Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_028584210.1 G494_RS0108610 aspartate aminotransferase family protein
Query= BRENDA::B1A0U3 (469 letters) >NCBI__GCF_000429965.1:WP_028584210.1 Length = 398 Score = 251 bits (642), Expect = 2e-71 Identities = 146/390 (37%), Positives = 218/390 (55%), Gaps = 12/390 (3%) Query: 47 NYHPLPIVFAHAKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSR 106 NY P +G +WD +G +Y+DFL+G + + GHCHP++ +A+ QA L S Sbjct: 17 NYSRFPATMVRGQGCRLWDEDGREYLDFLAGIAVCSLGHCHPRVTEAVVAQARSLVHVSN 76 Query: 107 AFYNDRFPVFAEYLTALFGYDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVSC 166 F+ AE LTA D V N+GAE E A+KLAR E + I+S Sbjct: 77 LFHTRPQIELAELLTANTFADRVFMANSGAEVNEAAIKLARIHSGEGRYE------IISL 130 Query: 167 CGCFNGRTLGVISMSCDNEATRGFGPLMPGHLKVDFGDAEAIERIFKEKGDRVAAFILEP 226 G F+GRTL ++ + + +GF P+ G +GD +E++ GD+ A + EP Sbjct: 131 TGSFHGRTLATVAATAQPKFHQGFEPMPQGFRYAPYGDPGEVEQLI---GDQTCAILCEP 187 Query: 227 IQGEAGVVIPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDVRPDVVILG 286 +QGE GV+ + YL+A+RDLC ++ +L+I DEIQTG+ RTG + A + V PD++ Sbjct: 188 LQGEGGVLPLGNEYLQALRDLCDQHGLLLIFDEIQTGMGRTGTLFAYEQTGVVPDIMTSA 247 Query: 287 KALGGGILPVSAVLADKDVMLCIKPGQHGSTFGGNPLASAVAIAALEVIKEERLTERSTK 346 KAL G LP+ A+L ++ + PG HGSTFGGNP+A+A A+A LE + E + Sbjct: 248 KALANG-LPLGALLTTDEIAASLVPGTHGSTFGGNPVAAAAAVAVLEEMLAPGFLEGVQQ 306 Query: 347 LGGELLGLLHKIQKKHPEHVKEVRGKGLFIGVELNSESLSPVSGFELSEKLKERGVLAKS 406 G G L+++ + P VRG+GL +G+ L E ++ G E+ ++L RG++ Sbjct: 307 TGAYFSGKLNELAARFPVLASGVRGQGLLLGLILTEEGIA--HGGEIVQRLFGRGMVINF 364 Query: 407 THDTIIRFTPPLCISADEIQQGSKALAEVL 436 +T++RF PPL +S EI Q LAEVL Sbjct: 365 AGNTVLRFAPPLVVSRAEIDQLIAELAEVL 394 Lambda K H 0.319 0.137 0.409 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: 425 Number of extensions: 23 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: 469 Length of database: 398 Length adjustment: 32 Effective length of query: 437 Effective length of database: 366 Effective search space: 159942 Effective search space used: 159942 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 (21.8 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