Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_013450014.1 SULKU_RS13855 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000183725.1:WP_013450014.1 Length = 388 Score = 271 bits (692), Expect = 3e-77 Identities = 155/393 (39%), Positives = 222/393 (56%), Gaps = 13/393 (3%) Query: 34 YVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLH 93 Y+++TY R + RG +TL D+EGK Y+DF AG+A C++GH + L RA+SDQ K+ Sbjct: 5 YLLSTYKRQEVCFERGDNATLCDSEGKEYIDFAAGVAVCSVGHGNCRLARAISDQAAKIL 64 Query: 94 HVSNLYYIPEQGELAKWIVEHSCAD-RVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPV 152 HVSNLY I Q E A+ IVE S D R FF NSG EANE AIK+ RKY +++ Sbjct: 65 HVSNLYRIEPQEECARRIVELSGYDMRCFFGNSGTEANEGAIKIARKYGERD-GSIKRYK 123 Query: 153 ILTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRV 212 I+T + SFHGRT+ + ATGQ YF P GF Y ++ +E+ + + Sbjct: 124 IITLENSFHGRTITALKATGQASKHDYFGPYPDGFVYAA--NVEEIESLI------DETT 175 Query: 213 AAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVE 272 A+ +E +QGEGGV+P D + + + DILL+ DEVQ G+ R G + G+ Sbjct: 176 VAVMIELVQGEGGVQPLDKQKVQNLSALLKSKDILLIVDEVQTGIYRCGSFLASHYYGIT 235 Query: 273 PDIFTSAKGLAGGVPIGAMMCKKFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRLL 332 PD+ T AKGL GGVPIG +M + ++F G+H STFGGN L+ A VL +E Sbjct: 236 PDVITLAKGLGGGVPIGVVM-TRLKEIFSYGDHGSTFGGNYLSTVAANEVLDILEAYNKS 294 Query: 333 DNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAMEQGLL 392 + + L YP +FTE G G++ GL + L+ +I+ +A E G+L Sbjct: 295 GEMMEHQNYFETSLKSFALHYPDIFTERVGIGMMQGLRVIDSEVLS--KIIDSAFEIGVL 352 Query: 393 LAPAGPKVLRFVPPLVVTEAEIAQAVEILRQAI 425 + +G LRFVPPL ++++E+ + L A+ Sbjct: 353 VIKSGRNTLRFVPPLTISKSEMDEGFRRLNSAM 385 Lambda K H 0.320 0.137 0.405 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: 363 Number of extensions: 15 Number of successful extensions: 6 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: 429 Length of database: 388 Length adjustment: 31 Effective length of query: 398 Effective length of database: 357 Effective search space: 142086 Effective search space used: 142086 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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