Align shikimate dehydrogenase (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 15811 b1692 quinate/shikimate 5-dehydrogenase, NAD(P)-binding (NCBI)
Query= BRENDA::Q6PUG0 (521 letters) >FitnessBrowser__Keio:15811 Length = 288 Score = 115 bits (287), Expect = 3e-30 Identities = 97/299 (32%), Positives = 140/299 (46%), Gaps = 32/299 (10%) Query: 236 MDTDTK--VFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDD--LKEFFRVYSSPD 291 MD K + GL++ P+ HS P + N G Y+ VD+ + Sbjct: 1 MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALK 60 Query: 292 FAGFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDA 351 G V +P K+ + DE+ P AK +GA+NTI+ DG L GYNTD I AI+++ Sbjct: 61 MRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVND--DGYLRGYNTDGTGHIRAIKES 118 Query: 352 LKVNGLTNGAAFLPSPLAGKLFVLVGAGGAGRAL-AFGAKSRRAEIVIF---DIDFDRAK 407 + GK VL+GAGGA A+ A GA EI +F D FD+A Sbjct: 119 -------------GFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKAL 165 Query: 408 ALAAAVSGE---ALPFENLASFQPEKGA-----ILANATPIGMHPNKDRIPVSEAS-LKD 458 A A V+ + +LA Q A IL N T +GM P ++ V++ S L Sbjct: 166 AFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHP 225 Query: 459 YVVVFDAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFTRTKAPEEFMRDIV 517 ++V + VY P T LL+ A+ AG T+ G M L Q QF L+T P E+++ ++ Sbjct: 226 GLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVM 284 Lambda K H 0.320 0.138 0.405 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: 8 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: 521 Length of database: 288 Length adjustment: 30 Effective length of query: 491 Effective length of database: 258 Effective search space: 126678 Effective search space used: 126678 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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