Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_028949958.1 Q385_RS0101465 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000619805.1:WP_028949958.1 Length = 457 Score = 163 bits (413), Expect = 9e-45 Identities = 124/429 (28%), Positives = 193/429 (44%), Gaps = 59/429 (13%) Query: 43 PIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLHHVSNLYYIP 102 P A+ +GS L+D EGK YLD + C G+ + + + +Q+ L +++ + Sbjct: 26 PKIFAKSEGSYLYDLEGKQYLDLQMWYSACNFGYNNKRINDGIKNQMDTLGQLASQFLTK 85 Query: 103 EQGELAKWIVEHSCADR------VFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVILTA 156 E+ L + + S DR V F G++A E ++K+VR Y L+F Sbjct: 86 EK-ILLSYKIAKSVEDRFKVKGRVHFNVGGSQAIEDSLKIVRNYTKKNLNF-------AF 137 Query: 157 KASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPY------------------------ 192 +HGRT+ T +Y++ + ++P+ Sbjct: 138 MGGYHGRTIGATNITSSYRYRERYGHFSDRAFFIPFPYCFRCPYGKDKETCDLYCAKEFE 197 Query: 193 NDIRSLENKVADLDEGNSRVAAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDE 252 S V + N A ++EP+QG GG YFK+++ + D+ +LLV DE Sbjct: 198 KLFESEYYTVCNPKTKNCEFGAFYIEPIQGTGGYIIPPKDYFKKIKPVLDEYKVLLVSDE 257 Query: 253 VQVGVGRTGKLWGYEHLGVEPDIFTSAKGLAGGV-PIGAMMCKKFC---DVFEPGNHAST 308 +Q+G RTGKLW EH GV PDI K L G+ P+ + K+ ++F PG+ ST Sbjct: 258 IQMGFYRTGKLWSIEHFGVVPDIIVFGKSLTNGMNPLSGLWAKEELINPEIFPPGSTHST 317 Query: 309 FGGNPLACAAGLAVLKTIEGDRLLDNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLING 368 F NP+ AGL V K IE V+ +GE+ + L ++K +YP +V G GL Sbjct: 318 FSSNPIGVRAGLEVFKIIEEKDYEKIVKEKGEKFLNYLKDLKKKYP-FIGDVDGLGLALR 376 Query: 369 LEISAESSLT-SVEIVKAAMEQGL------------LLAPAG---PKVLRFVPPLVVTEA 412 +EI + T S ++ +E+GL L+ G VL P L +T+ Sbjct: 377 VEICEKDGYTPSKKLTDKIVEEGLKANLNLNEKTYGLVLDVGGYYKNVLTLAPSLDITDE 436 Query: 413 EIAQAVEIL 421 EI AVE L Sbjct: 437 EINLAVEFL 445 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: 467 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 429 Length of database: 457 Length adjustment: 32 Effective length of query: 397 Effective length of database: 425 Effective search space: 168725 Effective search space used: 168725 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 10 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