Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_012282524.1 HM1_RS06545 acetylornithine transaminase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000019165.1:WP_012282524.1 Length = 432 Score = 288 bits (737), Expect = 2e-82 Identities = 156/392 (39%), Positives = 235/392 (59%), Gaps = 11/392 (2%) Query: 12 LLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVK 71 ++E K Y + + +V+GQGAR+WDA+G EY+D + G V +LGH +P+VV+A++ Sbjct: 6 IVELGKKYVMNTYGRLPISLVKGQGARLWDADGREYLDFLAGLAVNSLGHCHPKVVDALQ 65 Query: 72 RQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHT--- 128 +QA TL+ + + + + L + ++VF NSG EANE A+K AR + Sbjct: 66 QQAATLLHVSNLYWIEPQVQLAQVL--VENSFADKVFFCNSGAEANEGAIKLARKYAKKT 123 Query: 129 -GRKKF--VAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEE 185 G K+ + + F GRT+ +++ T +PKY++ + PL + ++P+ D++AL+RA+ Sbjct: 124 WGSDKYEIITMEKSFHGRTLATVTATAQPKYQKDYEPLPQGFRYVPFGDLKALERAISPH 183 Query: 186 TAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGI 245 T A+++EPVQGEGGV A P F + ++ LLI DE+Q G+GRTGK FA EH+G+ Sbjct: 184 TCAILVEPVQGEGGVNLAEPSFWQGLAKLAAANKLLLIFDEVQCGLGRTGKLFAHEHYGV 243 Query: 246 VPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTR 305 P I+TLAKAL GG P+G + ++VA + G H +TFGGNPL AA VA + L Sbjct: 244 TPHIMTLAKALAGGAPMGALLATDDVANAFQPGDHASTFGGNPLVAAAAVAVMDVLLNDG 303 Query: 306 LWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLAL 363 L + E+ +FM LR + P I EVRG+GLMV EL A +A ++ ++ Sbjct: 304 LMDNCREMAAYFMGHLRRLQEKYPFITEVRGLGLMVACELDRPGADIVANCLEKGLIINC 363 Query: 364 QAGPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395 AG V+RFLPPL+I K D++ V + VLA Sbjct: 364 TAG-NVLRFLPPLIINKADVDEAVAVLEEVLA 394 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: 387 Number of extensions: 15 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: 432 Length adjustment: 31 Effective length of query: 364 Effective length of database: 401 Effective search space: 145964 Effective search space used: 145964 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