Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase 1; ADH synthase 1; ADHS 1; ADTH synthase 1; EC 2.2.1.10 (uncharacterized)
to candidate 15638 b1517 hypothetical protein (NCBI)
Query= curated2:O30009 (260 letters) >FitnessBrowser__Keio:15638 Length = 291 Score = 135 bits (340), Expect = 1e-36 Identities = 83/251 (33%), Positives = 139/251 (55%), Gaps = 5/251 (1%) Query: 6 GKRRRMSRIM--KNGRTVILPMDHGITK-PEKGIEKVDRVVEEVQDYIDAVIVHKGVAKR 62 G + R+SRI K G+TV+L DHG + P G+E++D + + ++ D ++ +G+ R Sbjct: 35 GMQSRLSRIFNPKTGKTVMLAFDHGYFQGPTTGLERIDINIAPLFEHADVLMCTRGIL-R 93 Query: 63 SAVLADIDAALIIHLSASTSLAPDPNDKRIVTSVEKAIALGADAVSIHVNIGSKTEAEQI 122 S V + +++ S + S+ + +++ + S++ A+ L + AV+ V IGS+ E + I Sbjct: 94 SVVPPATNRPVVLRASGANSILAELSNEAVALSMDDAVRLNSCAVAAQVYIGSEYEHQSI 153 Query: 123 EKAGTISEICDDYGIPLLAMMYPRGSIDVTTETVRHAARIGYELGADILKVPYVQS-FEE 181 + + + G+P +A+ + A RI E+GA I+K YV+ FE Sbjct: 154 KNIIQLVDAGMKVGMPTMAVTGVGKDMVRDQRYFSLATRIAAEMGAQIIKTYYVEKGFER 213 Query: 182 VVAVCDIPVVVAGGSKGSEHEFLKRVEDAIAKGAAGVAAGRNVFNSDHPVRIAKALHMIV 241 +VA C +P+V+AGG K E E L+ AI +GA+GV GRN+F SDHPV + KA+ +V Sbjct: 214 IVAGCPVPIVIAGGKKLPEREALEMCWQAIDQGASGVDMGRNIFQSDHPVAMMKAVQAVV 273 Query: 242 HGNMHMEEVME 252 H N + E Sbjct: 274 HHNETADRAYE 284 Lambda K H 0.319 0.135 0.377 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: 151 Number of extensions: 10 Number of successful extensions: 5 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: 260 Length of database: 291 Length adjustment: 25 Effective length of query: 235 Effective length of database: 266 Effective search space: 62510 Effective search space used: 62510 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 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