Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate RR42_RS06250 RR42_RS06250 dihydrodipicolinate synthase
Query= SwissProt::P39359 (301 letters) >FitnessBrowser__Cup4G11:RR42_RS06250 Length = 294 Score = 151 bits (381), Expect = 2e-41 Identities = 97/300 (32%), Positives = 158/300 (52%), Gaps = 8/300 (2%) Query: 1 MKKFSGIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMA 60 M + +G I + + DG+LD A+R + D+ + +G DG+ +GT GE +N + Sbjct: 1 MTQINGSIVAIVTPMQEDGSLDFPALRALVDWHVAEGTDGIVIVGTTGESPTVNVDEHCE 60 Query: 61 LAEEAVTIVDGRVPVLIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDY 120 L AV D R+P++ G G ST EA++L A+ GAD + + PYY K + + Sbjct: 61 LIRVAVEQADKRIPIIAGTGGNSTKEAIELTAFAKQVGADASLQVVPYYNKPTQEGMYRH 120 Query: 121 YQQIARSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTV 180 ++ IA +V LPV+LYN P T D+ +T+ RLA Q I+G+K ++ G++ + Sbjct: 121 FRTIAEAVELPVVLYNVPGRTVADMQHDTILRLA-QVPGIIGVK---EATGNIDRAAQLI 176 Query: 181 KSVRPSFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNK 240 K FS++ G D + MLLGG G I+ +AN AP + A +GD TA ++ Sbjct: 177 KDAPQGFSIYSGDDPTAIALMLLGGHGNISVTANVAPRKMHELCVAALKGDAITARRIHM 236 Query: 241 KLLQL-PAIYALETPFVSLIKYSMQCVGLPVETYCLPPILEASEEAKDKVHVLLTAQGIL 299 +L+ L A++ P +K+++Q +G ++ P+ S E D V L+A G+L Sbjct: 237 ELVALNKAMFVEANPIP--VKWALQQMG-RMQGGIRLPLTPLSPEYHDVVRKALSAAGLL 293 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: 224 Number of extensions: 15 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