Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate CCNA_00886 CCNA_00886 aspartokinase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Caulo:CCNA_00886 Length = 415 Score = 258 bits (658), Expect = 5e-73 Identities = 151/417 (36%), Positives = 254/417 (60%), Gaps = 21/417 (5%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLI-------ELA 391 S +VMKFGG +++D+E++ +VA + +G + VV+SAM T+ L+ A Sbjct: 2 SRLVMKFGGTSVADLERIRRVARLVAAEVATGKQVAVVVSAMSGKTNELVAWTDGAGRAA 61 Query: 392 KTIDENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARII 451 + E+ D E D ++++GE + L+++ LR G+KA SF G Q+ I+TD+ +G ARI Sbjct: 62 AGLPESDD--EYDAVVASGEQVTAGLLAMTLRNMGHKARSFLGWQVPILTDEAHGRARIE 119 Query: 452 DINTDIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKD 511 +I + + I V+AGFQG+T ITTLGRGGSD +A+A+A ++ D C++Y D Sbjct: 120 EIPPENLEECFANGEIAVIAGFQGVTPNRRITTLGRGGSDTSAVAIAAAVKGD-CDIYTD 178 Query: 512 VDGVYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE 571 VDGVYT DPRI AR + ++S+EEM+E++ GA+VLQ R+ E A + V V + ++ E Sbjct: 179 VDGVYTTDPRIESKARRLAKISYEEMLEMASLGAKVLQTRSVEMAMAHRVPVRVLSSFVE 238 Query: 572 T-----RGTLIWEGTKV-ENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVN 625 +GT++ + ++ E IV V + AK+ L +PD PGV+++I L++ VN Sbjct: 239 PGEAPGQGTIVCDEEEIMEKRIVSGVAYSRDEAKITLLGLPDHPGVSSQIFGRLAEANVN 298 Query: 626 IDMIIQG-MKSGEYNTVAFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGV 681 +DMI+Q +S + + F V + + +++++ + + + + + +AKVS++GV Sbjct: 299 VDMIVQSRARSADTANMEFTVGKRDATRA-VEIVQAAQKEIGFEAVAVNEDVAKVSVIGV 357 Query: 682 NLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 + S ++ ++F+ LA + INI +IS S +ISV+ID Y E AV+A+H+ + LD+ Sbjct: 358 GMRSHAGVAQSMFQALAEKNINIQVISTSEIKISVLIDAAYTELAVRALHAVYGLDQ 414 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: 618 Number of extensions: 24 Number of successful extensions: 5 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: 415 Length adjustment: 36 Effective length of query: 703 Effective length of database: 379 Effective search space: 266437 Effective search space used: 266437 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