Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF3387 PGA1_c34400 aminotransferase class-III
Query= reanno::WCS417:GFF5299 (454 letters) >FitnessBrowser__Phaeo:GFF3387 Length = 464 Score = 597 bits (1540), Expect = e-175 Identities = 295/453 (65%), Positives = 347/453 (76%), Gaps = 3/453 (0%) Query: 3 SNNPQTREWQALSSDHHLAPFSDFKQLKEKGPRIITKAHGVYLWDSEGNKILDGMAGLWC 62 +N+ T E QAL + HH+ PF+ +L EKG RIIT+A GV L DSEGN+ILD MAGLWC Sbjct: 5 TNHLPTAELQALDAAHHMHPFTANGELAEKGARIITRARGVTLTDSEGNEILDAMAGLWC 64 Query: 63 VAIGYGRDELADAAAKQMKELPYYNLFFQTAHPPVLELAKAISDIAPAGMNHVFFTGSGS 122 V IGYGRDELAD AA+QM+ELPYYN FFQT H P + LA I+++AP G+NHVFF GSGS Sbjct: 65 VNIGYGRDELADVAARQMRELPYYNTFFQTTHAPAIALAAKIAELAPDGLNHVFFAGSGS 124 Query: 123 EGNDTMLRMVRHYWAIKGQPNKKTIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIT 182 E NDT +RMVRHYWA+K +P K IISRKNGYHGS+V SLGGMT MHEQG LPIP I Sbjct: 125 EANDTNIRMVRHYWAMKAKPTKSVIISRKNGYHGSSVGSGSLGGMTAMHEQGGLPIPDIH 184 Query: 183 HIAQPYWFGEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIVPPATY 242 HI QP W+ EGGDMS E+FG+ A +LE+ ILELG D V AFIAEP+QGAGGVIVPPATY Sbjct: 185 HINQPNWWAEGGDMSAEDFGLARAQELEQAILELGEDRVAAFIAEPVQGAGGVIVPPATY 244 Query: 243 WPRIKEILAKYDILFIADEVICGFGRTGEWFGSDFYDLKPHMMTIAKGLTSGYIPMGGLI 302 WP I+ I KY+IL IADEVICGFGRTG WFGS ++P +MTIAKGL+SGY P+GG I Sbjct: 245 WPEIQRICDKYEILLIADEVICGFGRTGNWFGSQSVGIRPDIMTIAKGLSSGYAPIGGSI 304 Query: 303 VRDEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRIMRDEKIVNRVHDETAPYLQKRLR 362 V DE+ V+ G+FNHG+TYSGHPVAAAVALEN+RI+ +E I+ V D APYL+++ Sbjct: 305 VSDEIASVIG-SGEFNHGYTYSGHPVAAAVALENLRILEEENIIGHVRDVAAPYLKEKWE 363 Query: 363 ELADHPLVGEVRGVGMLGAIELVQDKATRKRY--EGKGVGMICRTFCFENGLIMRAVGDT 420 LADHPLVGE + VGM+G+I L +KATR + EG VG ICR CF N L+MR VGD Sbjct: 364 ALADHPLVGEAKIVGMMGSIALTPNKATRAGFAAEGGTVGYICRERCFANNLVMRHVGDR 423 Query: 421 MIISPPLVISKAEIDELVTKARQCLDLTLAALQ 453 MIISPPLVI+ EID L+ +ARQ LD AALQ Sbjct: 424 MIISPPLVITPEEIDTLIARARQSLDECYAALQ 456 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: 751 Number of extensions: 26 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: 454 Length of database: 464 Length adjustment: 33 Effective length of query: 421 Effective length of database: 431 Effective search space: 181451 Effective search space used: 181451 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 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