Align Predicted lysZ by GapMind curators (no experimental data)
to candidate WP_011937170.1 GURA_RS01130 acetylglutamate kinase
Query= predicted:D4GYN9 (327 letters) >NCBI__GCF_000016745.1:WP_011937170.1 Length = 292 Score = 111 bits (278), Expect = 2e-29 Identities = 87/260 (33%), Positives = 123/260 (47%), Gaps = 13/260 (5%) Query: 50 VVVKIGGAKAVDP---KGAVSDVAHLVANGTDVVVVHGGSTAVDETLEELGEEPTYVESP 106 +V+K GG D K DV L G + V+VHGG ++ETL+ G +V+ Sbjct: 26 IVIKYGGHAMADEALKKSFAMDVILLKYIGINPVIVHGGGPQINETLKRYGIVSEFVKGM 85 Query: 107 SGVSGRFTDERAMEVFSMVMPGKLNTDLTALFREAGVDALGLSGVDGGLLTGPRKSAVRV 166 R TD M V MV+ G++N ++ + G A+GLSG DGGLL + Sbjct: 86 -----RVTDAATMGVVEMVLTGQVNKEVVGYINQHGGRAVGLSGKDGGLLLCRKLLQEVK 140 Query: 167 VEDGK-KKIKRGDHSGKITSVNATLLETLLDGGYTPIVTVPMLADDGVPVNADADRAAAA 225 +DG +K+ G G IT V++T+L TL GG+ P++ + G N +AD A Sbjct: 141 KDDGTIEKVDIG-FVGDITDVDSTILVTLEAGGFIPVIAPVGVGAGGESYNINADLVAGK 199 Query: 226 VAGALGA-KLVVLTDVKGVYADPDDESTLIETADTPEEFSALESAAEGFMTKKVMAAKEA 284 VA AL A KL++LTDV GV + I AD P G M KV +A Sbjct: 200 VAAALKAEKLILLTDVPGVKDQEGHLLSSIALADVPALID--NGTITGGMIPKVTCCTDA 257 Query: 285 LDGGAAEVVVADANLNDPIV 304 L GG + + D + I+ Sbjct: 258 LTGGVHKAHIVDGRVEHAIL 277 Lambda K H 0.310 0.131 0.359 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: 277 Number of extensions: 21 Number of successful extensions: 5 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: 327 Length of database: 292 Length adjustment: 27 Effective length of query: 300 Effective length of database: 265 Effective search space: 79500 Effective search space used: 79500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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