Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate HSERO_RS16395 HSERO_RS16395 dihydrodipicolinate synthase
Query= SwissProt::P39359 (301 letters) >FitnessBrowser__HerbieS:HSERO_RS16395 Length = 292 Score = 150 bits (379), Expect = 3e-41 Identities = 100/294 (34%), Positives = 157/294 (53%), Gaps = 6/294 (2%) Query: 6 GIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAEEA 65 G I + + H+DG+LD +R++ D+ I +G D + +GT GE ++ + L + A Sbjct: 4 GSIVAIVTPMHQDGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELIKVA 63 Query: 66 VTIVDGRVPVLIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQIA 125 V R+P++ G G ST EA++L + A+ GAD + + PYY + + ++++IA Sbjct: 64 VEHTAKRIPIIAGTGGNSTSEAIELTEFAKKVGADASLQVVPYYNRPTQEGMYLHFKKIA 123 Query: 126 RSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSVRP 185 SV LPVILYN P T D++ ET+ RLA Q + IVG+K D+ G++ + ++ Sbjct: 124 ESVDLPVILYNVPGRTVADMSNETILRLA-QVKGIVGVK---DATGNIARGTDLIRLAPK 179 Query: 186 SFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLLQL 245 SF+V+ G D + ML GG G I+ +AN AP + A G++A A LN KLL L Sbjct: 180 SFAVYSGDDATAIALMLYGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELNNKLLPL 239 Query: 246 PAIYALETPFVSLIKYSMQCVGLPVETYCLPPILEASEEAKDKVHVLLTAQGIL 299 +E V L K++MQ +GL + + P+ D V L G+L Sbjct: 240 HNKLFVEPNPVPL-KWAMQEMGL-IPSGMRLPLAPLGAAYHDTVRAALRESGVL 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: 221 Number of extensions: 17 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