Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013135532.1 ARNIT_RS08635 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000092245.1:WP_013135532.1 Length = 402 Score = 305 bits (781), Expect = 3e-87 Identities = 165/399 (41%), Positives = 255/399 (63%), Gaps = 2/399 (0%) Query: 342 VMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPR 401 V+KFGG ++ +E+++ VA I K K G + V+SAM T+ LIE A++ + P P Sbjct: 4 VLKFGGTSVGTLERIQNVATIIKKIKDDGHDVIAVVSAMSGETNKLIEYAESYSKMPAPS 63 Query: 402 ELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISRY 461 E+D+LLS+GE + AL+SIAL + GY AIS +G + I+TD+R+ ARI I+T + Sbjct: 64 EMDMLLSSGERVTSALLSIALNEAGYSAISMSGGRAGIVTDERHTKARIEYIDTKNMKES 123 Query: 462 LKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADPR 521 + + + VVAGFQG+T+ G +TTLGRGGSDLTA+A+A ++ AD+CE+Y DVDG+YT DPR Sbjct: 124 IAEGKVVVVAGFQGVTQKGRVTTLGRGGSDLTAVAIAGAIEADVCEIYTDVDGIYTTDPR 183 Query: 522 IVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAH-KETRGTLIW-E 579 I A+ + ++S++EM+EL+ GA+VLQ R+ E A+K V ++ +++ E GTLI E Sbjct: 184 IEPKAKKLDKISYDEMLELASLGAKVLQNRSVEMAKKLNVNLISRSSFTPEVEGTLITKE 243 Query: 580 GTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYN 639 +E PIV + + +V + V D+PG+A+ I L+ +N+DMI+Q + Sbjct: 244 ENIMEQPIVSGIALDKNQVRVGMYGVTDRPGIASYIFTALADANINVDMIVQTVAVDGKT 303 Query: 640 TVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFETLAN 699 ++ F +P + L + K E ++ + + KVSIVGV + S +++ F LAN Sbjct: 304 SLDFTIPTTDLEICKTIMHKFEDEVEKFDYNEKICKVSIVGVGMKSHTGVASKAFTALAN 363 Query: 700 EGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 E INI +IS S +ISVI++ KY E AV+A+H ++LD+ Sbjct: 364 ENINIRIISTSEIKISVIVEEKYAELAVRALHDAYDLDK 402 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: 684 Number of extensions: 31 Number of successful extensions: 2 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: 402 Length adjustment: 35 Effective length of query: 704 Effective length of database: 367 Effective search space: 258368 Effective search space used: 258368 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: 52 (24.6 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