Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate GFF530 Psest_0535 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__psRCH2:GFF530 Length = 427 Score = 137 bits (344), Expect = 8e-37 Identities = 100/289 (34%), Positives = 139/289 (48%), Gaps = 19/289 (6%) Query: 29 LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPM 88 L + GA V D + Y+D VG +G LGH +PEV++AV+RQ E + PT M Sbjct: 34 LFLKHAAGAYVIDEDDKRYVDYVGSWGPMILGHSHPEVLDAVRRQLEH--GLSYGAPTAM 91 Query: 89 RGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK---KFVAAMRGFSGRTM 145 E L L P + V V+SGTEA +A++ AR +TGR KF G S + Sbjct: 92 ETEMAE-LVCRLVPSMEMVRMVSSGTEATMSAIRLARGYTGRDAIIKFEGCYHGHSDSLL 150 Query: 146 -----GSLSVTWEPKYREPFLPLVEPVEFIPYND---VEALKRAVDEETAAVILEPVQGE 197 G+L++ P + + YND VEA + E+ A +I+EPV G Sbjct: 151 VKAGSGTLTLGVPSSAGVP-ADFAKHTLTLAYNDLAEVEATLKEKGEQVACIIVEPVAGN 209 Query: 198 GGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALG 257 P P FL R + G +LI DE+ TG R A ++G+ PD+ T K +G Sbjct: 210 MNCVPPAPGFLEGLRSLCDAHGVVLIFDEVMTGF-RVALGGAQAYYGVTPDLSTFGKIIG 268 Query: 258 GGVPLG-VAVMREEVARSMPKGG--HGTTFGGNPLAMAAGVAAIRYLER 303 GG+P+G R + R P G T GNPLAMAAG+ + + R Sbjct: 269 GGMPVGCFGGKRAIMERIAPLGPVYQAGTLSGNPLAMAAGLTTLGLISR 317 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: 353 Number of extensions: 19 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: 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 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