Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_057507751.1 ABB28_RS05895 aspartate aminotransferase family protein
Query= BRENDA::P04182 (439 letters) >NCBI__GCF_001431535.1:WP_057507751.1 Length = 450 Score = 155 bits (393), Expect = 2e-42 Identities = 132/423 (31%), Positives = 194/423 (45%), Gaps = 57/423 (13%) Query: 59 PVALERGKGIYMWDVEGRQYFDFLSAYGAVSQGHCHPKIIEAMKSQVDKLTLTSRAFYNN 118 P L R +G+Y DVEGRQ D + + GH KI++A+ Q L + Sbjct: 36 PRLLVRAQGMYYEDVEGRQILDGTAGLWCCNAGHGRKKIVQAIAEQAGTLDFAPTFQMGS 95 Query: 119 ----VLGEYEEYITKLFNYNKVLPMNTGVEAGETACKL------ARRWGYTVKGIQKYKA 168 VL + + N V N+G EA ++A K+ AR G + I + KA Sbjct: 96 PLPFVLAQRLAALAPA-GLNHVFFTNSGSEAVDSAMKIVLAHHRARGEGQRTRFIGREKA 154 Query: 169 KIVFAVGNFWGRTLSAVSSSTDPTSYDGFGPFMPGFETIPYN----------DLP----- 213 VG F G + + P + FG + G +P+ LP Sbjct: 155 --YHGVG-FGGMAIGGL-----PNNRRQFGLQLGGSAHLPHTLDLQRNAFSQGLPRHGAE 206 Query: 214 ---ALER--ALQDPN-VAAFMVEPIQGEAGVIVPDPGYLTGVRELCTRHQVLFIADEIQT 267 ALER AL D + +AA VEPI G AGVI+P PGYL +RE+C H ++ + DE+ T Sbjct: 207 LADALERLIALHDASTIAAVFVEPIAGSAGVILPAPGYLQRLREICDHHGIVLVFDEVIT 266 Query: 268 GLARTGRWLAVDHENVRPDIVLLGKALSGGLYPVSAVLCDDDIMLTIKPGE-------HG 320 G R G A V PD++ K S G P+ VL D I +++ G HG Sbjct: 267 GFGRVGMPFAAQRFGVTPDLITFAKGASNGAVPLGGVLVGDAIHSSLQQGPTQAIDLFHG 326 Query: 321 STYGGNPLGCRIAIAALEVLEEEHLAENADKMGAILRKELMKLPS-DVVTAVRGKGLLNA 379 TY G+PL C A+A L+V EE L E A ++G ++ L L V +R GL+ A Sbjct: 327 YTYSGHPLACAAALATLDVYAEERLFERAIELGEHWQRALHGLQGLPNVVDIRNFGLVGA 386 Query: 380 IVIRETKDC------DAWKVCLRLRDNGLLAKPTHGDIIRLAPPLVIKEDEIRESVEIIN 433 + + +D + ++ C D LL + T GD I L+PPL+++ +I + +++ Sbjct: 387 VELAPRRDAPGSRGYEVFRRC--FHDGNLLVRQT-GDTIALSPPLIVEPAQIDQIADVLG 443 Query: 434 KTI 436 I Sbjct: 444 AMI 446 Lambda K H 0.319 0.137 0.406 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: 407 Number of extensions: 22 Number of successful extensions: 4 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: 439 Length of database: 450 Length adjustment: 32 Effective length of query: 407 Effective length of database: 418 Effective search space: 170126 Effective search space used: 170126 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 09 2024. 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