Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_003173355.1:WP_109969613.1 Length = 384 Score = 217 bits (552), Expect = 6e-61 Identities = 130/405 (32%), Positives = 199/405 (49%), Gaps = 51/405 (12%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 I+I +G G V D DG + D +G+ V + GH HP+VV+AI +QA + H S F+ Sbjct: 23 IMITKGSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNL-FYVP 81 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQA 157 + LA+KL+E++ K + NSGAEA E A+KL + TGRK+F+A FHGRT Sbjct: 82 HQGALAKKLVEISGLPGNAKAFFSNSGAEAMEGALKLARIRTGRKEFIACEGGFHGRTMG 141 Query: 158 VLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR 217 L+ T +++ F P P + +PY + + Sbjct: 142 SLACTHKPAIREP-FMPLQPFTSFVPYG--------------------------DVQALK 174 Query: 218 HVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWA 277 E A+ EPIQGEGG ++PP G+ K +++ D G+LL DEVQ G+GRTG ++A Sbjct: 175 GAITEETAAVILEPIQGEGGVIIPPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFA 234 Query: 278 IEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAIAAGIEVVEI 337 + G+ PD+I KA+ G P+ ++ R + F K H +TF G P+A AA + +++ Sbjct: 235 FQEEGIHPDIITMAKAMASGFPMGAIVAREGLEFGK-SEHGSTFAGGPIACAAALASIDV 293 Query: 338 VKELLPHVQEVGDYLHKYLEEFKEKYE--VIGDARGLGLAQAVEIVKSKETKEKYPELRD 395 + ++LP V G+ L + + +IG G A Sbjct: 294 IGKVLPEVAAKGERFRAALAHLNPRVKGLMIGITIGDHCAD------------------- 334 Query: 396 RIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEAL 440 + KE A GL++ ++R +PPL +T EID A I A+ Sbjct: 335 -VQKECAVHGLLVNCAAHGNLRLVPPLTITNAEIDKATGIINAAV 378 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: 26 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: 384 Length adjustment: 31 Effective length of query: 414 Effective length of database: 353 Effective search space: 146142 Effective search space used: 146142 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 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