Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate CCNA_01253 CCNA_01253 dihydrodipicolinate synthase
Query= SwissProt::P39359 (301 letters) >FitnessBrowser__Caulo:CCNA_01253 Length = 294 Score = 147 bits (370), Expect = 4e-40 Identities = 102/293 (34%), Positives = 154/293 (52%), Gaps = 18/293 (6%) Query: 4 FSGIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAE 63 F G+IP + + F RDG +D+KA + + I GV GL +GT GE S ++ + + E Sbjct: 6 FKGVIPALVTPF-RDGEVDEKAFVALVERQIAGGVHGLVPVGTTGETSTLSHEEHRRVVE 64 Query: 64 EAVTIVDGRVPVLIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQ 123 V GRVPV+ G GS STDEA++LA+HA+ GAD + + PYY + + + +Y+ Sbjct: 65 LCVKTTAGRVPVIAGAGSNSTDEAIELARHAKTVGADACLVVTPYYNRPSQEGMYQHYKA 124 Query: 124 IARSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSV 183 I +V LP+ +YN P TG D++ +T+ RLA + NIVGIK D+ G L + Sbjct: 125 INDAVELPIFVYNVPGRTGVDISNDTLERLA-KLPNIVGIK---DATGDLTRISFQRLMC 180 Query: 184 RPSFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLL 243 P + + G D L M GG G I+ ++N AP+ A +G+ +L+ Sbjct: 181 GPEWVMLSGDDPTALGYMAHGGHGVISVTSNVAPDACSAFMNACMQGEWEKGLYWQDRLV 240 Query: 244 QL-PAIYALETPFVSLIKYSMQCVGLPVE------TYCL----PPILEASEEA 285 +L A++ +P + K++M +GL E T C P ILEA EA Sbjct: 241 RLHKALFLDSSP--APTKFAMAQLGLCTEDVRLPITACAEGVRPAILEAMREA 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: 203 Number of extensions: 12 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: 294 Length adjustment: 26 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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