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_012504789.1 PAES_RS00970 glutamate-1-semialdehyde 2,1-aminomutase
Query= metacyc::MONOMER-18314 (387 letters) >NCBI__GCF_000020625.1:WP_012504789.1 Length = 431 Score = 144 bits (362), Expect = 6e-39 Identities = 104/308 (33%), Positives = 155/308 (50%), Gaps = 29/308 (9%) Query: 8 GDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISILSTSF 67 G + + KG+ Y+ D++G YLD+ G LG +P I L++ L I TSF Sbjct: 33 GGTPIYMAKGQGAYMTDVDGNTYLDYVGSWGPFILGSMHPRITAALEHTLTKIG---TSF 89 Query: 68 STPIKDEM--LQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHG 125 TPI+ E+ + L ++ P ++ ++NSGTEA +A++ AR T R KII F+ +HG Sbjct: 90 GTPIEMEIEIAELLCQIVPS-IEMVRMVNSGTEATMSAVRLARGYTSRDKIIKFEGCYHG 148 Query: 126 R------TAGSLSVTWNKKYREPFEPLV-----GPVEFLTFNNIEDLSKIDNET----AA 170 AGS ++T P P V +N+IE + + NE AA Sbjct: 149 HGDSFLIKAGSGALTLGA----PDSPGVTKGTANDTLNAKYNDIESVRLLVNENKGNIAA 204 Query: 171 VIVEPIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPD 230 +I+EP+ G +GVIPA F++AL++ G +LIFDE+ GF R A + Y + PD Sbjct: 205 IIIEPVAGNTGVIPAKPGFLQALRDLCTEEGIVLIFDEVMCGF-RVALGGAQERYGVTPD 263 Query: 231 ILTAGKAIGGGFPVSVVFLPDHIANKLEE-GD--HGSTYGGNPMAMAAVTAACKVIEKEN 287 + T GK IGGG PV I ++ GD T GNP+A+ A K++ EN Sbjct: 264 LTTMGKIIGGGLPVGAFGGKREIMERIAPLGDVYQAGTLSGNPLALTAGLETLKILRDEN 323 Query: 288 VVEQANQK 295 + +K Sbjct: 324 PYPELERK 331 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: 385 Number of extensions: 9 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: 387 Length of database: 431 Length adjustment: 31 Effective length of query: 356 Effective length of database: 400 Effective search space: 142400 Effective search space used: 142400 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