Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_014449307.1 LFE_RS05800 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000284315.1:WP_014449307.1 Length = 417 Score = 315 bits (806), Expect = 4e-90 Identities = 165/402 (41%), Positives = 258/402 (64%), Gaps = 3/402 (0%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V KFGG ++ +E++ VA + K SG + VVV+SAM TD L++LA + +P Sbjct: 2 ALIVQKFGGTSVGSIERIRLVAGIVQKTLSSGDQVVVVVSAMAGETDRLVKLAHELSPDP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RE+D+L+S+GE + AL++I L G A S TG Q+ I TD + ARI I+++ + Sbjct: 62 PEREMDMLMSSGERVTSALLAICLNNMGIPARSMTGRQVGIKTDNVHTKARIESISSEPL 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 ++ L+ +P+VAGFQGI+ ++TTLGRGGSD TA+A+A ++GA C++Y DV GV+T Sbjct: 122 AQSLEAGIVPIVAGFQGISPQENVTTLGRGGSDTTAVAIAVAIGAQRCDIYTDVTGVFTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DP +V AR I +++EEM+E++ GA+VLQ R+ EFA KY + V +++ + GTL+ Sbjct: 182 DPNLVPQARKIDRIAYEEMLEMASLGAKVLQTRSVEFAMKYKMPVRVRSTFSDDPGTLVT 241 Query: 579 EGTK-VENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 E K +E +V VT + AK+ + DVPD+PG+AAR+ +S + +DMI+Q + + Sbjct: 242 EEEKGMEQIVVSGVTLDKNQAKITVSDVPDRPGLAARLFEDISGHSIIVDMIVQNIGQDQ 301 Query: 638 YNTVAFIVPESQLGKLDIDLLKTRSE--AKEIIIEKGLAKVSIVGVNLTSTPEISATLFE 695 ++F VP S+ K + L E A EI +++ + K+SIVGV + S ++A +F Sbjct: 302 MTDISFTVPRSESRKAERIALDFSKEIGAGEIRVKEDIVKISIVGVGMRSHSGVAARMFS 361 Query: 696 TLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 LA EGINI MIS S +IS +I+ +Y E +V+ +H FEL+ Sbjct: 362 ALAKEGINIVMISTSEIKISCLIEDRYAELSVRTLHKEFELE 403 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: 650 Number of extensions: 29 Number of successful extensions: 4 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: 417 Length adjustment: 36 Effective length of query: 703 Effective length of database: 381 Effective search space: 267843 Effective search space used: 267843 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