Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900105005.1:WP_090271605.1 Length = 417 Score = 235 bits (600), Expect = 2e-66 Identities = 133/408 (32%), Positives = 217/408 (53%), Gaps = 14/408 (3%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 + ERGEG + DG + DF +G+GV + GH HP VV A ++Q K H T ++ Sbjct: 14 VCAERGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTTVTHQ 73 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQA 157 + LAE+L+ P I+ V + N+G+EA E A++L ++ T R + F FHGRT Sbjct: 74 PMLDLAERLVGKMPDGID-SVAFSNAGSEAVEMALRLARHATRRANVIVFNGGFHGRTMG 132 Query: 158 VLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR 217 S+T S ++ + P M GV P+P+ +R W +E T L ++ + Sbjct: 133 AASMTTSGTKVRNAYHPMMAGVVVAPFPHSWRYGWS------EEEATRFCLAELDHILKT 186 Query: 218 HVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWA 277 P + A+ EP+QGE GY F + L + ++GILL DE+Q G GR+GKFW+ Sbjct: 187 QTAPEDTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWS 246 Query: 278 IEHFGVEPDLIQFGKAIGGGLPLAGV-IHRADITFDKPGRHATTFGGNPVAIAAGIEVVE 336 +HFG+ PD++ K + G PL+ + + + G T+G N V+ AA + + Sbjct: 247 HQHFGITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLR 306 Query: 337 IV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELR 394 ++ + L+ + G L +L+ +++Y + D RG GL +EI +S + + +L Sbjct: 307 VMDNENLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPD--KPLADLA 364 Query: 395 DRIVKESAKRGLVLLGCGDNS--IRFIPPLIVTKEEIDVAMEIFEEAL 440 + S + GL+LL CG +S IR++PPL+V++ E+D A++ F L Sbjct: 365 ASLTTASEEEGLLLLRCGTDSQIIRWLPPLVVSEAEVDDAVQRFTRVL 412 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: 411 Number of extensions: 18 Number of successful extensions: 5 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: 417 Length adjustment: 32 Effective length of query: 413 Effective length of database: 385 Effective search space: 159005 Effective search space used: 159005 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