Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__SB2B:6937472 Length = 405 Score = 250 bits (639), Expect = 4e-71 Identities = 145/384 (37%), Positives = 215/384 (55%), Gaps = 15/384 (3%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y ++ V+G G+R+WD +G E+ID GG V LGH +P +V A+ QA+ L + T Sbjct: 16 YAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSALTEQAQKLWHLSNT 75 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARA------HTGRKKFVAAM 137 + + L E +V+ NSG EANEAALK R + + +A Sbjct: 76 MTNEPALMLAKHLVDNTFAE--KVYFANSGAEANEAALKLVRRVALNKFGADKSQIIAFK 133 Query: 138 RGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGE 197 +GF GRT+ ++SV +P Y + F P ++ YN++++LK + + T AV+LEP+QGE Sbjct: 134 QGFHGRTLFTVSVGGQPAYSDGFGPKPADIDHAEYNNLDSLKALISDRTCAVVLEPLQGE 193 Query: 198 GGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALG 257 GG+ TPEF++ RE+ + ALL+ DE+QTG+GRTG+ +A+ G+ PD+LT AKALG Sbjct: 194 GGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVTPDVLTTAKALG 253 Query: 258 GGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWF 317 GG P+G + E+A+ + G HG+T+GGNPLA A G+AA + + E F Sbjct: 254 GGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEVLNGVKEREQLF 313 Query: 318 MEKLRAIPS--PKIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVIR 371 + L AI EVRG GL++G L KA ++ +E VL L AG V+R Sbjct: 314 RDGLNAINDKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEE-GVLLLMAGQNVVR 372 Query: 372 FLPPLVIEKEDLERVVEAVRAVLA 395 F P L+I + D+ + A +A Sbjct: 373 FAPSLIIPEADVREGLARFDAAIA 396 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: 361 Number of extensions: 13 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: 395 Length of database: 405 Length adjustment: 31 Effective length of query: 364 Effective length of database: 374 Effective search space: 136136 Effective search space used: 136136 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 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