Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate WP_013645701.1 METBO_RS10535 glutamate-1-semialdehyde-2,1-aminomutase
Query= metacyc::MONOMER-18314 (387 letters) >NCBI__GCF_000191585.1:WP_013645701.1 Length = 420 Score = 134 bits (338), Expect = 4e-36 Identities = 97/326 (29%), Positives = 160/326 (49%), Gaps = 25/326 (7%) Query: 16 KGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISILSTSFSTPIKDEM 75 K E + D++G Y+D+ G LGH NP ++ ++ QL + +++ P + E+ Sbjct: 34 KAEGSKLTDVDGNSYIDYCLAYGPMVLGHSNPEVVSEVEKQL----VKGSAYGVPTEKEI 89 Query: 76 LQALDKVKPDKM---DNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGRTAGSLS 132 L K+ +++ D +NSGTEA +A++ AR + KII F+ A+HG L Sbjct: 90 --ELAKMVVNRVPCADMVRFVNSGTEATMSAIRLARAAKSKNKIIKFEGAYHGAHDNVLV 147 Query: 133 VTWNKKYREPFEPLVGPVE------FLTFNNIEDLSKIDNET----AAVIVEPIQGESGV 182 + + P P V P E + FNN E + +I N+ AA+I+EPI G G+ Sbjct: 148 KSGSGAAGLPDSPGV-PEETTRNTLLIPFNNEESVIEIINKNKDSIAAIIIEPIMGNVGL 206 Query: 183 IPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGKAIGGGF 242 IP F++ L++ T LIFDE+ TGF R + A +++ + PD++T GK +GGGF Sbjct: 207 IPPKNGFLEFLRKITLENDITLIFDEVITGF-RIAQGGAQEYFKVTPDLVTFGKILGGGF 265 Query: 243 PVSVVFLPDHIANKLEEGD---HGSTYGGNPMAMAAVTAACKVIEKENVVEQANQKGQQF 299 P+ + + T+ GNP+++ A A K ++++ N KG+ F Sbjct: 266 PMGAITGKKEYMEMIAPSGSVYQAGTFNGNPISITAGLATLKQLDQQ-FYSDMNSKGKNF 324 Query: 300 SNILVKNLADLKVVREVRGKGLMIGI 325 + L D + +V G M I Sbjct: 325 REGIRNILEDKNLNYQVAGVSSMFQI 350 Lambda K H 0.317 0.136 0.385 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: 387 Number of extensions: 13 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: 387 Length of database: 420 Length adjustment: 31 Effective length of query: 356 Effective length of database: 389 Effective search space: 138484 Effective search space used: 138484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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