Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate AO356_13150 AO356_13150 aminotransferase
Query= reanno::pseudo5_N2C3_1:AO356_13150 (454 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_13150 Length = 454 Score = 934 bits (2413), Expect = 0.0 Identities = 454/454 (100%), Positives = 454/454 (100%) Query: 1 MTRNNPQTREWQALSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGL 60 MTRNNPQTREWQALSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGL Sbjct: 1 MTRNNPQTREWQALSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGL 60 Query: 61 WCVAVGYGREELADAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGS 120 WCVAVGYGREELADAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGS Sbjct: 61 WCVAVGYGREELADAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGS 120 Query: 121 GSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPG 180 GSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPG Sbjct: 121 GSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPG 180 Query: 181 IVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPD 240 IVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPD Sbjct: 181 IVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPD 240 Query: 241 SYWPRMKEILAKYDILFVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGG 300 SYWPRMKEILAKYDILFVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGG Sbjct: 241 SYWPRMKEILAKYDILFVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGG 300 Query: 301 LIVRDDVVAVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKR 360 LIVRDDVVAVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKR Sbjct: 301 LIVRDDVVAVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKR 360 Query: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQFCFDNGLIMRAVGDT 420 LRELNDHPLVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQFCFDNGLIMRAVGDT Sbjct: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQFCFDNGLIMRAVGDT 420 Query: 421 MIIAPPLVISKAEIDELVTKARHCLDLTLSALQG 454 MIIAPPLVISKAEIDELVTKARHCLDLTLSALQG Sbjct: 421 MIIAPPLVISKAEIDELVTKARHCLDLTLSALQG 454 Lambda K H 0.320 0.139 0.431 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: 918 Number of extensions: 28 Number of successful extensions: 1 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: 454 Length adjustment: 33 Effective length of query: 421 Effective length of database: 421 Effective search space: 177241 Effective search space used: 177241 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