Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 246 bits (627), Expect = 1e-69 Identities = 145/381 (38%), Positives = 211/381 (55%), Gaps = 14/381 (3%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 V+++ D++ +G+GA + ++G ++D G V LGH +P +V A++ QA L Sbjct: 9 VFDRTDVIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSN 68 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAH------TGRKKFVAA 136 P + L I + F N+G EA E +K AR + R + VA Sbjct: 69 LYRVPGQERVAERL--IKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVAC 126 Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQG 196 F GRT+ +L+ PKY E F P+ + + +PY D+EA + A+ TAA+++EPVQG Sbjct: 127 TGSFHGRTIATLAAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAIGSNTAALLVEPVQG 186 Query: 197 EGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKAL 256 EGG+RPA P +LR R + + G LL++DE+QTG+GRTGK FA E GI PD++ LAK L Sbjct: 187 EGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMGLAKGL 246 Query: 257 GGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPW 316 GGG P+G + E+ A M G HG TFGGNPLAMA A + + ER + Sbjct: 247 GGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQAVAAL 306 Query: 317 FMEKL----RAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRF 372 +L R P I +VRG GLM+GL+ + A+L +LA+ AG V+R Sbjct: 307 LRGRLDDLARRYPG-AIAQVRGQGLMLGLKTVPVNTEFNAKLFAA-GLLAVGAGDNVVRL 364 Query: 373 LPPLVIEKEDLERVVEAVRAV 393 +PPL+I + ++ER VE + V Sbjct: 365 VPPLIIGEAEVERAVEIIDGV 385 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: 391 Number of extensions: 16 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: 388 Length adjustment: 31 Effective length of query: 364 Effective length of database: 357 Effective search space: 129948 Effective search space used: 129948 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