Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011317641.1 AVA_RS03950 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000204075.1:WP_011317641.1 Length = 429 Score = 160 bits (406), Expect = 9e-44 Identities = 109/314 (34%), Positives = 169/314 (53%), Gaps = 12/314 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 V++GI GLGTVG ++L++ + ++ I +V RSP K + + E I D Sbjct: 3 VKLGILGLGTVGTGTVQLLQDAVGR--HPLLQEIEIYRVGVRSPNKSRDVQLQPEVITTD 60 Query: 80 FDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKRK 137 + ++ + D+VVE +GG + A L+ +A+ G+ VVT NK I+ +G E + Sbjct: 61 LESIVNDPAVDIVVEVMGGLEPARSLILQAINNGKHVVTANKAAIARFGAEIFTAANQAG 120 Query: 138 LF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEA 194 ++ EA+VGGGIP+I L+ L ++ + GI+NGTTNYILT M ++G F +VL +A Sbjct: 121 VYVMLEAAVGGGIPVIQPLKQALSVNRLHTVTGIVNGTTNYILTRMQTEGSDFGDVLADA 180 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q LGYAEADPT D++G D K+++LA + + V EGI ++ + + G Sbjct: 181 QRLGYAEADPTADVDGLDAGDKIAILASLAFDGRINLEDVYCEGIRQVSKTDIAYAEKLG 240 Query: 255 KKLKLIG-----ELDFSTNRYEVRLREVTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRG 309 +KL+ D + V V P +++GV NAI V + G + G G Sbjct: 241 FVIKLLAIAKNQAQDATKLSVRVHPTFVPKTHPLASINGVYNAILVEGEPIGQVMFFGPG 300 Query: 310 AGGYPTASAVIADL 323 AG TASAV +D+ Sbjct: 301 AGAGATASAVTSDI 314 Lambda K H 0.318 0.137 0.377 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: 685 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 429 Length adjustment: 36 Effective length of query: 703 Effective length of database: 393 Effective search space: 276279 Effective search space used: 276279 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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