Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_012566210.1 RC1_RS04730 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000016185.1:WP_012566210.1 Length = 467 Score = 184 bits (468), Expect = 4e-51 Identities = 137/425 (32%), Positives = 224/425 (52%), Gaps = 29/425 (6%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHY-SLTDFF 95 P+VI G G+ V D G + + +G+ ++G PR+VEA +Q Y + Sbjct: 35 PMVITGGRGVTVVDDAGREYIEGVAGLWCTSLGFDEPRLVEAAVRQLRTLPFYHAFAHKS 94 Query: 96 YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTG------RKQFLAFYH 149 +E I LAEKL+ LAP + K + SG+EAN+ A+KLV Y +K+ + Sbjct: 95 HEPGIELAEKLVALAPVPMS-KAFFACSGSEANDTAVKLVWYYNNALGRPQKKKIIGRIK 153 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 A+HG T A SLT +D P + + H P+ YR + +G E+ + +R+ Sbjct: 154 AYHGVTVASASLTGLPNNHRDFDLP-IDRILHTDCPHWYR--FHEEG-EDEEAFASRLAA 209 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 +E + R P + A EP+ G GG +VPP+ +F+ ++ ++ +LL DEV G Sbjct: 210 SLEALIQRE-GPETVAAFIAEPVMGAGGVIVPPRTYFEKIQAVLRKHDVLLIADEVICGF 268 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV-----IHRADIT-FDKPG--RHATT 320 GRTG + E FG++PD++ KA+ +PL+ V I+RA + +K G H T Sbjct: 269 GRTGAMFGSETFGLKPDIMTMAKALTSAYMPLSAVLVSEPIYRACVAESEKIGVFGHGYT 328 Query: 321 FGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378 + G+PV+ A +E ++I +E ++ H + VG L + L ++ + ++G+ RG+GL V Sbjct: 329 YSGHPVSCAVALETLKIYEERDIVAHTRAVGARLQEGLARYR-SHPLVGEVRGVGLIAGV 387 Query: 379 EIVKSKETKEKY-PEL--RDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEI 435 E+V K T++ + P+L R+ + G +L GD ++ F PPLI+T EE+D + Sbjct: 388 ELVADKATRQPFDPKLGVAARLAGFAQGHGAILRPIGD-TLGFSPPLIITPEEVDELVAR 446 Query: 436 FEEAL 440 F AL Sbjct: 447 FGRAL 451 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: 534 Number of extensions: 30 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: 467 Length adjustment: 33 Effective length of query: 412 Effective length of database: 434 Effective search space: 178808 Effective search space used: 178808 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