Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013010710.1 DACET_RS07130 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000025725.1:WP_013010710.1 Length = 439 Score = 182 bits (461), Expect = 4e-50 Identities = 127/339 (37%), Positives = 183/339 (53%), Gaps = 19/339 (5%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRS---PQKYELLGVPKEEI 76 V VG+ G GTVG +L + N I + G + V + + ELL + E+ Sbjct: 5 VNVGLIGYGTVGKGTAEVLLKNKNLIFENTGIDIRLKTVADLAIDTANPDELLSLC--EV 62 Query: 77 AFDFDDLILNS---DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEY- 132 + + ILN D+VVE IGG A D + AL + VV+ NK L + YG E + Sbjct: 63 VTNNAEDILNDQDIDIVVELIGGYTFAKDFIISALNKKKHVVSANKALFAMYGTEIYQAA 122 Query: 133 -IKKRKLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEV 190 + + FE +VGGGIP++ ++++ L + I GI+NGT NYIL++M K G+ FEEV Sbjct: 123 ELNNVSVCFEGAVGGGIPVLRVIKEDLAGNNINEIFGIINGTANYILSKMEKEGKEFEEV 182 Query: 191 LKEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGIT---RIDPEYL 247 LK AQELGYAEADPT DIEG D A+K+++LA + + EGIT +ID E+ Sbjct: 183 LKVAQELGYAEADPTFDIEGIDSAHKIAILASMAFNTLIPFEKIYVEGITSIKQIDIEFA 242 Query: 248 KEIVRSGKKLKLIGELDFSTNRYEVRLREVTPEDP--FFNVDGVDNAIEVSTDLAGDFLL 305 K++ K+KL+ N EVR+ D VDGV NA+E+ D++ + Sbjct: 243 KKL---DCKIKLLAIAKKHENDLEVRVHPTMVPDVELMAQVDGVFNAVEIIGDMSDKTMH 299 Query: 306 KGRGAGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMK 344 GRGAGG PT SAV D+ +A+ G ++ ++ K Sbjct: 300 YGRGAGGKPTGSAVAGDVISIARDIAAGCTKRTPILGFK 338 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: 774 Number of extensions: 49 Number of successful extensions: 6 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: 739 Length of database: 439 Length adjustment: 36 Effective length of query: 703 Effective length of database: 403 Effective search space: 283309 Effective search space used: 283309 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 Jul 25 2024. The underlying query database was built on Jul 25 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