Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__PS:Dsui_0132 Length = 385 Score = 157 bits (396), Expect = 6e-43 Identities = 113/363 (31%), Positives = 169/363 (46%), Gaps = 7/363 (1%) Query: 23 RALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERH 82 RA QG +I+ + VG+PDF TP PI+ AA + L G Y G LR+ I+ + Sbjct: 22 RARELEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFYTPALGLPELREAISGFY 81 Query: 83 RRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVP 142 R+R G AV A ++ + AGA AL + CL PG E ++ +P Y A V Sbjct: 82 RQRYGIAVPASRIAITAGASGALTLALACLAAPGSEWLLTDPGYPCNRHFVRAFEGVPVS 141 Query: 143 VPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMI 202 +PV + + F+ ++ RT SP NP+G L A +A+ +I Sbjct: 142 IPVGAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAAELADIADFVRQRQGQLI 201 Query: 203 SDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENL 262 DE+Y L ++G+ +P +L D + S SK MTGWR+GW+V P +E L Sbjct: 202 IDEIYHGLTYNGD--APTAL-AAGDNIFVVQSFSKYFQMTGWRLGWLVIPEPFVRDVEKL 258 Query: 263 ALCMLYGSPEFIQDAACTALE-APLPELEAMREAYRRRRDLVIECLADSPGLR-PLRPDG 320 A + + Q AA A + + LE R ++ RRD + L ++ G R +P+G Sbjct: 259 AQNLFISASTPAQHAALAAFQPETIALLEQRRAEFKARRDYLAPAL-EAIGFRITAQPEG 317 Query: 321 GMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFG-PSAAGHIRLGLVLGAEPLREAC 379 ++ D + FA RLL+ GV++ G FG A+ H+R L E Sbjct: 318 AFYLYADCSTLTDDSFGFARRLLEEAGVAITPGIDFGNHGASSHVRFAYTNAQARLAEGV 377 Query: 380 RRI 382 RI Sbjct: 378 ERI 380 Lambda K H 0.322 0.136 0.411 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: 418 Number of extensions: 28 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: 393 Length of database: 385 Length adjustment: 30 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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