNLEAAIALLATIGVVGFSV 69 Query: 318 TIPHKEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQN 377 TIPHK+A + E+ PVA++IGAVN + R+ + + G NTD G I+ ++ + + Sbjct: 70 TIPHKQAIIPLLAEISPVAQAIGAVNTVTRQNN--QWVGTNTDIEGFIAPLQTTYKRDWS 127 Query: 378 GNSAGASPLNGKLFVVIGAGGAGKALGYGAKEKG-ARVVIANRTYDRARELAETIGGDAL 436 A V++G GGA +A+ G + G A + + R R E + D Sbjct: 128 QQIA----------VILGNGGAARAVVAGCYQLGFAEIHVVGRNVQRLEEFRHS--WDNS 175 Query: 437 SLADLENFHPEDGM--------ILANTTSIGMQPKVDETPIPKHALKHY---SLVFDAVY 485 +A+ H D + +L NTT IGM P+VDE+P+ L + ++ +D +Y Sbjct: 176 PIAENLQVHTWDYLAKLVPQANLLVNTTPIGMYPQVDESPLSTEELANLQTGAIAYDLIY 235 Query: 486 TPKITRLLKEAEECGATIVSGLEMFIGQ 513 PK T+ L++A++ GA + GLEM + Q Sbjct: 236 IPKPTQFLQKAQQQGAIAIDGLEMLVQQ 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: 316 Number of extensions: 15 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: 293 Length adjustment: 31 Effective length of query: 507 Effective length of database: 262 Effective search space: 132834 Effective search space used: 132834 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 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