Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_012991510.1 THAL_RS02335 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000025605.1:WP_012991510.1 Length = 424 Score = 139 bits (349), Expect = 2e-37 Identities = 100/300 (33%), Positives = 148/300 (49%), Gaps = 23/300 (7%) Query: 29 LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPM 88 +++ +G R+WD EG EYID + +G LGH +P VV V+RQ M+ T + Sbjct: 33 IVVREAKGCRLWDVEGKEYIDFLMSWGPLILGHAHPYVVSEVERQLSRGMSYGLTCYEEI 92 Query: 89 RGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK---KFVAAMRGF----- 140 R L P + V V+SGTEA +A++ AR +TGRK KF G Sbjct: 93 R---LAELVVSSVPSVEMVRFVSSGTEATMSAIRLARGYTGRKFVVKFEGCYHGHYDGLL 149 Query: 141 --SGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD---EETAAVILEPVQ 195 +G + +L + P E L +PYND +A+ + E+ A VI+EPV Sbjct: 150 VSAGSGVATLGIPGTPGVPEEIAGL---TLVLPYNDTDAVLSTFERYGEDIACVIVEPVA 206 Query: 196 GEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKA 255 G GV + FL RE+T++ GA+LI DE+ T R A E++ I PDI + K Sbjct: 207 GNMGVVLPSEGFLEVLREVTRKYGAVLIFDEVITNF-RLSVGGAQEYYAIDPDITCMGKI 265 Query: 256 LGGGVPLGVAVMREEVARSMPKGG---HGTTFGGNPLAMAAGVAAIRYLERTRLWERAAE 312 LGGG+PLG ++E+ + G T GNP+++ G A + L R + ++ E Sbjct: 266 LGGGMPLGAYGGKKEIMSHVAPEGKVYQAGTLSGNPVSVVCGRATLEELLRLKPYQLLEE 325 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: 396 Number of extensions: 21 Number of successful extensions: 3 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: 424 Length adjustment: 31 Effective length of query: 364 Effective length of database: 393 Effective search space: 143052 Effective search space used: 143052 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