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 CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Pedo557:CA265_RS15205 Length = 378 Score = 249 bits (637), Expect = 7e-71 Identities = 137/374 (36%), Positives = 221/374 (59%), Gaps = 20/374 (5%) Query: 12 LTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLE---NISILSTSFS 68 L V+ + Y++D + ++++D GIGV+ +GH +P +++ ++ Q E ++ + Sbjct: 2 LEFVRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMHLMVYGEYVQ 61 Query: 69 TPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGRTA 128 TP + +AL + P+ + LNSGTEAVE A+K A++ TGRK IA KNA+HG T Sbjct: 62 TP-QVNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKGFIACKNAYHGSTQ 120 Query: 129 GSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDLSKIDNETAAVIVEPIQGESGVIPANIE 188 G+ S+ + Y + P + V F+ NN+ DL KI NE AAV +EPIQGE+G+ +++ Sbjct: 121 GAESLMESDFYSSGYGPFLPHVSFIEHNNLADLEKITNEIAAVFIEPIQGEAGIRVSDLS 180 Query: 189 FMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGKAIGGGFPVSVVF 248 +M+AL+ K TG+LLIFDEIQ+GFGR+GK++A++HYN+VPD+L K IGGG P+ Sbjct: 181 YMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAKGIGGGMPIGAFI 240 Query: 249 LPDHIANKLEEG---DHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQKGQQFSNILVK 305 I + L H +T+GG+P+ AA A + + +++V++ +KGQ F K Sbjct: 241 SSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEVEEKGQLF-----K 295 Query: 306 NLADLKVVREVRGKGLMIGIDIRFQPGQVLKYLQEKGILAVKAG------STVIRFLPSY 359 L ++E+RGKGLM+ ++ F+ ++ K + + IL S +R P Sbjct: 296 QLLQHPAIKEIRGKGLMLAVE--FENFEINKKIIDACILDGVLSDWFLHCSNSMRIAPPL 353 Query: 360 LITYENMEEASNVL 373 +IT E + EA ++ Sbjct: 354 IITKEEIAEACTII 367 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: 366 Number of extensions: 15 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: 378 Length adjustment: 30 Effective length of query: 357 Effective length of database: 348 Effective search space: 124236 Effective search space used: 124236 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