Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_035242472.1 Q366_RS19250 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000745975.1:WP_035242472.1 Length = 398 Score = 342 bits (876), Expect = 2e-98 Identities = 182/393 (46%), Positives = 244/393 (62%), Gaps = 8/393 (2%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 +V TY R KG G +L+D +G Y DF+AGIA C LGH HP + A+SAQ L Sbjct: 9 HVFKTYARQGRPFVKGRGTQLYDDQGNVYTDFLAGIAVCNLGHCHPDITAAISAQAGTLV 68 Query: 83 HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 H+SNL+Y Q LA+ + E S AD+VFF NSGAEANEAAIKL R++ + + I Sbjct: 69 HVSNLFYTRPQAELAKVLTEKSFADRVFFANSGAEANEAAIKLARRFFQAKGE-AGRFKI 127 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202 ++ + SFHGRT+AT++ATGQ K +K F PL DGF +VP+NDI AL+ + + V Sbjct: 128 VTMQQSFHGRTMATLSATGQDKIKKGFFPLLDGFIHVPFNDIEALKAVM------DGTVC 181 Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262 A+M+E +QGEGGV P D EY KAVR++C + G LL+ DE+Q G+GR G + +E+ + P Sbjct: 182 AVMMEPVQGEGGVIPADPEYIKAVRQLCTDTGTLLIFDEIQTGMGRCGTLFAHESYDVVP 241 Query: 263 DIFTSAKGLAGGIPIGAMMCKDSCAV-FNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 DI T AK LA G+PIGAM+ + A+ F G H STFGG P + AAAL VV + ++ L Sbjct: 242 DIMTLAKALANGVPIGAMLASEEAALGFEVGSHGSTFGGTPLATAAALEVVRLISEQGFL 301 Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381 +V + A L L EK+ DVRG GL+ GME+ T+ + V +KG ++ Sbjct: 302 ASVREKSAYFLAQLNGLKEKHKKVVDVRGKGLLIGMELDISKGKTATDYVSECFKKGFII 361 Query: 382 APAGPKVLRFVPPLIVSAAEINEAIALLDQTLA 414 KVLRF PPLI+ EIN+ +A LD LA Sbjct: 362 NAIQDKVLRFAPPLIIGTVEINQLVAELDSLLA 394 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: 392 Number of extensions: 18 Number of successful extensions: 4 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: 398 Length adjustment: 31 Effective length of query: 387 Effective length of database: 367 Effective search space: 142029 Effective search space used: 142029 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