Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_072908061.1 BUB13_RS08945 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_900142125.1:WP_072908061.1 Length = 427 Score = 154 bits (389), Expect = 5e-42 Identities = 101/298 (33%), Positives = 162/298 (54%), Gaps = 19/298 (6%) Query: 29 LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPM 88 + I + G++++DA+GNEYID VG +G +GH +P+VVEA+++ A + + PT Sbjct: 36 IFIEKAAGSKIYDADGNEYIDYVGSWGPMIMGHCHPKVVEAIQKTAASGASFGA--PTAR 93 Query: 89 RGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGRTMGSL 148 + ++ P + +V V+SGTEA +A++ AR +TGR K + + G L Sbjct: 94 ETQLAEMVSEAYP-NIEKVRMVSSGTEATMSAIRLARGYTGRDKILKFDGCYHGHADSLL 152 Query: 149 SVTWE--PKYREPFLPLVEPVEFIPY------NDVEALKRAV---DEETAAVILEPVQGE 197 + P P V P +F Y ND++ +K+ V D+E A +ILEP+ G Sbjct: 153 VKAGSGLATFGVPTSPGV-PADFAKYTLTATYNDLDEVKQMVAANDKEIACIILEPIAGN 211 Query: 198 GGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALG 257 G P P FL RE+ ++G +LI+DE+ TG R A E F + D++ L K +G Sbjct: 212 MGCVPPVPGFLEGLRELCTQEGIVLIVDEVMTGF-RVAFGGAQERFNVRGDLVCLGKIIG 270 Query: 258 GGVPLGVAVMREEVARSM-PKGG--HGTTFGGNPLAMAAGVAAIRYLERTRLWERAAE 312 GG+P+G ++E+ S+ P+GG T GNPLAM+AG+A + L+ +++ E Sbjct: 271 GGLPVGAFGGKKEIMDSLSPEGGVYQAGTLSGNPLAMSAGIATLNILKEEGFYQQLEE 328 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: 382 Number of extensions: 22 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: 395 Length of database: 427 Length adjustment: 31 Effective length of query: 364 Effective length of database: 396 Effective search space: 144144 Effective search space used: 144144 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