Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_086509870.1 BZY95_RS10460 aspartate aminotransferase family protein
Query= reanno::WCS417:GFF5299 (454 letters) >NCBI__GCF_002151265.1:WP_086509870.1 Length = 485 Score = 574 bits (1479), Expect = e-168 Identities = 281/462 (60%), Positives = 348/462 (75%), Gaps = 18/462 (3%) Query: 8 TREWQALSSDHHLAPFSDFKQLKEKGPRIITKAHGVYLWDSEGNKILDGMAGLWCVAIGY 67 T ++ L DHHL PF+DFK L E+G RI+T A G+Y+ DSEGN+ILD MAGLWCV +GY Sbjct: 3 TETYRQLDRDHHLHPFTDFKALGEEGSRIVTHAEGIYIHDSEGNRILDAMAGLWCVNLGY 62 Query: 68 GRDELADAAAKQMKELPYYNLFFQTAHPPVLELAKAISDIAPAGMNHVFFTGSGSEGNDT 127 GR+EL AA Q++ELPYYN FF++ HPP ++LA+ + +APA MN VFFTGSGSE NDT Sbjct: 63 GREELVAAATAQLRELPYYNNFFKSTHPPAVKLAEMLCRLAPAHMNRVFFTGSGSEANDT 122 Query: 128 MLRMVRHYWAIKGQPNKKTIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGITHIAQP 187 +LRMVR YWA++G+P+K+ +I+R+N YHGSTVAG SLGGM MH QG +P I H+ QP Sbjct: 123 VLRMVRRYWALEGKPDKQWVIARENAYHGSTVAGLSLGGMAPMHAQGGPLVPKIAHVRQP 182 Query: 188 YWF----------GEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIV 237 YWF GEG D SPE FG A LE KIL LG +NV AFIAEP+QGAGG I+ Sbjct: 183 YWFGEGKVAQGRVGEGRDTSPEAFGRECAAALEAKILALGEENVAAFIAEPVQGAGGAII 242 Query: 238 PPATYWPRIKEILAKYDILFIADEVICGFGRTGEWFGSDFYDLKPHMMTIAKGLTSGYIP 297 PP +YWP +KE+LA+YDIL + DEVICGFGR GEWFGS YDLKP +M IAKGL+SGY+P Sbjct: 243 PPQSYWPAVKEVLARYDILLVVDEVICGFGRLGEWFGSIHYDLKPDLMPIAKGLSSGYLP 302 Query: 298 MGGLIVRDEVVEVLNE-GGDFNHGFTYSGHPVAAAVALENIRIMRDEKIVNRVHDETAPY 356 +GG++V D V E L E GG+F HGFTYSGHPV AAVAL+N+ +M+ E IV RV D+ PY Sbjct: 303 IGGVLVGDRVAETLIERGGEFFHGFTYSGHPVCAAVALKNLELMQAEGIVERVRDDVGPY 362 Query: 357 LQKRLRELADHPLVGEVRGVGMLGAIELVQDKATRKRYE------GKGVGMICRTFCFEN 410 L +R LADHPLVGEVR +G++GA+EL+ D T +R++ G GVG +CR CF++ Sbjct: 363 LAERWATLADHPLVGEVRSLGLIGALELI-DPDTGERFDKARFPKGFGVGTLCRDICFDH 421 Query: 411 GLIMRAVGDTMIISPPLVISKAEIDELVTKARQCLDLTLAAL 452 GL+MR+VGDTMIISPPLVI++AEIDELV A + LD T L Sbjct: 422 GLVMRSVGDTMIISPPLVITRAEIDELVRLAWEALDETARRL 463 Lambda K H 0.320 0.139 0.426 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: 790 Number of extensions: 33 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: 454 Length of database: 485 Length adjustment: 33 Effective length of query: 421 Effective length of database: 452 Effective search space: 190292 Effective search space used: 190292 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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