Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_011802239.1 PNAP_RS14300 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000015505.1:WP_011802239.1 Length = 465 Score = 153 bits (387), Expect = 9e-42 Identities = 133/429 (31%), Positives = 205/429 (47%), Gaps = 57/429 (13%) Query: 35 IAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHHISNLYY---IP 91 I K E +WD+EG LD ++G+ +G+ L A Q+ L + ++ + +P Sbjct: 36 ITKAENIYVWDSEGHKILDAMSGLWCVNVGYGREELASAAYRQMMLLSYYNSFFQTTNVP 95 Query: 92 ------EQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQP---VI 142 + ALA + S VF+ +SG+E+N++ +++VR+Y D L QP VI Sbjct: 96 AVQLAAKLAALAPEVGGRSFRH-VFYSSSGSESNDSNVRMVRRYW----DLLGQPQRKVI 150 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFD-PLP-----------------DGFAYVPYNDI 184 +S +++HG T+A + G D P+P + A Sbjct: 151 ISRNNAYHGSTMAGASLGGMSGMHAQGDLPIPNITHIEQPYFYELGQPGESSAEFGLRAA 210 Query: 185 RALEEAITDIDEGNRRVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQV 244 R LEE I I+ G +VAA + E +QG GGV Y+ ++RI D+ GILL+ DEV Sbjct: 211 RWLEEKI--IETGPDKVAAFIAEPVQGAGGVIIAPDSYWPEIQRIVDKYGILLISDEVIC 268 Query: 245 GVGRTGKYWGYENLGIEPDIFTSAKGLAGG-IPIGAMMCKDSCA---VFNPGE--HASTF 298 GR G ++ YE G PD+ T AKG+ G IP+G +M D A + GE H T+ Sbjct: 269 AFGRLGYWFAYEKFGYRPDLVTFAKGVTSGYIPLGGVMVGDRVATVLIEQGGEFNHGYTY 328 Query: 299 GGNPFSCAAALAVVETLEQENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGME 358 G+P +CA ALA +E +E+ENL V A T ++P G + G+ Sbjct: 329 SGHPVACAVALANLELMEKENLPGRVRDDIGPYLARRFTELGEHPLVGLAETCGFMAGLV 388 Query: 359 I---KADLELTSIEVVKAAM------EKGLLLAPAGPKVLRFVPPLIVSAAEINEAIAL- 408 + KA E E+ + GL++ G +++ PPL+++ +I+E IAL Sbjct: 389 LVRNKATQEAFKPELGVGMLCRSHCFRLGLIMRAVGDRMI-IAPPLVMTHDQIDEMIALI 447 Query: 409 ---LDQTLA 414 LD TLA Sbjct: 448 RRCLDATLA 456 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: 24 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 418 Length of database: 465 Length adjustment: 32 Effective length of query: 386 Effective length of database: 433 Effective search space: 167138 Effective search space used: 167138 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