Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >FitnessBrowser__Koxy:BWI76_RS14020 Length = 461 Score = 225 bits (574), Expect = 2e-63 Identities = 138/439 (31%), Positives = 234/439 (53%), Gaps = 51/439 (11%) Query: 27 KTADFDTYVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVS 86 + A+F++ V + + P+AI + +G L D + K YLD +AG T LGH HP +++++ Sbjct: 26 RQAEFESNVRSYPRKLPLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQ 85 Query: 87 DQIQK---LHHVSNLYYIPEQGELAKWIVEHSCADRVFFC-----NSGAEANEAAIKLVR 138 I LH + P + +++++ + +C SGA+A EAA+KL + Sbjct: 86 SVITSGLPLHTLD--LTTPLKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAK 143 Query: 139 KYAHTVLDFLEQPVILTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYND---- 194 KY + +++ +HG T ++ TG + + ++P ++PY Sbjct: 144 KYTG-------RSSVISFSGGYHGMTHGALSVTGNLSPKAAVNGMMPEVQFMPYPHQYRC 196 Query: 195 ---------IRSL----ENKVADLDEGNSRVAAIFLEPLQGEGGVRPGDLAYFKRVREIC 241 +++L EN + D++ G + AA+ LE +QGEGGV P + + +R+R++ Sbjct: 197 PLGIGGEAGVKALTYYFENLINDVESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVT 256 Query: 242 DQNDILLVFDEVQVGVGRTGKLWGYEHLGVEPDIFTSAKGLAGGVPIGAMMCKKFCDVFE 301 ++ ILL+ DEVQ G RTGK + +EH G+EPDI +K + GG+P+ + KK D +E Sbjct: 257 QEHGILLIIDEVQAGFARTGKFFAFEHAGIEPDIIVMSKAVGGGLPLAVLGIKKQFDAWE 316 Query: 302 PGNHASTFGGNPLACAAGLAVLKTIEGDRLLDNVQARGEQLRSGLAEIKNQYPTLFTEVR 361 PG+H TF GN LA A GL L+ ++ +++ D A+GE L+ LAE++ +YP + VR Sbjct: 317 PGHHTGTFRGNQLAMATGLTTLRHLKDNKIADKTAAQGEWLKGKLAEMQKRYPVI-GHVR 375 Query: 362 GWGLINGLEI-------------SAESSLTSVEIVKAAMEQGLLLAPAGPK--VLRFVPP 406 G GL+ G+EI A+ L+++ + K E GL+L G VLR +P Sbjct: 376 GLGLMIGIEIVKPNEAPDHMGCYPADGELSAL-LQKKCFEAGLILERGGRHGCVLRLLPS 434 Query: 407 LVVTEAEIAQAVEILRQAI 425 L+++ AE+ + QA+ Sbjct: 435 LLISNAELEIFFDKFEQAL 453 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: 488 Number of extensions: 30 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: 429 Length of database: 461 Length adjustment: 32 Effective length of query: 397 Effective length of database: 429 Effective search space: 170313 Effective search space used: 170313 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 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