Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_084201012.1 C0029_RS15270 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_002869505.1:WP_084201012.1 Length = 426 Score = 134 bits (336), Expect = 7e-36 Identities = 96/307 (31%), Positives = 148/307 (48%), Gaps = 29/307 (9%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+ I+R +G RVYD +G + D+ G + +GH+HP V EA+ KQ+EK + Sbjct: 33 PVFIDRSDGARVYDCEGKAYIDYVLSWGPMIMGHNHPAVREAVIKQSEKGLSFGAPT--- 89 Query: 97 ENAIILAEKLIELAPG-DIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRT 155 E I LA+++ E+ PG D+ R V NSG EA +A++L + TGR + F +HG + Sbjct: 90 ELEIQLADRICEIMPGMDLVRMV---NSGTEATMSAIRLARGYTGRDTIVKFEGCYHGHS 146 Query: 156 QAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215 ++L S + P+ PGV + T Y +P+ + + + Sbjct: 147 DSLLVKAGSGALTMG--VPSSPGVPAALADHTMTLT-----YNDPEGVRAAFAEHGD--- 196 Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275 I + EP+ G + P GF + L++ D G +L DEV G R G Sbjct: 197 -------SIACVIVEPVAGNMNCIPPEPGFLETLRECCDVSGAVLILDEVMTGF-RFGLQ 248 Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD----KPGRHATTFGGNPVAIAAG 331 A FGVE DL GK +GGG+P+ + +I P A T GNP+A+AAG Sbjct: 249 GAQGFFGVEADLTTLGKVVGGGMPVGAFGGKREIMEQIAPLGPVYQAGTLSGNPIAMAAG 308 Query: 332 IEVVEIV 338 + ++I+ Sbjct: 309 LATLDII 315 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: 19 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: 426 Length adjustment: 32 Effective length of query: 413 Effective length of database: 394 Effective search space: 162722 Effective search space used: 162722 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 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