Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate 14406 b0268 2-keto-3-deoxy gluconate (KDG) aldolase; CP4-6 prophage (NCBI)
Query= SwissProt::Q57695 (289 letters) >FitnessBrowser__Keio:14406 Length = 302 Score = 158 bits (400), Expect = 1e-43 Identities = 101/296 (34%), Positives = 155/296 (52%), Gaps = 8/296 (2%) Query: 1 MFKGVYPAIITPFK-NKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVI 59 +F G+ P + T F + ++D G I+ LI+ GV G+ +G+ GE L EE K + Sbjct: 6 LFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIA 65 Query: 60 EKVVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFG 119 +D V+ RV V+ G G E IELS A+ GAD ++ I PYY K ++ L ++F Sbjct: 66 RFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFE 125 Query: 120 KVAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAK- 178 +VA+S+ LP++LYN P+ T +L P VK LA+ SNI +K+ +++ + +IH K Sbjct: 126 QVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKG 185 Query: 179 ----ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKL 234 TVL G D+ + LGG G IS N P+ V ++ +GD KA H L Sbjct: 186 AHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTL 245 Query: 235 FPLMKAMFIETNPIPV-KTALNMMGRPAGELRL-PLCEMSEEHKKILENVLKDLGL 288 + + ++T + V K A+ + GRP L P + E K L+ +L+ L L Sbjct: 246 LQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKL 301 Lambda K H 0.315 0.135 0.374 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: 182 Number of extensions: 9 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: 289 Length of database: 302 Length adjustment: 26 Effective length of query: 263 Effective length of database: 276 Effective search space: 72588 Effective search space used: 72588 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: 48 (23.1 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