Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate WP_011841396.1 RSPH17029_RS10240 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q84P52 (520 letters) >NCBI__GCF_000015985.1:WP_011841396.1 Length = 455 Score = 389 bits (1000), Expect = e-113 Identities = 184/418 (44%), Positives = 271/418 (64%), Gaps = 2/418 (0%) Query: 85 LVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYHSFWNRST 144 +V+ +G Y+YDV+G+ YLDA +GLW G + P L+ AA Q YH+F+ R + Sbjct: 33 VVLTHGKGPYIYDVHGRAYLDANSGLWNMVAGFDHPGLIEAAKAQYERFPGYHAFFGRMS 92 Query: 145 KPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKKFIARTKS 204 ++ L+++L+++ + + F+TNSGSEANDT VK++W+ A G P+++K I R S Sbjct: 93 DQTVMLSEKLVEVSPFAR-GRVFYTNSGSEANDTMVKMLWFLGAAEGHPERRKIITRVNS 151 Query: 205 YHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFSTRLANNLENL 264 YHG T +SAS++G P + F LP P +H CPH+WRF Q GETE EF+ RLA LE Sbjct: 152 YHGVTAVSASMTGKP-YNSLFGLPLPGFIHVGCPHYWRFGQAGETEAEFTQRLARELEAT 210 Query: 265 ILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDILFIADEVICGFGRLGTM 324 I+KEGP+TIA F AEPVMGAGGVIPP YF+ +Q +L++Y I IADEVICGFGR G Sbjct: 211 IIKEGPDTIAGFFAEPVMGAGGVIPPSEGYFQAIQPVLQRYGIPLIADEVICGFGRTGNT 270 Query: 325 FGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFSHGFTYSGHPV 384 +GC+ Y+ PD + +K +++G+ P+GAV++ PE++D + + S + F HGFT SGHPV Sbjct: 271 WGCQTYDFMPDAIISSKNITAGFFPMGAVILGPELADRLQAASEAVEEFPHGFTASGHPV 330 Query: 385 SCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEIRGTGLLHGTEFTDNKS 444 CA+AL+ + + + E V ++PKF+ GL +++P IGE RG GL+ E +K+ Sbjct: 331 GCAIALKAIDVVMNEGLAENVRALTPKFEAGLAYLAENPNIGEWRGKGLMGALEAVKDKA 390 Query: 445 PNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEIDELIIKYGKALK 502 PFP + + C HG++ R G +I++ PP+I++ ++DE+ K G ALK Sbjct: 391 TKTPFPGDLSVSERIANSCTDHGLICRPLGQSIVLCPPFIMTEAQMDEMFEKLGAALK 448 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: 641 Number of extensions: 23 Number of successful extensions: 3 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: 455 Length adjustment: 34 Effective length of query: 486 Effective length of database: 421 Effective search space: 204606 Effective search space used: 204606 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 Apr 10 2024. 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