Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate Dsui_1977 Dsui_1977 dihydrodipicolinate synthase
Query= SwissProt::P39359 (301 letters) >FitnessBrowser__PS:Dsui_1977 Length = 292 Score = 155 bits (393), Expect = 8e-43 Identities = 98/295 (33%), Positives = 159/295 (53%), Gaps = 6/295 (2%) Query: 5 SGIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAEE 64 +G I + + DG LD +++++ DF + +G DG+ +GT GE +N + L Sbjct: 3 TGSIVAIVTPMSDDGRLDYDSLKKLIDFHVQEGTDGIVIVGTSGESPTVNVDEHAELIRT 62 Query: 65 AVTIVDGRVPVLIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQI 124 V GR+PV+ G G+ ST EA++L + A++ GAD +++ PYY K L +++ I Sbjct: 63 TVKHAAGRIPVIAGTGANSTSEAIELTRFAKSVGADAALSVVPYYNKPTQEGLYQHFRSI 122 Query: 125 ARSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSVR 184 A +V +PVILYN P T D++ +T RLA Q +N+VGIK D+ G+L + + Sbjct: 123 AEAVDIPVILYNVPGRTVADMSNDTALRLA-QIDNVVGIK---DATGNLERGADLIARAP 178 Query: 185 PSFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLLQ 244 F+V+ G D + +LLGG G I+ +AN AP L + A GD+A A ++ KLL Sbjct: 179 ADFAVYSGDDASAVALILLGGKGDISVTANVAPRLMHEMCAAALAGDVAKAREIHFKLLG 238 Query: 245 LPAIYALETPFVSLIKYSMQCVGLPVETYCLPPILEASEEAKDKVHVLLTAQGIL 299 L E + +K+++Q +GL + P+ S E ++V + G+L Sbjct: 239 LHRHLFCEANPIP-VKWAVQQLGL-IPGGIRLPLTTLSPECHERVRSAMRQAGVL 291 Lambda K H 0.319 0.137 0.398 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: 239 Number of extensions: 14 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: 301 Length of database: 292 Length adjustment: 26 Effective length of query: 275 Effective length of database: 266 Effective search space: 73150 Effective search space used: 73150 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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