Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_011319592.1 AVA_RS14370 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000204075.1:WP_011319592.1 Length = 493 Score = 256 bits (653), Expect = 1e-72 Identities = 158/452 (34%), Positives = 239/452 (52%), Gaps = 17/452 (3%) Query: 7 VKELPGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVI 66 V LPG + + +ER + P +PI I +GI + D DGNV+ D +G G + Sbjct: 36 VHSLPGEASSQYLERQQARESNARSYPRRIPIAISEAQGIYIKDADGNVYIDCLAGAGTL 95 Query: 67 NVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVY---GNS 123 +GH+HP +EA++K + D E+L P + + V G S Sbjct: 96 ALGHNHPVAIEAMRKVLDGGLPLHTLDLTTPVKDKFVEELFASLPPEFAQNVKIQFCGPS 155 Query: 124 GAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIP 183 GA+A EAA+KLVK TG + L+F+ +HG T LSLT + +Q MP V +P Sbjct: 156 GADAVEAAIKLVKTATGNRSVLSFHGGYHGMTHGALSLTGNLNPKQ-AVTGLMPDVHFLP 214 Query: 184 YPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPK 243 YP YR +G+ G + + +++ V P A+ E +QGEGG + P Sbjct: 215 YPYHYRCPFGLGGEAGQRTSSRYIESILDDPESGIVTP---AAMILEVVQGEGGVIPAPD 271 Query: 244 GFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGV 303 + + +++ + I L DE+Q G+GRTGK +A EH G+ PD++ KAIGG LPL+ V Sbjct: 272 DWLREMRRITRDRHIPLIVDEIQTGLGRTGKLYAFEHSGIMPDVLLLSKAIGGSLPLSVV 331 Query: 304 IHRADITFDKPGRHATTFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKE 361 ++ ++ PG HA TF GN +A+AAG ++ + E L H +GD L K+L + + Sbjct: 332 LYNKELDKWSPGAHAGTFRGNQMAMAAGTATLQYILENSLTEHAAAMGDRLLKHLHQIQG 391 Query: 362 KYEVIGDARGLGLAQAVEIVKSKETKEK------YPELRDRIVKESAKRGLV--LLGCGD 413 + IG+ RG GL VEI+ + + ++ +P+L RI E +RGL+ L G Sbjct: 392 ETYCIGEVRGRGLMVGVEIINPQASADRRGKYPAHPQLASRIQAECLRRGLIVELGGRFG 451 Query: 414 NSIRFIPPLIVTKEEIDVAMEIFEEALKAALK 445 + +RF+PPLIVT +ID EIF A++AA K Sbjct: 452 SVVRFLPPLIVTPAQIDSICEIFASAVQAAEK 483 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: 587 Number of extensions: 43 Number of successful extensions: 7 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: 493 Length adjustment: 33 Effective length of query: 412 Effective length of database: 460 Effective search space: 189520 Effective search space used: 189520 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