Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_038218346.1 Q392_RS30555 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000745855.1:WP_038218346.1 Length = 400 Score = 335 bits (860), Expect = 1e-96 Identities = 170/388 (43%), Positives = 248/388 (63%), Gaps = 11/388 (2%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 +VM+TYGR P+A+ +G+GCR+WDT GK+YLD + GIA TLGH HP L+ A++ Q+ ++ Sbjct: 10 HVMNTYGRLPIALERGQGCRVWDTNGKAYLDGLGGIAVNTLGHNHPELVPALAEQLGRII 69 Query: 83 HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 H SN Y++P Q LA + + FFC +G EANEAAIKL RK+ H +E+P I Sbjct: 70 HSSNYYHVPGQETLAARLTALAGMTNAFFCCTGLEANEAAIKLARKFGH--GKGIEKPQI 127 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202 + + +FHGR++AT++ATG PK Q F PL +GF VP ND+ AL++A EGN V Sbjct: 128 VVYEHAFHGRSIATLSATGNPKIQAGFGPLLEGFIRVPLNDVDALKQA----TEGNPNVV 183 Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262 A+MLE +QGEGG+ +Y K VR +CD N L+++DE+Q G+GRTGK++ ++ GI P Sbjct: 184 AVMLETIQGEGGIHEMRADYLKQVRALCDANDWLMMIDEIQTGIGRTGKWFAHQWAGIVP 243 Query: 263 DIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 D+ + AKGL G+P+GA++ A +F PG H +TFGGNP + A + + +E++ LL Sbjct: 244 DVMSLAKGLGSGVPVGAVLAGPKAADLFQPGNHGTTFGGNPLAMRAGIETLRIMEKDGLL 303 Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381 +N G L+ L+ E +VRG GL+ G+E+ + ++ A E GLL Sbjct: 304 DNAAKVGAHLKGALQAAFEGVAGVKEVRGQGLMLGIELDRPCGV----LLGRACEAGLLF 359 Query: 382 APAGPKVLRFVPPLIVSAAEINEAIALL 409 + V+R VPPLI++ AE +E +ALL Sbjct: 360 SVTADSVIRLVPPLILTVAEADEIVALL 387 Lambda K H 0.319 0.136 0.406 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: 462 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: 418 Length of database: 400 Length adjustment: 31 Effective length of query: 387 Effective length of database: 369 Effective search space: 142803 Effective search space used: 142803 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 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