Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011939064.1 GURA_RS11050 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000016745.1:WP_011939064.1 Length = 436 Score = 185 bits (470), Expect = 4e-51 Identities = 120/418 (28%), Positives = 222/418 (53%), Gaps = 20/418 (4%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 ++++++G+ G GT+G + ++L + +E+++G + + K+ + + V + Sbjct: 1 MKEIKIGLLGFGTIGAGVVKLLTKNSALLEEKLGARLSLKKIADLDITTDRGVSVEPGVL 60 Query: 77 AFDFDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 + D+++ + ++ V+E IGG + A V +A+ G+ ++T NK L++ +G E Sbjct: 61 TTNVDEVLCDPEISIVIELIGGYEPARSFVLKAIANGKHIITANKALLAVHGEEIYAAAA 120 Query: 135 KR--KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVL 191 ++ ++ FEA+VGGGIP++S ++ + + + GI+NGT NYIL++M++ G F EVL Sbjct: 121 QKGVEILFEAAVGGGIPVLSAIKGNMAGNNFSTVLGILNGTCNYILSKMTQDGVDFAEVL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 + AQELGYAEADPT D+EG D A+K+ +L + G + + EGI+ I + Sbjct: 181 QTAQELGYAEADPTFDVEGIDTAHKLCLLLSLCFGTRVDLKDISTEGISSISAVDINFAR 240 Query: 252 RSGKKLKL--IGELDFSTNRYEVRLREVTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRG 309 G K+KL IG+ D V + P +V+GV NAI ++ D G + GRG Sbjct: 241 DFGYKIKLLAIGKRDGERIEARVHPTMIPVNYPLADVNGVFNAIRLTGDFVGPVMFYGRG 300 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKS 369 AG PTASAVI D+ +A+ + G + + + + ++ + ++ K R + Sbjct: 301 AGMEPTASAVIGDVVDIARNMLAGISRRSAPLGYLDDRVKKLTIKPMGEIVSKYYIRFNA 360 Query: 370 GVKPVVV------LSAMGDTTDHLIELAKTIDE-------NPDPRELDLLLSTGEIQS 414 +P V+ L A + + +++ A++ E + RE+D+ + EI + Sbjct: 361 VDRPGVLAKISGALGASNISIESMMQTARSASETVPIVIMTHEAREMDVRKALAEIDA 418 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: 731 Number of extensions: 48 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: 436 Length adjustment: 36 Effective length of query: 703 Effective length of database: 400 Effective search space: 281200 Effective search space used: 281200 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