Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_022948199.1 H035_RS0106595 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000421465.1:WP_022948199.1 Length = 415 Score = 288 bits (738), Expect = 2e-82 Identities = 157/409 (38%), Positives = 233/409 (56%), Gaps = 14/409 (3%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 +++ERGEG +YD G + DF SG+GV GH HP VV A +KQ H T + Sbjct: 14 VLVERGEGAYLYDAAGTKYLDFTSGIGVTATGHCHPTVVAAAQKQVATLVHAQYTTVKHP 73 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQA 157 + L ++L E P +++ + + NSG+EA E+A++L + TGR +AF FHGRT Sbjct: 74 RMLELTDRLYERLPAELDA-IAFWNSGSEAVESAVRLARQATGRANIIAFQGGFHGRTMG 132 Query: 158 VLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR 217 SLT S + GF P M GV + P+P+ YR W +E T L ++ Sbjct: 133 AASLTTSTPKVRTGFHPMMAGVVYAPFPHTYRYGWS------EEETTRFCLQELDHLFVT 186 Query: 218 HVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWA 277 P + AI EP+QGE GY +GF + L++ D +GI+L DE+Q G GRTG+FW+ Sbjct: 187 QSAPSDTAAIIVEPVQGEYGYYPATEGFMQGLRERCDRHGIVLICDEIQAGYGRTGQFWS 246 Query: 278 IEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDK-PGRHATTFGGNPVAIAAGIEVVE 336 EHF V PD++ K + G PL+ + AD+ PG T+G N VA AA + ++ Sbjct: 247 HEHFDVRPDILITAKGLASGYPLSAIAASADLMKQGFPGSQGGTYGANAVACAAALATLD 306 Query: 337 IVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELR 394 + ++ LL +V+E G YL + LE + Y I + RG+GL +EIV K K+ E Sbjct: 307 VFEQENLLANVRENGAYLRQQLERLQSAYRFIDEIRGMGLMLGMEIVDDK--KQPSGERA 364 Query: 395 DRIVKESAKRGLVLLGCGDNS--IRFIPPLIVTKEEIDVAMEIFEEALK 441 +++KES GL++L CG + +R++PPLIVT+E+ID A+ +FE+AL+ Sbjct: 365 AQLLKESEAAGLLMLRCGTHGQVVRWLPPLIVTREQIDEAVGLFEQALQ 413 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: 466 Number of extensions: 28 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: 415 Length adjustment: 32 Effective length of query: 413 Effective length of database: 383 Effective search space: 158179 Effective search space used: 158179 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