Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_001584165.1:WP_128083232.1 Length = 420 Score = 263 bits (671), Expect = 1e-74 Identities = 150/399 (37%), Positives = 225/399 (56%), Gaps = 17/399 (4%) Query: 48 VYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLI 107 ++DV+G F DFA+G+ V+N GH HP++V AI++Q KFTH + Y + + LAE++ Sbjct: 29 IWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFTHTAYQIVPYGSYVELAERIN 88 Query: 108 ELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWV 167 + PGD +K + ++GAEA E A+K+ + TGR +AF AFHGRT ++LT Sbjct: 89 AVTPGDHAKKTTFFSTGAEAVENAVKIARAATGRSAVIAFSGAFHGRTMMGMALTGKVVP 148 Query: 168 QQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAI 227 + GF P V H+P+P E L ++ V P + AI Sbjct: 149 YKVGFGPFPAEVYHVPFP-----------VELHGVSIENSLAALQSLFKADVDPKRVAAI 197 Query: 228 FFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDL 287 EP+QGEGG+ P F +AL+K DE+GILL DEVQ G RTGK +A+EH GV PDL Sbjct: 198 ILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEHSGVIPDL 257 Query: 288 IQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVKE--LLPH 344 + K++ GG+PL+ V RA+I PG T+ GNP+A+A+ + V+++++E L+ Sbjct: 258 MTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVASALAVLDVIEEEKLVER 317 Query: 345 VQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKR 404 +G L + LE + I D RGLG AVE + +K+ + ++ E+ K Sbjct: 318 ANVLGGRLKQVLEGLRADVPQIADIRGLGAMVAVEFTQ-PGSKQPDADFTKKVQAEALKN 376 Query: 405 GLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441 GL+LL CG N+IRF+ PL + +D A+ I +A++ Sbjct: 377 GLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAMR 415 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: 487 Number of extensions: 25 Number of successful extensions: 6 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: 420 Length adjustment: 32 Effective length of query: 413 Effective length of database: 388 Effective search space: 160244 Effective search space used: 160244 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 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