Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate CA265_RS07530 CA265_RS07530 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__Pedo557:CA265_RS07530 Length = 433 Score = 187 bits (474), Expect = 9e-52 Identities = 129/433 (29%), Positives = 217/433 (50%), Gaps = 31/433 (7%) Query: 77 WH-----STDLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLN 131 WH L + I + EG YV+D +GK+Y+DA++ W G + P + +QLN Sbjct: 25 WHPYTQMKNALPHIPIVRGEGVYVFDESGKRYIDAVSSWWVNIHGHSHPYIAQKVAEQLN 84 Query: 132 ELAFYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALG 191 L + F + +P++ LA+ LL + K K F+T++GS A + +K+ Y + G Sbjct: 85 VLE-HVIFAGFTHEPAVLLAERLLPILPG-KQDKVFYTDNGSTAVEVALKMCLQYWDNKG 142 Query: 192 RPDKKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEE 251 P K K +A +YHG T + S+SG F+ V D P+ + Sbjct: 143 TP-KTKILAFKNAYHGDTFGAMSVSGRSIFTDAFNSLLFDVEFIDLPNEYNI-------- 193 Query: 252 EFSTRLANNLENLILKEGPETIAAFIAEP-VMGAGGVIPPPATYFEKVQAILKKYDILFI 310 + L ++L NL A FI EP ++G+GG++ A Y +++ + K+ IL I Sbjct: 194 ---SHLTSHLSNL------SDTACFIFEPLILGSGGMLMYEAKYLDQLLSACKEAGILTI 244 Query: 311 ADEVICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKL 370 ADEV+ GFGR GT F CEK KPD++ ++K L+ G MP+G + E+ + S +KL Sbjct: 245 ADEVMTGFGRTGTYFACEKLINKPDIICLSKGLTGGTMPLGVTTCTNEIFEAFLS-DDKL 303 Query: 371 GTFSHGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEIRG 430 T HG +++ +P++C +L +L I + ++ + R+ K L+ P + IR Sbjct: 304 KTLYHGHSFTANPIACVASLASLDILLKSETLQNIKRVEAKHAVFLEEIKTHPKVKAIRQ 363 Query: 431 TGLLHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEI 490 TG + E+ + + AYF + G+++R G+ I + PPY++S E++ Sbjct: 364 TGTIIAIEWETGNETSYLSNLRNLLYAYFLDK----GIILRPLGNIIYILPPYVISDEDL 419 Query: 491 DELIIKYGKALKD 503 D + AL++ Sbjct: 420 DYIYATIKLALEE 432 Lambda K H 0.317 0.135 0.401 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: 527 Number of extensions: 28 Number of successful extensions: 6 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: 520 Length of database: 433 Length adjustment: 33 Effective length of query: 487 Effective length of database: 400 Effective search space: 194800 Effective search space used: 194800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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