Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate GFF1478 Psest_1515 dihydrodipicolinate synthase
Query= SwissProt::P39359 (301 letters) >FitnessBrowser__psRCH2:GFF1478 Length = 292 Score = 146 bits (369), Expect = 5e-40 Identities = 91/281 (32%), Positives = 153/281 (54%), Gaps = 6/281 (2%) Query: 19 GTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAEEAVTIVDGRVPVLIG 78 G LD ++ ++ DF + +G + + +GT GE + ++ A+ + + V V+GR+PV+ G Sbjct: 17 GGLDWDSLSKLVDFHLQEGTNAIVAVGTTGESATLSVAEHIEVIRRVVDQVNGRIPVIAG 76 Query: 79 VGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQIARSVTLPVILYNFP 138 G+ ST EAV+L ++A+ GAD + + PYY K L +++ IA +V +P ILYN P Sbjct: 77 TGANSTSEAVELTENAKTAGADACLLVTPYYNKPTQEGLYLHFKHIAEAVAIPQILYNVP 136 Query: 139 DLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSVRPSFSVFCGYDDHLL 198 T D+ P+TV RL+ + NI+GIK ++ G L+ + V F V+ G D + Sbjct: 137 GRTVCDMLPDTVERLS-KISNIIGIK---EATGDLKRGQEVLDRVSGDFLVYSGDDPTAV 192 Query: 199 NTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLLQLPAIYALETPFVSL 258 ML+GG G I+ +AN AP + A GD ATA +N++L+ L LE + Sbjct: 193 ELMLMGGKGNISVTANVAPRAMSDLCAAAMAGDAATARAINERLMPLHRALFLEANPIP- 251 Query: 259 IKYSMQCVGLPVETYCLPPILEASEEAKDKVHVLLTAQGIL 299 +K+++ +GL L P+ S+ ++ + + G+L Sbjct: 252 VKWALHEMGLMGNGIRL-PLTWLSQSYQEPLRQAMRQTGVL 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: 181 Number of extensions: 10 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