Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_084057642.1 B9A12_RS09455 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900176285.1:WP_084057642.1 Length = 442 Score = 195 bits (496), Expect = 4e-54 Identities = 127/387 (32%), Positives = 207/387 (53%), Gaps = 7/387 (1%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 + VRVG+ G GTVG + R+L+E + I+ R+G + +V + + V +E++ Sbjct: 1 MESVRVGLIGWGTVGCGVIRVLEENASAIQARLGFPLELVRVADLDLDSPRPVSVGREKL 60 Query: 77 AFDFDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 + D++ + +VVE IGG + A + +AL+ G+ VVT NK L++ +GNE + Sbjct: 61 TTNVRDILEDPHIQIVVELIGGLEPARTFILQALDQGKHVVTANKALLAHHGNELFAHAA 120 Query: 135 KRK--LFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVL 191 +R + FEASV GGIP++ +++ L +V I GI+NGT NYILT M++ G FEE L Sbjct: 121 RRGCCIGFEASVAGGIPLLKSIREGLAANRVDTIFGILNGTGNYILTRMTEEGLGFEEAL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 +EAQE GYAEADPT D++G D A+K+++ + G + V EGI DP ++ Sbjct: 181 REAQERGYAEADPTLDVDGIDTAHKLAIAGAMAFGTPIQFDQVYVEGIRHTDPLDVQFAS 240 Query: 252 RSGKKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRG 309 G +LKL+ + E+R+ + +V G NA+ + + G+ +L G G Sbjct: 241 EFGYQLKLLAIGRHVNGQLEMRVHPTLIPSSHVLASVRGAYNAVHLHGNAVGNIMLYGLG 300 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKS 369 AG PT SAV+AD+ +A+ GG + + + V +E+V + R + Sbjct: 301 AGMMPTGSAVVADMVDIARDLTSGGINRVPPLSFLPERTQDTPVRPMEEVVTRYYFRFSA 360 Query: 370 GVKPVVVLSAMGDTTDHLIELAKTIDE 396 +P V+ G ++ I +A I + Sbjct: 361 VDRPGVLSKISGILGENAISIAAVIQK 387 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: 746 Number of extensions: 44 Number of successful extensions: 7 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: 442 Length adjustment: 36 Effective length of query: 703 Effective length of database: 406 Effective search space: 285418 Effective search space used: 285418 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