Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011386084.1 AMB_RS18865 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000009985.1:WP_011386084.1 Length = 428 Score = 202 bits (515), Expect = 2e-56 Identities = 143/391 (36%), Positives = 206/391 (52%), Gaps = 14/391 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKF-IISKVINRSPQKYELLGVPKEEIAF 78 +++ IAGLGTVGG ++L + + R G ++ P L GVP A Sbjct: 6 LKIAIAGLGTVGGGTVQLLHDHAPLLAARAGRPLALVGAAALAKPADLPLDGVPFFTDAR 65 Query: 79 DFDDLILNSDVVVEAIGGTD-VAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKR- 136 D + DV+VE IGG +A+D+VR ALE G+ VVT NK +I+ +G E + + + Sbjct: 66 DMAKTC-DYDVLVELIGGAKGIALDVVRTALERGKSVVTANKAMIAHHGIELARIAEAKG 124 Query: 137 -KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEA 194 + FEASVGGGIP+I L++ L +VT++ GI+NGT NYILT M GR F +VL EA Sbjct: 125 GNIGFEASVGGGIPVIKSLREGLAGNRVTKVMGILNGTCNYILTTMRDSGRDFSDVLAEA 184 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q LGYAEADP+ DI+G D A+K+++LA + I++V EGI + ++ G Sbjct: 185 QALGYAEADPSFDIDGTDTAHKLAILASLAFAMPLDIDAVSCEGIRNVSALDIRYADELG 244 Query: 255 KKLKLIGELDFSTNRYEVRL--REVTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 ++KL+G S E R+ V P +V G NAI D G +L+GRGAG Sbjct: 245 YRIKLLGVASLSDQGVETRVYPAMVPLSFPLAHVSGPFNAIVTEGDFVGRTVLEGRGAGA 304 Query: 313 YPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVK 372 PTASAV+ADL +A +V G +V +K AA S + +++ + Sbjct: 305 RPTASAVVADLMDLATGRV-GPTFGIAVDALKALPAAPSGTHRSAYYIRLMVRD-----E 358 Query: 373 PVVVLSAMGDTTDHLIELAKTIDENPDPREL 403 P V G H + + + I P E+ Sbjct: 359 PGVFADVAGILKAHKVSMEQIIQRGRSPSEV 389 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: 681 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: 428 Length adjustment: 36 Effective length of query: 703 Effective length of database: 392 Effective search space: 275576 Effective search space used: 275576 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 09 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