Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_052665669.1 NITAL_RS08275 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_000969705.1:WP_052665669.1 Length = 416 Score = 263 bits (671), Expect = 9e-75 Identities = 148/397 (37%), Positives = 217/397 (54%), Gaps = 8/397 (2%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80 G AE++ DG+RY+DF GIGVL+ GH +P VV A Q Q R+ H + H P L L Sbjct: 17 GSGAELFGHDGRRYLDFTAGIGVLSTGHGHPRVVAAAQEQIGRIVHAQYTTVRHQPLLEL 76 Query: 81 MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLN 140 E+L++ +P A ++G EA E AL++ R ATG+ +IAFDGGFHGRT+ L++ Sbjct: 77 SERLTEVMPAGID-AFFFASAGTEAVEAALRLVRQATGRPNVIAFDGGFHGRTMGALSMT 135 Query: 141 GKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQ-----ALKAMDRLFSVELAVEDVAAFI 195 + + L G V+ P+P+A E AL +D L + A ++ AA Sbjct: 136 TSKTALRSGLAPLMGGVHTAPFPTAHRYGWSEAEATRFALAELDHLLATHTAPDETAAIF 195 Query: 196 FEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLL 255 EPV GEGG++ AF + LR CD G+L++IDEIQ+G GRTG+ + GI PDL+ Sbjct: 196 VEPVLGEGGYVPAPDAFLRGLRERCDRHGMLLVIDEIQTGIGRTGRFWGHDHAGIVPDLV 255 Query: 256 LLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWG 315 + AK +A G PL LMA G GGTY GN +SCAAALA+L + +E L Sbjct: 256 VSAKGLASGFPLSTFGAPAALMAQGRPGSQGGTYGGNAVSCAAALATLDVVAEEGLVARA 315 Query: 316 ERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARG 375 E ++ R +G + G G M G+E + +G+P A +V++ A RG Sbjct: 316 EVLGDRLLDGLRRSTLD--IDAVGDVRGRGLMVGVELRDPEGAPDGAAAGRVLKEAEQRG 373 Query: 376 LLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 LLL+ G ++RL+ PL ++ ++ + I+ + + Sbjct: 374 LLLLACGAYGQVVRLIPPLVVDEAQVDTAIAIVTEAI 410 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: 502 Number of extensions: 31 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: 416 Length of database: 416 Length adjustment: 31 Effective length of query: 385 Effective length of database: 385 Effective search space: 148225 Effective search space used: 148225 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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