Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_041313646.1 HM1_RS08880 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000019165.1:WP_041313646.1 Length = 433 Score = 152 bits (384), Expect = 2e-41 Identities = 105/306 (34%), Positives = 158/306 (51%), Gaps = 23/306 (7%) Query: 26 KHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLP 85 ++ + I R +GA ++D +GN+Y+D VG +G +GH +PEV EA+K + P Sbjct: 32 RNPVFIERAEGAYLYDVDGNKYVDYVGSWGPMIVGHAHPEVSEALKAAIDR--GTSYGAP 89 Query: 86 TPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGRT- 144 T + + + P ++ V VNSGTEA +AL+ AR +TGR K V + G Sbjct: 90 TELESRLAKLILEAFPA-MDMVRMVNSGTEATMSALRLARGYTGRSKIVKFEGCYHGHAD 148 Query: 145 -----MGSLSVTWEPKYREPFLP--LVEPVEFIPYNDVEALKRAVDE---ETAAVILEPV 194 GS ++T P +P + PYND+E LK E + AA+I+E V Sbjct: 149 SLLIKAGSGALTLGVP-TSPGVPANIANNTITAPYNDLETLKAIFQEAGDDIAAIIIEGV 207 Query: 195 QGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAK 254 G GV P P +L+ RE+T++ GAL+I+DE+ +G R A +G+ PD+ L K Sbjct: 208 PGNMGVVPPAPGYLQGVRELTRQYGALMIVDEVMSGF-RVDFGGAQTLYGVEPDLTCLGK 266 Query: 255 ALGGGVPLGVAVMREEVARSMPKGG---HGTTFGGNPLAMAAGVAAIRYLER----TRLW 307 +GGG+P+G + E+ + G T GNPLAM AG+ + L+R L Sbjct: 267 IIGGGLPVGAYGGKAEIMEKVSPAGPIYQAGTLSGNPLAMTAGIITLEILKRPGTYAALD 326 Query: 308 ERAAEL 313 E+AA L Sbjct: 327 EKAAYL 332 Lambda K H 0.319 0.137 0.403 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: 392 Number of extensions: 22 Number of successful extensions: 6 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: 395 Length of database: 433 Length adjustment: 31 Effective length of query: 364 Effective length of database: 402 Effective search space: 146328 Effective search space used: 146328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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