Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 214 bits (546), Expect = 3e-60 Identities = 148/425 (34%), Positives = 224/425 (52%), Gaps = 55/425 (12%) Query: 26 LAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEK 85 LA TT P L I IE+ EGI +Y G + D SG+GV NVGH HP+V++AI+ Q +K Sbjct: 11 LAQTTDFP--LLIEIEKAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDK 68 Query: 86 FTHYSLTDFFYENAII-LAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQF 144 + H + + ++ LA+ L + P ++ V NSG+EA E A+KL K TGR++ Sbjct: 69 YMHLMVYGEYVQSPQTQLAKALTDTLPKKLDN-VYLVNSGSEAVEGALKLAKRYTGRREI 127 Query: 145 LAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELT 204 L+ +A+HG + LS+ ++ + + + P +PG+ H+ + EPD+L Sbjct: 128 LSCVNAYHGSSHGALSVGGNE-IFKRAYRPLLPGIRHLDF-------------NEPDQL- 172 Query: 205 NRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDE 264 D I E E AI E +QGE G V K +FKAL+ DE G LL DE Sbjct: 173 ----DQITE---------ETAAIMVETVQGEAGIRVGTKEYFKALRHRCDETGTLLILDE 219 Query: 265 VQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGR----HATT 320 +Q G GRTGKFWA +H+ + PD++ K +GGG+P+ I I H TT Sbjct: 220 IQAGFGRTGKFWAFQHYDIVPDIVVCAKGMGGGMPIGAFIAPQSIMSVFKNNPLLGHITT 279 Query: 321 FGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378 FGG+PV+ AA + ++I+++ L+ HV+ + K+L K I + R GL AV Sbjct: 280 FGGHPVSCAAALATIDILRDEKLIQHVERKANLFKKHLNHPK-----IQEIRNKGLMMAV 334 Query: 379 EIVKSKETKEKYPELRDRIVKESAKRGLV---LLGCGDNSIRFIPPLIVTKEEIDVAMEI 435 + E + L+ I+ + + G++ L C D S+R PPL +T EEI+ A I Sbjct: 335 KF-------EAFEVLKP-IIDRAIELGIITDWFLFCED-SMRIAPPLTITDEEIEKACAI 385 Query: 436 FEEAL 440 +++ Sbjct: 386 ILQSI 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: 416 Number of extensions: 23 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: 393 Length adjustment: 32 Effective length of query: 413 Effective length of database: 361 Effective search space: 149093 Effective search space used: 149093 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: 50 (23.9 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