Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate WP_028313382.1 G491_RS0101915 hypothetical protein
Query= curated2:Q2S0A0 (285 letters) >NCBI__GCF_000429905.1:WP_028313382.1 Length = 345 Score = 104 bits (259), Expect = 3e-27 Identities = 95/312 (30%), Positives = 138/312 (44%), Gaps = 43/312 (13%) Query: 1 MPLDATTQLVTLLGH-PVEHSLSPRIHNTAFRAQDVNAAYVATPVRPEALGDAVAGLRA- 58 + LDAT +LG P + + SP + N AF +++ V PE L A L+A Sbjct: 13 LDLDATEMYAAILGESPSKGAKSPSLWNAAFDGLNISGFMHPMDVVPEKLEQVAAALKAD 72 Query: 59 LQFLGANVTTPHKEAVLPVLDEVTERARAVGAVNTIVRDGGRLHGDNTDIAGFLRPLEER 118 +++G VT P+K ++P LD + A A+GAVN I RDG L G NTD AG + L+ Sbjct: 73 KRYMGGAVTMPYKITLIPFLDRLEPEAEAIGAVNCIYRDGDDLVGTNTDGAGAIHCLKAD 132 Query: 119 GGDALEGAPMLVFGAGGAARAV-VYGLLSHYRPERLTIVARRPDQAEGLAADLAAH---- 173 G+ L G +L+ G GGA AV Y + L + R P+ AE LAA L+ Sbjct: 133 YGEDLAGKTVLLIGTGGAGYAVAAYVAAAIGAGGSLYLANRSPEPAEKLAAKLSVQCKTK 192 Query: 174 ------------DPDGALRVSS--FEEAALSVRTSRLVVNATPLGMAPDR----RGQTPW 215 D D + SS FE + R + ++ TPLG D G+ Sbjct: 193 SVPFPLEAGSFGDVDIVINCSSLGFESSKRDRRGAYSHLHFTPLGPVDDSLRVPLGENVQ 252 Query: 216 PNPVDFTADHV------------------VYDLVYTPEETRLLREAAAEGATPIGGLDML 257 ++ + V V D++Y P ET +L A + G G+ M Sbjct: 253 ARFLEAAREAVSANFAASASRLAGMGKAYVMDIIYQPRETLMLWLAKSLGLRTQNGVAMN 312 Query: 258 VEQAAAAYRQWT 269 +EQA A+ + T Sbjct: 313 LEQAVIAFDKAT 324 Lambda K H 0.318 0.134 0.393 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: 241 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 285 Length of database: 345 Length adjustment: 27 Effective length of query: 258 Effective length of database: 318 Effective search space: 82044 Effective search space used: 82044 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: 48 (23.1 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