Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate 15422 b1302 GABA aminotransferase, PLP-dependent (NCBI)
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__Keio:15422 Length = 421 Score = 326 bits (835), Expect = 9e-94 Identities = 175/397 (44%), Positives = 240/397 (60%), Gaps = 11/397 (2%) Query: 23 NAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALME 82 NA + D +G YIDF GI VLN GH +P +V A++ Q + TH A+ P+ Y+ L E Sbjct: 31 NATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVTLAE 90 Query: 83 QLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGK 142 +++ PVS +GAEA ENA+K+AR TG+ +IAF GGFHGRT T+ L GK Sbjct: 91 KINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMTMALTGK 150 Query: 143 VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQGE 202 VAPYK G PG VYH+PYPS G++ + +L A++RLF ++ + VAA IFEPVQGE Sbjct: 151 VAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAIIFEPVQGE 210 Query: 203 GGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIA 262 GGF A+RR CDE GI++I DE+QSGF RTG+ FA +PDL+ +AKS+A Sbjct: 211 GGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLMTMAKSLA 270 Query: 263 GGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLA----TWGERQ 318 GGMPL VVG +M A GGLGGTY+GNP++ AAA A L + E+L G+R Sbjct: 271 GGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCERANQLGQRL 330 Query: 319 EQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANAD-GSPAPAQLAKVMEAARARGLL 377 + ++ E P I + G+G+M +EF + G P+ A K+ + A A+GLL Sbjct: 331 KNTLIDAKES------VPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQGLL 384 Query: 378 LMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 L+ G ++IR L PLTI + + IL+ L++ Sbjct: 385 LLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALSD 421 Lambda K H 0.320 0.137 0.402 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: 515 Number of extensions: 17 Number of successful extensions: 3 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: 416 Length of database: 421 Length adjustment: 32 Effective length of query: 384 Effective length of database: 389 Effective search space: 149376 Effective search space used: 149376 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 (21.8 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