Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate NP_444087.1 NGR_a01380 hypothetical protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000018545.1:NP_444087.1 Length = 467 Score = 212 bits (540), Expect = 2e-59 Identities = 139/430 (32%), Positives = 226/430 (52%), Gaps = 28/430 (6%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHY-SLTDFF 95 P ++E G+GIR+ D GN D +G+ +NVG+ V EAI +QA + +Y S Sbjct: 34 PTIVETGKGIRIQDARGNQLIDGFAGLYCVNVGYGRTEVAEAISRQAYRLAYYHSYAAHT 93 Query: 96 YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTG------RKQFLAFYH 149 + IL+++L+++APG + KV YG SG++ANE KLV Y +K+ ++ Sbjct: 94 TDELAILSDRLVKMAPGKMS-KVFYGMSGSDANETQAKLVWYYNNLRGKPTKKKIISRER 152 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 +HG + S+T + P +P + H P+ Y WG + E E + R Sbjct: 153 GYHGCSVVSGSMTGMSFYHDHMDLP-LPQICHTGVPHHY---WGANPGETEREFSARRAA 208 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 ++E + + P +GA EP+ G GG PP+G+++A++ ++ +LL DEV G Sbjct: 209 ELDEMI-ETLGPDNVGAFIAEPVLGTGGITPPPEGYWEAIQAVLKKHDVLLIADEVITGF 267 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADI------TFDKPG--RHATT 320 GRTG + +H+G+EPDLI K + PL+ I + D+ G H T Sbjct: 268 GRTGSMFGSQHYGIEPDLITVAKGLTSAYFPLSASIVGEKVYKVLEDGADRVGAFSHGYT 327 Query: 321 FGGNPVAIAAGIEVVEIV-KELLP-HVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378 + G+P+ AA V++IV KE LP + +EVG Y L+E + ++G+ RG+GL A+ Sbjct: 328 YSGHPIGAAAANAVLDIVEKEDLPGNAREVGGYFQAQLKEKFAQLPIVGEVRGVGLMGAI 387 Query: 379 EIVKSKETKEKYPELRD---RIVKESAKRGLVLLGCGDNSI-RFIPPLIVTKEEIDVAME 434 E V +E K+++ L R+ K + RGL+ I F PPL+ TKEE+D + Sbjct: 388 EFVGDRENKKRFDPLLKVGARVSKAARDRGLIARAMPHGDILGFAPPLVTTKEEVDEIVA 447 Query: 435 IFEEALKAAL 444 + E+A+++ + Sbjct: 448 MAEKAVRSVM 457 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: 582 Number of extensions: 28 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: 467 Length adjustment: 33 Effective length of query: 412 Effective length of database: 434 Effective search space: 178808 Effective search space used: 178808 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