Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_013721656.1 ALIDE2_RS06730 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000204645.1:WP_013721656.1 Length = 442 Score = 196 bits (498), Expect = 1e-54 Identities = 140/421 (33%), Positives = 212/421 (50%), Gaps = 18/421 (4%) Query: 34 ENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTD 93 + P + +G V D G DF SG +GH+HP +V+A+++ EK H + Sbjct: 19 DTFPSLFRSAKGCVVTDDTGREILDFTSGQMCATIGHNHPAIVQAVQEAGEKAYHM-FSG 77 Query: 94 FFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHG 153 E LA+ + K ++ N+G+E+NE A+++ K T + LA ++HG Sbjct: 78 MIPEVVARLAQTMARDWMPQGLSKSIFINTGSESNEVALRMAKMYTQGFEILAVGGSWHG 137 Query: 154 RTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRN-TWGIDGYEEPDELTNRVLDFIE 212 T A + AS + G+ +PGV +P PN YR G+DG E + I Sbjct: 138 VTGAASA--ASFASDRKGYGVHVPGVFVMPEPNMYRPYIQGMDG-----EASALACLEIG 190 Query: 213 EYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRT 272 ++ AI EPI GG +VPPK + +AL+K ADE G+LL DE Q GR Sbjct: 191 LKMYDMASTGRRSAIIIEPIISAGGVLVPPKSYMQALRKAADERGMLLIFDEAQTAFGRI 250 Query: 273 GKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD---KPGRHATTFGGNPVAIA 329 G A + FGV PD++ K +GGGLPLA V +I D K T+ +P+ Sbjct: 251 GHRHAADFFGVTPDIMAVSKTMGGGLPLAAVSTTPEIEEDIHAKGFTFYTSHVSDPLPAT 310 Query: 330 AGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETK 387 G+ V+ +++ L+ Q +G YL + LEE + +YE IGD RG G+ VE+VKS+ET+ Sbjct: 311 VGLAVLRTIQQERLIERAQSMGAYLRRRLEELQSRYEAIGDVRGEGMLLGVELVKSRETR 370 Query: 388 EKYPELRDRIVKESAKRGL---VLLGCGDNSI-RFIPPLIVTKEEIDVAMEIFEEALKAA 443 E Y L + + GL + S+ R PPL T+ EID +++ +EAL+ + Sbjct: 371 EPYHALGAITTQRCYELGLSMNIRRRPERGSVWRIAPPLTATQGEIDRGVDMLDEALRRS 430 Query: 444 L 444 + Sbjct: 431 I 431 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: 478 Number of extensions: 20 Number of successful extensions: 6 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: 442 Length adjustment: 32 Effective length of query: 413 Effective length of database: 410 Effective search space: 169330 Effective search space used: 169330 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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