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 N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Dyella79:N515DRAFT_3307 Length = 426 Score = 136 bits (342), Expect = 1e-36 Identities = 89/286 (31%), Positives = 143/286 (50%), Gaps = 22/286 (7%) Query: 16 KGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISILSTSFSTPIKDE- 74 + + Y+WD+EG+RY+D+ G +GH +P + E ++ +++ SF TP E Sbjct: 37 RADGAYLWDVEGKRYIDYVGSWGPMIVGHNHPRVREAVERAVKD----GLSFGTPCPAEI 92 Query: 75 -MLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGR------T 127 M + + ++ P +D ++NSGTEA +A++ AR TGR KI+ F+ +HG Sbjct: 93 TMAETITRLVPS-VDMVRMVNSGTEATMSAIRLARGATGRSKIVKFEGCYHGHGDSFLVK 151 Query: 128 AGSLSVTWNKKYREPFEPLVGPVEF-LTFNNIEDLSKIDNE----TAAVIVEPIQGESGV 182 AGS ++T+ + L +N++ + E A +I+EP+ G Sbjct: 152 AGSGALTFGVPTSPGVPKAAADLTLTLAYNDLAAAEALFAEHGADIAGLIIEPVAGNMNC 211 Query: 183 IPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGKAIGGGF 242 IP +++ L+ G+LLIFDE+ TGF R A HY I PD+ T GK IGGG Sbjct: 212 IPPKDGYLQGLRALCTRHGALLIFDEVMTGF-RVALGGAQAHYGITPDLSTFGKIIGGGM 270 Query: 243 PVSVVFLPDHIANKLEEGD---HGSTYGGNPMAMAAVTAACKVIEK 285 PV + ++ T GNP+AMAA A ++I++ Sbjct: 271 PVGAYGGRRELMEQIAPAGPIYQAGTLSGNPVAMAAGLAMLELIQE 316 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: 356 Number of extensions: 13 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: 426 Length adjustment: 31 Effective length of query: 356 Effective length of database: 395 Effective search space: 140620 Effective search space used: 140620 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 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