Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate PP_1237 PP_1237 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::P39359 (301 letters) >FitnessBrowser__Putida:PP_1237 Length = 295 Score = 126 bits (317), Expect = 5e-34 Identities = 87/284 (30%), Positives = 144/284 (50%), Gaps = 9/284 (3%) Query: 19 GTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAEEAVTIVDGR---VPV 75 G +D ++ ++ DF + G + +GT GE + ++ + + + + V V +PV Sbjct: 17 GRVDWGSLDKLVDFHLENGTHAIVAVGTTGESATLDVEEHILVIKHVVERVKRSAKPIPV 76 Query: 76 LIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQIARSVTLPVILY 135 + G G+ ST EAV L Q+A+ GAD + + PYY K L +++ IA +V +P ILY Sbjct: 77 IAGTGANSTAEAVHLTQNAKNAGADACLLVVPYYNKPTQEGLYQHFKHIAEAVDIPQILY 136 Query: 136 NFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSVRPSFSVFCGYDD 195 N P T D+ ETV RL+ NI+GIK+ + + +++ V F V G D Sbjct: 137 NVPGRTSCDMQAETVIRLSTV-PNIIGIKEATGDLARAKAILD---GVSKDFIVMSGDDP 192 Query: 196 HLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLLQLPAIYALETPF 255 + +L+GG G I+ +AN AP + A EG+ A +N+KL+ L E+ Sbjct: 193 TAVELILMGGKGNISVTANVAPREMADLCEAALEGNAEKARAINEKLMPLHKDLFCESNP 252 Query: 256 VSLIKYSMQCVGLPVETYCLPPILEASEEAKDKVHVLLTAQGIL 299 + +K+++ +GL + L P+ SE +KV L G+L Sbjct: 253 IP-VKWALVEMGLMQKGIRL-PLTWLSEGCHEKVRTALRQSGVL 294 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: 180 Number of extensions: 10 Number of successful extensions: 3 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: 295 Length adjustment: 26 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 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