Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Putida:PP_4481 Length = 406 Score = 266 bits (680), Expect = 8e-76 Identities = 153/385 (39%), Positives = 220/385 (57%), Gaps = 17/385 (4%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y+ + VRG+G+RVWD G E ID GG V LGH +P +V+A+ QA TL + Sbjct: 21 YSPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVNALGHCHPALVKALTEQANTLWHVSNV 80 Query: 84 LPT-PMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR--AHTG----RKKFVAA 136 P ++ + A +R F NSG E+NEAA K AR AH + + +A Sbjct: 81 FTNEPALRLAHKLVDATFA---DRAFFCNSGAESNEAAFKLARRVAHDRFGPQKHEIIAT 137 Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQG 196 + F GRT+ ++SV +PKY + F P + + +PYND+EALK + ++T AV++EP+QG Sbjct: 138 VNSFHGRTLFTVSVGGQPKYSDGFGPKITGISHVPYNDLEALKAQISDKTCAVVIEPIQG 197 Query: 197 EGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKAL 256 E GV PA +L AR++ E ALLI DE+QTG+GRTG +A++H+G++PDILT AK+L Sbjct: 198 ESGVVPADKAYLEGARKLCDEHNALLIFDEVQTGVGRTGSLYAYQHYGVIPDILTSAKSL 257 Query: 257 GGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPW 316 GGG P+G + E+A+ + G HGTT+GGNPL A A + + Sbjct: 258 GGGFPIGAMLTTTELAKHLAVGTHGTTYGGNPLGCAVACAVLDVVNTPETLAGIKAKHER 317 Query: 317 FMEKLRAIPSP--KIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVI 370 F +L I +VRG+GL++G L E KA + EKE V+ LQAGP V+ Sbjct: 318 FKTRLEQIGQQYNLFSQVRGVGLLLGCVLTEAWKGKAKDVLNAAEKE-GVMVLQAGPDVV 376 Query: 371 RFLPPLVIEKEDLERVVEAVRAVLA 395 RF P LV+E D++ ++ +A Sbjct: 377 RFAPSLVVEDADIDEGLDRFERAVA 401 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: 382 Number of extensions: 18 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: 406 Length adjustment: 31 Effective length of query: 364 Effective length of database: 375 Effective search space: 136500 Effective search space used: 136500 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