Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate BWI76_RS14455 BWI76_RS14455 aspartate aminotransferase family protein
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__Koxy:BWI76_RS14455 Length = 447 Score = 258 bits (660), Expect = 2e-73 Identities = 151/435 (34%), Positives = 239/435 (54%), Gaps = 15/435 (3%) Query: 84 PLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYHSFWNRS 143 P V ++G+Y+ D +G++YLDA G + LG P ++AA +Q++ LA+ H+ + Sbjct: 13 PAVAVSAQGAYITDASGQRYLDACGGAAVSCLGHAHPDVLAAMHRQIDRLAYAHTSF--F 70 Query: 144 TKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKKFIARTK 203 T +++ E L + A+F + GSEA +T +KL Y +G+PD+ FIAR + Sbjct: 71 TSDTVEQLAEQLVRTAPGSLNYAYFVSGGSEAVETALKLARQYFVEIGQPDRTLFIARKQ 130 Query: 204 SYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFSTRLANNLEN 263 SYHG+TL + ++ G +QF V+ + +R + GE++++++ RL LE Sbjct: 131 SYHGNTLGALAVGGNEWRRRQFAPLLMDVVRVSACNEYRDREAGESQQQYTERLLGELEA 190 Query: 264 LILKEGPETIAAFIAEPVMGA-GGVIPPPATYFEKVQAILKKYDILFIADEVICGFGRLG 322 IL GPE I FIAE V+GA G +PP Y + V+ + KY IL+IADEV+CG GR G Sbjct: 191 AILDAGPEKIIGFIAETVVGATTGAMPPTPGYLQGVRRLCDKYGILYIADEVMCGMGRTG 250 Query: 323 TMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFSHGFTYSGH 382 T+ E+ + PD+V++AK L GY PIGAVL S ++ + + S G F HG TY H Sbjct: 251 TLHAFEQDGVVPDIVTIAKGLGGGYQPIGAVLASEQIVAALQAGS---GMFQHGHTYICH 307 Query: 383 PVSCAVALETLKIYKERNIIEQVNRISPKFQEGL-KAFSDSPIIGEIRGTGLLHGTEFTD 441 P + A AL ++ + ++EQV + Q+ L P +G+ RG GL G E Sbjct: 308 PTAAAAALAVQQVIERDRLLEQVQQQGAYLQQALHDVLGGLPYVGDTRGRGLFAGVELVC 367 Query: 442 NKSPNDPFPPEWGIGAYFGARCEKHGVLV--------RVAGDNIMMSPPYILSLEEIDEL 493 +K F P + A A+C HG+LV GD+I+++PP+I+S E+D + Sbjct: 368 DKERKTAFDPLLKLHAAIKAQCMGHGLLVYPMGGTIDGQRGDHILIAPPFIVSRSELDFV 427 Query: 494 IIKYGKALKDTENRV 508 + K + + +++ Sbjct: 428 VDTLHKVISEETHKL 442 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: 534 Number of extensions: 25 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: 447 Length adjustment: 34 Effective length of query: 486 Effective length of database: 413 Effective search space: 200718 Effective search space used: 200718 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: 52 (24.6 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