Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011735216.1 PPRO_RS06410 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000015045.1:WP_011735216.1 Length = 438 Score = 191 bits (486), Expect = 5e-53 Identities = 122/402 (30%), Positives = 213/402 (52%), Gaps = 10/402 (2%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 ++VG+ G G +G + ++L I ++G ++ ++ +R + V + D Sbjct: 4 IKVGLIGFGNIGAGVVKLLTNNAEVIRGKVGAGIVLKRIADRDITTDRGVAVDPSCMTTD 63 Query: 80 FDDLILNSD--VVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNE-FSEYIKKR 136 +D+ + + VV+E +GG + A V RA+E G+ +VT NK L++ +G + F+ +K Sbjct: 64 VNDIFDDPEISVVIELVGGYEPAKSFVLRAIEKGKHIVTANKALLALHGQDIFAAAARKN 123 Query: 137 -KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVLKEA 194 ++ FEA+VGGGIP+++ ++ + + GIMNGT NYILT M++ G F ++L A Sbjct: 124 VEVQFEAAVGGGIPVLTAIKGNMAANNFGSVFGIMNGTCNYILTRMTQEGADFADMLTAA 183 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 QELGYAE DPT DIEG D A+K+++L + G N++ EGI+RI +K G Sbjct: 184 QELGYAEPDPTFDIEGVDTAHKLAILVSLCFGTRIDFNAIHTEGISRISGLDVKFARDFG 243 Query: 255 KKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 ++KL+ S + E R+ + +P +V+GV NAI ++ D G + GRGAG Sbjct: 244 YRIKLLAIGKLSDGKVEARVHPTMIPLHNPMADVNGVFNAIRLTGDFVGAVMFYGRGAGQ 303 Query: 313 YPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVK 372 PTASA++ DL +++ + G + + + + V+ + + K + R + Sbjct: 304 DPTASAIVGDLIGLSRSMLAGAGRRMAPLGLMDEQVRDLPVKPMADIVSKYMLRFSTRDI 363 Query: 373 PVV---VLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGE 411 P V + A+G + + +T E D + +++ T E Sbjct: 364 PGVLGTITGALGKHGISISSMVQTAHEANDNAPVPIVIMTHE 405 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: 739 Number of extensions: 32 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: 438 Length adjustment: 36 Effective length of query: 703 Effective length of database: 402 Effective search space: 282606 Effective search space used: 282606 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