Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate WP_011384093.1 AMB_RS08515 aspartate aminotransferase family protein
Query= SwissProt::Q84P52 (520 letters) >NCBI__GCF_000009985.1:WP_011384093.1 Length = 459 Score = 450 bits (1157), Expect = e-131 Identities = 220/440 (50%), Positives = 298/440 (67%), Gaps = 1/440 (0%) Query: 69 MLAPFTAGWHSTDLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATK 128 +L P+T ++ PLVI + +G VYD G+ Y++ LAGLWCTSLG E RLV AA + Sbjct: 18 VLHPYTNLKRHPEVGPLVITRGQGVRVYDEAGRDYIEGLAGLWCTSLGWGEERLVEAAAR 77 Query: 129 QLNELAFYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNN 188 Q+ +L FYH F +++ ++L LL + M+K F SGSEANDT +KL+ Y N Sbjct: 78 QMRQLPFYHLFSHKTHDVGVELCARLLAMAPV-PMSKVFLAGSGSEANDTAIKLIHYRAN 136 Query: 189 ALGRPDKKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGE 248 ALG PDKKK IAR K+YHG T+ +ASL+GL + FDLP P VL CPH +RF + GE Sbjct: 137 ALGTPDKKKIIAREKAYHGVTVATASLTGLVNNQRSFDLPIPGVLRAACPHHYRFAKDGE 196 Query: 249 TEEEFSTRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDIL 308 +EE+FSTRLA LE +IL EGP+T+AAF AEPVMGAGGVI PPA YF K+QA+L +YD+L Sbjct: 197 SEEDFSTRLAGELEAMILAEGPDTVAAFFAEPVMGAGGVIVPPAGYFPKIQAVLDRYDVL 256 Query: 309 FIADEVICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSN 368 + DEVICGFGR G MFG E + I+PD++++AK LSSGY PI A++V+ V + +S Sbjct: 257 LVVDEVICGFGRTGKMFGTETFGIRPDMMTLAKGLSSGYAPISALMVNERVYGPVAEESG 316 Query: 369 KLGTFSHGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEI 428 ++G F HG+TY GHPVS AVALETL IY ER+I+ QV + P Q+GL+A P++GE Sbjct: 317 RIGVFGHGYTYGGHPVSAAVALETLNIYAERDILAQVAEVGPVLQDGLRALRGHPLVGEA 376 Query: 429 RGTGLLHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLE 488 RG GL+ E +K+ PFPPE +GA A+ + GV++R GD + +PP ++S Sbjct: 377 RGVGLIGAVELVADKANRAPFPPELAVGARVVAKAQAKGVILRAMGDAVAFAPPLVISKA 436 Query: 489 EIDELIIKYGKALKDTENRV 508 +I E++ ++G AL + + Sbjct: 437 DIAEMLRRFGLALDEAHGEL 456 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: 615 Number of extensions: 24 Number of successful extensions: 2 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: 459 Length adjustment: 34 Effective length of query: 486 Effective length of database: 425 Effective search space: 206550 Effective search space used: 206550 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