Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate Pf1N1B4_2257 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4512 (454 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2257 Length = 400 Score = 742 bits (1916), Expect = 0.0 Identities = 351/375 (93%), Positives = 367/375 (97%) Query: 1 MTRNNPQTREWQALSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGL 60 MT NNPQTREWQALS+DHHLAPFSDFKQLKEKGPRIIT AKGVYLWDSEGNKILDGMAGL Sbjct: 1 MTSNNPQTREWQALSSDHHLAPFSDFKQLKEKGPRIITSAKGVYLWDSEGNKILDGMAGL 60 Query: 61 WCVAVGYGREELADAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGS 120 WCVA+GYGR+ELADAAS+QMRELPYYNLFFQTAHPPVLEL+K I+D+APEGMNHVFFTGS Sbjct: 61 WCVAIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKVISDVAPEGMNHVFFTGS 120 Query: 121 GSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPG 180 GSEGNDTMLRMVRHYWAIKGQP KKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPG Sbjct: 121 GSEGNDTMLRMVRHYWAIKGQPKKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPG 180 Query: 181 IVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIVPPD 240 IVHIAQPYWFGEGGDM+P EFG+WAANQLEEKILE+GVDNVGAFIAEPIQGAGGVI+PPD Sbjct: 181 IVHIAQPYWFGEGGDMTPNEFGIWAANQLEEKILEVGVDNVGAFIAEPIQGAGGVIIPPD 240 Query: 241 SYWPRMKEILAKYDILFVADEVICGFGRTGEWFGTDHYELKPHMMTIAKGLTSGYIPMGG 300 SYWPR+KEILAKYDILFVADEVICGFGRTGEWFGTD Y+LKPHMMTIAKGLTSGYIPMGG Sbjct: 241 SYWPRIKEILAKYDILFVADEVICGFGRTGEWFGTDFYDLKPHMMTIAKGLTSGYIPMGG 300 Query: 301 LIVRDDVVAVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKR 360 LIVRDDVV VLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKI+ERV +ETAPYLQKR Sbjct: 301 LIVRDDVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIVERVRTETAPYLQKR 360 Query: 361 LRELNDHPLVGEVRG 375 LREL+DHPLVGEVRG Sbjct: 361 LRELSDHPLVGEVRG 375 Lambda K H 0.320 0.139 0.428 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: 773 Number of extensions: 21 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: 400 Length adjustment: 32 Effective length of query: 422 Effective length of database: 368 Effective search space: 155296 Effective search space used: 155296 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