Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013450991.1 CALNI_RS04335 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000183405.1:WP_013450991.1 Length = 441 Score = 197 bits (500), Expect = 1e-54 Identities = 131/385 (34%), Positives = 203/385 (52%), Gaps = 8/385 (2%) Query: 18 RKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIA 77 R+V VGI G GTVG +L + N I+++ G + V + +++ + K Sbjct: 4 RRVNVGIVGYGTVGKGTVNVLIDNANVIKEKTGIDIFVKSVADLKINEFDDQFLRKVPNK 63 Query: 78 FDFDDLILNS---DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 + D+I+N D+VVE IGG + A ++ A+E + VVT NK L++ YG E + + Sbjct: 64 YTDADMIINDPVIDIVVELIGGYNAAKKVILDAIEKKKHVVTANKALLAVYGTEIFKKAE 123 Query: 135 KR--KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVL 191 ++ +L FE SVGGGIPII +L++ L + I GI+NGT NYILT M K G+ F+EVL Sbjct: 124 EKSVQLGFEGSVGGGIPIIKVLKEDLAANNIKEIYGIINGTANYILTRMEKEGKEFDEVL 183 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 K+AQ LGYAEADPT DIEG D A+K+++L+ + + V EGI+ I + Sbjct: 184 KDAQRLGYAEADPTFDIEGIDTAHKITILSSIAFNTIIPFDKVFVEGISSIKQVDIDFAK 243 Query: 252 RSGKKLKLIGELDFSTNRYEVRLREVTPEDPFF--NVDGVDNAIEVSTDLAGDFLLKGRG 309 + K+KL+ N EVR+ + + V+ V NAI + +D + GRG Sbjct: 244 KLNCKIKLLAIAKKHENDIEVRVHPTMIPERYILSKVENVFNAIYLVSDKLDRTIHYGRG 303 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKS 369 AGG PT SAV D+ +A+ + G ++ V+ + V+ ++ + R + Sbjct: 304 AGGLPTGSAVAGDIISIARDIICGCHKRVPVLGFTKEYRSYFPVKNIDDIRSSFYLRFMA 363 Query: 370 GVKPVVVLSAMGDTTDHLIELAKTI 394 KP V+ G + I ++ I Sbjct: 364 LDKPGVLSKIAGVLGKYNISISAAI 388 Score = 25.4 bits (54), Expect = 0.006 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 5/58 (8%) Query: 8 KMFTNSSQGVRKVRVGIAGLGTVGGSIYRILKERGNEIEKR-----IGEKFIISKVIN 60 K+F +++V + A + I K+ N+IE R I E++I+SKV N Sbjct: 225 KVFVEGISSIKQVDIDFAKKLNCKIKLLAIAKKHENDIEVRVHPTMIPERYILSKVEN 282 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: 857 Number of extensions: 40 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: 2 Length of query: 739 Length of database: 441 Length adjustment: 36 Effective length of query: 703 Effective length of database: 405 Effective search space: 284715 Effective search space used: 284715 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