Align ornithine aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_084456741.1 G494_RS0111850 L-lysine 6-transaminase
Query= CharProtDB::CH_122124 (454 letters) >NCBI__GCF_000429965.1:WP_084456741.1 Length = 437 Score = 147 bits (370), Expect = 9e-40 Identities = 123/397 (30%), Positives = 192/397 (48%), Gaps = 34/397 (8%) Query: 53 GRHYLDFLSAYSAVNQGHCHPKLVAALVDQASRLTLSSRAFYNDVFPKFAEMVTKYFGFD 112 G +LDF S Y+++ G+ HPKL+AA DQ + L + + + +AE + + Sbjct: 39 GAPFLDFFSMYASMAVGYNHPKLLAAQ-DQLAPLAVQKPSCSDVYTEAYAEFMATFASHA 97 Query: 113 M--VLP----MNTGAEAVETGIKIARKWGYK---VKGIPENEAI-ILSAENNFHGRTMAA 162 M LP + GA AVE G+K A W + KG +A ++ + FHGR+ Sbjct: 98 MPDYLPHAFFIEGGALAVENGLKTAFDWKVRKNLAKGNHRRQASQVIHFQQAFHGRSGYT 157 Query: 163 ISLSSDPESRENY------GPYVPNIGCTIPGTE---KPITYNDKAA---LREAFEKAGS 210 +SL++ + R+ P + N P + + ++ +K A L E ++AG Sbjct: 158 LSLTNTHDQRKTKFFPTFNWPRIINPKLRFPLDQAQLEEVSRREKLAMDQLTEVIKEAGD 217 Query: 211 NLAAFLVEPIQGEAGIIVPDDDYLQLARSLCDQHNVLLICDEIQTGIARTGKLLCHEWSG 270 +LAA ++EPIQGE G ++LQ R LCD H +L I DEIQTG+ TG+ HE Sbjct: 218 DLAALIIEPIQGEGGDNHFRPEFLQQLRDLCDNHELLYIMDEIQTGLGLTGRFWAHEHFN 277 Query: 271 IKPDMVLLGKAISGGMYPVSCVLGRKDVMLTVEPGTHGSTYGGNPLACAVAIRALEVVQE 330 ++PD++ GK S + + + E ST+GGN + A L+++ E Sbjct: 278 VRPDILCFGKKTQVCGILASKRIDQVADNVFAESSRINSTFGGNLIDMARCSHILKIIAE 337 Query: 331 ENMVERAEKLGQAFRSGLEAIQN---PIIQTVRGKGLLNAIVID--ESKTNGHTAWDLCM 385 + +V + G+ GL+A+ ++ RG+GL+ A +D ESK N A Sbjct: 338 DELVANSRIQGKRLLLGLKALAGEFPELVSNPRGRGLMCAFDLDKEESKNNFIQA----- 392 Query: 386 LMKEKGLLAKPTHQNIIRLAPPLVITEEEIAKALEII 422 KEK LL + IR P L + E EI +AL I+ Sbjct: 393 AFKEKFLLL-GCGEKTIRFRPHLTVAEAEIDEALTIL 428 Lambda K H 0.316 0.133 0.392 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: 395 Number of extensions: 24 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: 454 Length of database: 437 Length adjustment: 32 Effective length of query: 422 Effective length of database: 405 Effective search space: 170910 Effective search space used: 170910 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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