Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 226 bits (576), Expect = 1e-63 Identities = 144/425 (33%), Positives = 220/425 (51%), Gaps = 40/425 (9%) Query: 27 AMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKF 86 A Q P+ +ERGEG RV+D G + DF +G+ +GH+HP +V+AI Q K Sbjct: 25 ACVMQTYGRFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKL 84 Query: 87 THYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV-KYGTGRKQ-- 143 H S + E + A L +V + NSGAEANEAA+KL K+G + Sbjct: 85 HHVSNLYYIPEQGQLAAW----LTANSCADRVFFCNSGAEANEAAIKLARKHGNTVLEAE 140 Query: 144 ---FLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEP 200 L +FHGRT A ++ T + GF P + G ++PY + Sbjct: 141 NPIILTAQASFHGRTLAAVTATGQPKYHK-GFQPLVQGFRYVPYNDLAAL---------- 189 Query: 201 DELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILL 260 E T LD E V AI EP+QGEGG + +F+A+++ D+ +LL Sbjct: 190 -EATLAELDAAGETV---------AAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLL 239 Query: 261 ADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATT 320 DEVQ+G+GR+G+ W E+ G+EPD K +GGG+P+ ++ +A + G HA+T Sbjct: 240 ILDEVQVGMGRSGQLWGYENLGIEPDAFTVAKGLGGGVPIGALLVKASCNILQAGEHAST 299 Query: 321 FGGNPVAIAAGIEVVEIVK--ELLPHVQEVGDYLHKYLEEFKEKY-EVIGDARGLGLAQA 377 FGGNP+A AG+ + ++++ +LL +VQ G+ L L+E ++Y ++ RG GL Sbjct: 300 FGGNPLACRAGLAIAQVMERDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLING 359 Query: 378 VEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFE 437 + + +VK + ++GL+L+ G +RF+PPLIV+ EID A+ + E Sbjct: 360 LVLRNDPNVTP------IALVKAAIEQGLLLVPAGAEVVRFVPPLIVSAAEIDEALAMTE 413 Query: 438 EALKA 442 AL A Sbjct: 414 RALLA 418 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: 448 Number of extensions: 21 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: 422 Length adjustment: 32 Effective length of query: 413 Effective length of database: 390 Effective search space: 161070 Effective search space used: 161070 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 17 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