Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_086508150.1 BZY95_RS01045 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_002151265.1:WP_086508150.1 Length = 404 Score = 255 bits (651), Expect = 2e-72 Identities = 150/387 (38%), Positives = 227/387 (58%), Gaps = 20/387 (5%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y+ ++ VRG+G+R+WD EG EYID GG V +LGH +P +V+A+ Q L + Sbjct: 18 YSPQKVIPVRGEGSRLWDQEGREYIDFAGGIAVNSLGHCHPVLVKALTEQGNKLWHLSNV 77 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR--AHTG----RKKFVAAM 137 + +TL + ++ + +SG EANEAALK AR AH + + V+ Sbjct: 78 YTNEPSLKLAKTL--VERTFADKAYFCSSGGEANEAALKLARRWAHDNFGEHKHRIVSFY 135 Query: 138 RGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGE 197 + F GRT ++SV +PKY + F P+ + +N++++++ ++++T AV++EP+QGE Sbjct: 136 QSFHGRTFFTVSVGGQPKYSQGFGPVPGGIVHGEFNNLDSVRDLINDDTCAVMVEPMQGE 195 Query: 198 GGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALG 257 GG+ PAT EFL+ R++ ALLI DE+QTG+GRTG +A+ +GI PDILT AKALG Sbjct: 196 GGITPATQEFLQGLRDLCDAHDALLIFDEVQTGVGRTGSLYAYMEYGIEPDILTSAKALG 255 Query: 258 GGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWF 317 GG P+G + + VA ++ G HG+T+GGN LA A +AA+ +++ + + F Sbjct: 256 GGFPIGAMLTTDRVAPALAIGTHGSTYGGNALASAVALAAVEHIDTPEVLGGVKQRHDLF 315 Query: 318 MEKLRAIPSPK--IREVRGMGLMVGLELK---EKAAPYIARLEKEHRVLALQAGPTVIRF 372 E L AI RE+RGMGL++G E+ + A I L E ++AL AGP V+R Sbjct: 316 REHLEAINRKHGVFREIRGMGLLIGAEMTPEYKDRAKDILPLAIEEGLMALIAGPNVLRM 375 Query: 373 LPPLVIEKED-------LERVVEAVRA 392 P LVI + D LER +E + A Sbjct: 376 APSLVIPEADIAEGMARLERAIERLVA 402 Lambda K H 0.319 0.137 0.403 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: 439 Number of extensions: 14 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: 395 Length of database: 404 Length adjustment: 31 Effective length of query: 364 Effective length of database: 373 Effective search space: 135772 Effective search space used: 135772 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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