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 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 142 bits (359), Expect = 1e-38 Identities = 102/340 (30%), Positives = 167/340 (49%), Gaps = 23/340 (6%) Query: 4 IQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISIL 63 + + D L IV+GE ++WD GRRYLD + V +GH +P +++ + Q ++ Sbjct: 16 VPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNN--VPHVGHCHPRVVDAIARQARVLNTH 73 Query: 64 STSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAF 123 + + D ++ L + +D A+L+ +G+EAV+ AL+ AR TG+ +IA N + Sbjct: 74 TRYLHEGVLD-YIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAATGKTGLIATDNTY 132 Query: 124 HGRTAGSLSVTWNKK----YREPFEPLVGP---VEFLTF-----NNIEDLSKIDNETAAV 171 HG T ++ + Y + + P + F +L + AA+ Sbjct: 133 HGNTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAFGAHVARAAAELETAGHGVAAL 192 Query: 172 IVEPIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKL-WAYKHYNIVPD 230 IV PI G+ F++ G LLI DE+Q GFGR G + W Y+ I PD Sbjct: 193 IVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGYQALGIAPD 252 Query: 231 ILTAGKAIGGGFPVSVVFLPDHIANKLEEG-DHGSTYGGNPMAMAAVTAACKVIEKENVV 289 ++T GK++G G+PV+ V I E + +T+GG+P+A AA A V+E E +V Sbjct: 253 VVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVAAAAAMAVLDVLEDEGLV 312 Query: 290 EQANQKGQQFSNILVKNLADLK--VVREVRGKGLMIGIDI 327 E A + G+ ++ L L+ + VRG GL +D+ Sbjct: 313 ENAKRVGR----YTLERLQALRHPAIDGVRGYGLAFALDL 348 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: 354 Number of extensions: 20 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: 413 Length adjustment: 31 Effective length of query: 356 Effective length of database: 382 Effective search space: 135992 Effective search space used: 135992 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