Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase; ADH synthase; ADHS; ADTH synthase; EC 2.2.1.10 (uncharacterized)
to candidate WP_068171231.1 HTA01S_RS11570 aldolase
Query= curated2:Q9HSB8 (265 letters) >NCBI__GCF_001592305.1:WP_068171231.1 Length = 282 Score = 105 bits (263), Expect = 8e-28 Identities = 83/270 (30%), Positives = 131/270 (48%), Gaps = 21/270 (7%) Query: 6 KTARLNRISTDDRLLTIPMDHGITL--GAIDGLVDIEATIREVTANGADAVLTQPGIAPR 63 KTARLNR+ ++ R L I +DHG+ ++GL D+ + ++ A G DA+ G + Sbjct: 5 KTARLNRLLSNGRCLDIALDHGVCNEPSFLNGLEDMPQVMDKLVAAGPDAIQLNYGQSDL 64 Query: 64 VH--PNKGDAGYIVHL------NASTTLGPDQTDKRRTGTVEDAVRAGADAVSFHINVGS 115 + P + ++ + NA+ + V AV+ A V ++ + Sbjct: 65 LQDRPGRNKPALVMRIDMGNPYNATAHRVMWAVLQNEHDPVLPAVQRDAACVVVNLFMLP 124 Query: 116 DHEPDQ----ITALADVAADADRLGVP------VLAMAYARGPGVDEHDAANLGHAVRLA 165 D EPD + +A V AD DR G+P V+ A+G + + DA + VRLA Sbjct: 125 D-EPDLFRQCVQNIARVRADCDRYGMPLMIEPLVMRPHSAQGGYMVDGDAEKIVTLVRLA 183 Query: 166 EEVGADVIKTAYSGSTESFQRVVDATAKPVIIAGGDPAGDRETLQGIRDAMDAGAAGVST 225 E+GAD++K + F RVV A PV++ GG ++ R MD GA+G+ Sbjct: 184 REMGADIVKADPTTDPTDFHRVVQAARCPVLVRGGGREDLQQVFARSRVLMDQGASGMVY 243 Query: 226 GRTVFQHATPGAMTAAISAVVHDDADPEAA 255 GR V+QHA P A+ +A+ A++H A A Sbjct: 244 GRNVYQHANPSAVVSALMAMIHRGASASEA 273 Lambda K H 0.315 0.131 0.370 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: 202 Number of extensions: 6 Number of successful extensions: 2 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: 265 Length of database: 282 Length adjustment: 25 Effective length of query: 240 Effective length of database: 257 Effective search space: 61680 Effective search space used: 61680 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: 42 (22.0 bits) S2: 47 (22.7 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