Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate PP_4108 PP_4108 putative 4-aminobutyrate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Putida:PP_4108 Length = 416 Score = 226 bits (576), Expect = 9e-64 Identities = 154/418 (36%), Positives = 219/418 (52%), Gaps = 45/418 (10%) Query: 16 EKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAE 75 ++++ + H + + G+ A VWD +G YID VGG GV NLGH NP VVEA++ QA Sbjct: 3 QESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQAT 62 Query: 76 TLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPV---------NSGTEANEAALKFARA 126 L G + L +L++ PV NSG EA E ALK AR Sbjct: 63 RLTHY--AFNAAPHGPYLA-----LMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG 115 Query: 127 HTGRKKFVAAMRGFSGRTMGSLSVTWE-PKYREPFLPLVEPVEFIPYNDV------EALK 179 TG++ +A GF GRT+ +L++ + Y++ L PV +PY E Sbjct: 116 ATGKRAIIAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQAL 175 Query: 180 RAVD---------EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTG 230 +A+D E+ AA I EPVQGEGG P F +A R E+G L+I+DEIQ+G Sbjct: 176 KAMDRLFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSG 235 Query: 231 MGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLA 290 GRTG+RFAF GI PD+L LAK++ GG+PLG V R+E+ ++PKGG G T+ GNP++ Sbjct: 236 FGRTGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPIS 295 Query: 291 MAAGVAAIRYL--ERTRLW-ERAAELGPWFMEKLRAIP-SPKIREVRGMGLMVGLELK-- 344 AA +A++ + E W ER + E+ +A SP I + G+G M G+E Sbjct: 296 CAAALASLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANA 355 Query: 345 --EKAAPYIARLEKEHRVLALQAGPT-----VIRFLPPLVIEKEDLERVVEAVRAVLA 395 A +A++ + R L P+ +IR L PL IE E LE ++ + LA Sbjct: 356 DGSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLA 413 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: 409 Number of extensions: 21 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: 416 Length adjustment: 31 Effective length of query: 364 Effective length of database: 385 Effective search space: 140140 Effective search space used: 140140 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