Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_012502877.1 CPAR_RS08355 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000020505.1:WP_012502877.1 Length = 296 Score = 126 bits (316), Expect = 1e-33 Identities = 97/298 (32%), Positives = 142/298 (47%), Gaps = 38/298 (12%) Query: 241 KVFGLISKPVGHSKGPILHNPTFRHVGYNGIYV------PMFVDDLKEFFRVYSSPDFAG 294 KVFGLI + V +S P++HN F+ +G IY P V + R AG Sbjct: 8 KVFGLIGRNVDYSWSPLIHNTAFQALGLPSIYTIFNIAAPELVGNALTGARALG---IAG 64 Query: 295 FSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKV 354 F+V IPYK+ VV F DE+ P A++IGAVNTI+ +G+L G+NTD + Sbjct: 65 FNVTIPYKKTVVPFLDELSPEAQAIGAVNTIVND--NGRLTGHNTD-------------I 109 Query: 355 NGLTNGAAFLPSPLAGKLFVLVGAGGAGRAL--AFGAKSRRAEIVIFDIDFDRAKALAAA 412 G + + GK + G GGA A AF + + + + ++A+A+ Sbjct: 110 AGFAAPLLPMAEQIHGKPVCIFGNGGAALAAVEAFRLHFHPSSVRLMVRNLEKAEAMLEG 169 Query: 413 VSGEALPFENL-ASFQPEKG-------AILANATPIGMHPNKDRI----PVSEASLKDYV 460 + L L A G ++ NATPIG D I P L + Sbjct: 170 YAHRELVEPCLTAELDTPDGERLLGECCVIVNATPIGTAGRSDAIQSVVPARRKLLHEGQ 229 Query: 461 VVFDAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFTRTKAPEEFMRDIVM 518 +V+D VY P +T LL +A AAGA T+SG+EM + QA F ++T + P + +R V+ Sbjct: 230 IVYDMVYNPLETPLLAEARAAGAETISGIEMLIGQAARSFSIWTGQEMPVDTVRKTVL 287 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: 318 Number of extensions: 13 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: 521 Length of database: 296 Length adjustment: 31 Effective length of query: 490 Effective length of database: 265 Effective search space: 129850 Effective search space used: 129850 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 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