Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_012675586.1 PERMA_RS00880 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000021565.1:WP_012675586.1 Length = 388 Score = 336 bits (862), Expect = 6e-97 Identities = 177/393 (45%), Positives = 258/393 (65%), Gaps = 17/393 (4%) Query: 34 YVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLH 93 Y++ Y R+P++ +G+G L+DTEGK Y+D +AGIA TLG+ HP L A+ +QI+ + Sbjct: 11 YLIQNYARYPVSFVKGEGVYLYDTEGKRYIDMLAGIAVNTLGYNHPLLTEALCNQIKDVI 70 Query: 94 HVSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVI 153 HVSNL+YI Q ++AK +VE+SC DRVFFCNSGAEANE AIKLVRKY + E+ I Sbjct: 71 HVSNLFYIQPQIDVAKILVENSCLDRVFFCNSGAEANETAIKLVRKYFYD-KGKPEKFEI 129 Query: 154 LTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRVA 213 +T FHGRT+ ++TAT QPKY + F PL+ G Y +N++ SL++ V N A Sbjct: 130 VTFTGGFHGRTIGSLTATAQPKYHEGFKPLLQGIRYAEFNNVESLKSAV------NENTA 183 Query: 214 AIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVEP 273 A+ E +QGEGG+ P D + + +I + D+L+V DEVQ G+GRTGKL+ Y+H + P Sbjct: 184 AVMFEFIQGEGGINPIDRDFLSEIVKISREYDLLIVVDEVQTGIGRTGKLFAYQHYDICP 243 Query: 274 DIFTSAKGLAGGVPIGAMMCK-KFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRLL 332 DI T AKGL GGVPIGA++ K + +VF PG H STFGGN ++ A VL + D L Sbjct: 244 DIVTLAKGLGGGVPIGAVLAKEEVAEVFTPGTHGSTFGGNYISTTAAKVVLNEVLKDGFL 303 Query: 333 DNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAMEQGLL 392 ++V+ +GE L + E++N + + RG GL+ G + + + + +I K A+++GL+ Sbjct: 304 EDVEKKGEFL---IEELRN----IGLKPRGKGLMVGCPLPED--IKAGDIAKKALDEGLI 354 Query: 393 LAPAGPKVLRFVPPLVVTEAEIAQAVEILRQAI 425 + AG LRFVPPL++ + +I +AV IL++ + Sbjct: 355 IGTAGGNTLRFVPPLIIQKEQIQEAVNILKKVV 387 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: 397 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: 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