Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_084076407.1 BUB04_RS10885 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900129305.1:WP_084076407.1 Length = 442 Score = 395 bits (1015), Expect = e-114 Identities = 215/442 (48%), Positives = 295/442 (66%), Gaps = 11/442 (2%) Query: 4 RPNVKELP-GPKAKEVIERNFKYLAMT-TQDPENLPIVIERGEGIRVYDVDGNVFYDFAS 61 RP +K P GPKAK IER+ + ++ + T+D P+V+ERG G+ + DVDGNV+ DF S Sbjct: 3 RPLIKTPPPGPKAKAHIERDTRVVSPSYTRD---YPLVVERGRGLWIEDVDGNVYLDFTS 59 Query: 62 GVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYG 121 G+ V GH HPRVVEAI++Q+EK H S TDF+Y I LAE+L L +V +G Sbjct: 60 GIAVCATGHCHPRVVEAIRRQSEKLLHMSGTDFYYTPQIELAERLAALVSPKEPYRVYFG 119 Query: 122 NSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTH 181 NSGAEA EAA KL ++ T R+ +AF+ AFHGRT LSLTASK +Q+ + P +PG+TH Sbjct: 120 NSGAEAVEAAFKLARWHTRRELNIAFFGAFHGRTMGALSLTASKTIQKKHYNPFVPGITH 179 Query: 182 IPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR-HVPPHEIGAIFFEPIQGEGGYVV 240 IPY YR + + Y D + + ++E+ +FR +PP E+ AIF EPIQGEGGYVV Sbjct: 180 IPYAYCYRCPYNLT-YPACD---IQCVQWVEDTLFRTTMPPEEVAAIFVEPIQGEGGYVV 235 Query: 241 PPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPL 300 PP F + L A +YGIL DEVQ GIGRTGK +A+EH+GV PD++ K I GLPL Sbjct: 236 PPPEFHRKLYDIAHKYGILYVADEVQTGIGRTGKMFAMEHYGVVPDIVALAKGIASGLPL 295 Query: 301 AGVIHRADITFDKPGRHATTFGGNPVAIAAGIEVVEIVKE-LLPHVQEVGDYLHKYLEEF 359 ++ RADI + G HA+TFGGNPV+ A + +++V+E L+ + + G+ L + L Sbjct: 296 GAMVARADIMDWEAGSHASTFGGNPVSCTAALVTLDLVEEGLMENARLQGERLLEGLRAL 355 Query: 360 KEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFI 419 + +E +GD RG GL VE+VK +ETKE+ + R+ +V+ + ++GL+LLGCG N++RF Sbjct: 356 QRSHESMGDVRGKGLMVGVELVKDRETKERAGDWRNALVRRAFEKGLLLLGCGMNTVRFA 415 Query: 420 PPLIVTKEEIDVAMEIFEEALK 441 P L VT E+ID +EIFEEALK Sbjct: 416 PALTVTAEQIDTCLEIFEEALK 437 Lambda K H 0.320 0.141 0.418 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: 567 Number of extensions: 28 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: 445 Length of database: 442 Length adjustment: 32 Effective length of query: 413 Effective length of database: 410 Effective search space: 169330 Effective search space used: 169330 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: 51 (24.3 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