Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_057509166.1 ABB28_RS13775 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_001431535.1:WP_057509166.1 Length = 408 Score = 187 bits (474), Expect = 7e-52 Identities = 128/403 (31%), Positives = 200/403 (49%), Gaps = 47/403 (11%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 +V+ERG+G RV+D G + D A+G+ V +GH+ P + A+ +QA K H S F+ Sbjct: 24 VVLERGQGARVWDSQGREYIDLAAGIAVCGLGHNDPDLTAALVEQAGKLWHTSNV-FYSA 82 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTG-------RKQFLAFYHA 150 + LAE+L++ + +V NSGAEANE A+K+V+ R+ + F + Sbjct: 83 PPLHLAEELVKASR--FAERVFLCNSGAEANEVAIKMVRKWASSQGRPADRRVIVTFRGS 140 Query: 151 FHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDF 210 FHGRT A ++ TA Q+G+ P G R +DF Sbjct: 141 FHGRTLAAVTATAQP-KYQEGYEPLPQGF--------------------------RYVDF 173 Query: 211 IEEYVFRH-VPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 +E + ++ A+ EP+QGEGG + GF K +++ D++G LL DE+Q G+ Sbjct: 174 NDEVQLETAMAAGDVAAVMLEPVQGEGGVMPARPGFLKRVRELCDQHGALLVLDEIQAGM 233 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKP-GRHATTFGGNPVAI 328 GRTG +A GV PD++ KA+GGG P+ ++ + G H TTFGGNP+A Sbjct: 234 GRTGTLFAHWQDGVVPDMVTLAKALGGGFPIGAMLAGPKVAETMQFGAHGTTFGGNPLAA 293 Query: 329 A-AGIEVVEIVK-ELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKET 386 A A + + ++ E+ +V L + E ++ V G RG GL + K Sbjct: 294 AVARVALRKLASDEIAANVDRQSRALREGFERINAEFGVFGQVRGRGLMLGAVLSKDHLG 353 Query: 387 KEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEI 429 + I+ +A+ GL+ L G + +RF+P L +T EEI Sbjct: 354 QAGV------ILDHAAEHGLLTLQAGPDVLRFVPSLNITDEEI 390 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: 423 Number of extensions: 24 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: 408 Length adjustment: 32 Effective length of query: 413 Effective length of database: 376 Effective search space: 155288 Effective search space used: 155288 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