Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_085979190.1 SACCYDRAFT_RS09245 shikimate dehydrogenase
Query= BRENDA::A0A5H2WZU5 (532 letters) >NCBI__GCF_000244975.1:WP_085979190.1 Length = 284 Score = 95.9 bits (237), Expect = 2e-24 Identities = 88/284 (30%), Positives = 134/284 (47%), Gaps = 31/284 (10%) Query: 257 GVIGKPIGHSKSPHLYNAAFKSVNFNGIYLP---LLVDNVANFINAYSSPDFVGYSYTIP 313 GV+G P+ HS SP L+NAA+ ++ G + + +++ F++A ++VG S T+P Sbjct: 7 GVLGSPVRHSLSPVLHNAAYTALGLAGWHYDTHEVDAESLPEFVHALGD-EWVGLSVTMP 65 Query: 314 HKEDGLRCCDEVDPIAKAIGAISQMIRRPTDGKMIGYNVDYLGAIAAIEEALRASNGASP 373 K L DEV A A+ A + ++R P+ G + D + + ALRA+ G Sbjct: 66 GKRAALAVADEVTQRALAVEAANTLVRLPSGG----WRADCTD-VDGVAGALRAAGGLRS 120 Query: 374 TTTSPLAGKLFVVIGAGGAGKALAYGAMEKGA---RVVVANRTYEKAKELASKVGGQAIT 430 G+ VV+GAGG A E G VVV +A A++ G A++ Sbjct: 121 GE-----GRTAVVLGAGGTASAAVTALGELGVADVHVVVREPARAQATTEAARRAGLAVS 175 Query: 431 L---AELENFHPEDG-MVLANTTSV-GMKPNV-DLTPLPKNALSRYCLVFDAIYTPKLTR 484 + AE + G VL NT + P+V +L +P V D IY P T Sbjct: 176 VHRWAEADFGALATGAQVLVNTVPPEAVAPHVGELAAVP--------CVLDVIYHPWPTP 227 Query: 485 LLREAQEVGAIPVYGTEMFINQAFVQFERFTGYPAPKQLIRDTL 528 L G +M ++QAF Q E+FTG PAP++++RD L Sbjct: 228 LAEAVTARDGRVATGLDMLLHQAFGQVEQFTGRPAPREVMRDAL 271 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: 300 Number of extensions: 13 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: 532 Length of database: 284 Length adjustment: 30 Effective length of query: 502 Effective length of database: 254 Effective search space: 127508 Effective search space used: 127508 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 (21.7 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