Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_090446700.1 BLS63_RS16660 aspartate aminotransferase family protein
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >NCBI__GCF_900100495.1:WP_090446700.1 Length = 457 Score = 788 bits (2036), Expect = 0.0 Identities = 372/445 (83%), Positives = 415/445 (93%), Gaps = 1/445 (0%) Query: 5 NPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVA 64 NP+TREWQ +S EHHLAPFSD++QL E GPRIIT A GVYLWDSEGNKILDGMAGLWCVA Sbjct: 7 NPKTREWQAMSREHHLAPFSDYRQLAEVGPRIITKADGVYLWDSEGNKILDGMAGLWCVA 66 Query: 65 IGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEG 124 +GYGR+EL +AAS+QMRELP+YN FF TAHPPVLELAKAI++IAP GMNHVFFTGSGSEG Sbjct: 67 VGYGREELVEAASQQMRELPFYNTFFMTAHPPVLELAKAIAEIAPPGMNHVFFTGSGSEG 126 Query: 125 NDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHI 184 NDTMLR+VRHYWA+KGQP KKVII R+NGYHGSTVAGASLGGM +MHEQGDLPIPGIVHI Sbjct: 127 NDTMLRLVRHYWALKGQPQKKVIIGRVNGYHGSTVAGASLGGMKFMHEQGDLPIPGIVHI 186 Query: 185 PQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWP 244 PQPYWFGEGGDM+P+EFGIWAA+QLE+KILE+G + V AFIAEPIQGAGGVIIPPDSYWP Sbjct: 187 PQPYWFGEGGDMSPDEFGIWAADQLEQKILEVGEENVAAFIAEPIQGAGGVIIPPDSYWP 246 Query: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVR 304 RI+EILAKYDILFVADEVICGFGRTGEWFGSDFYG +PD+MTIAKGLTSGY+PMGGLIV Sbjct: 247 RIREILAKYDILFVADEVICGFGRTGEWFGSDFYGNRPDLMTIAKGLTSGYVPMGGLIVS 306 Query: 305 DEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLREL 364 D+V +V+N GGDFNHGFTYSGHPVAAAVALEN+RILREEKI+E V+A+TAPYLQ+RLREL Sbjct: 307 DKVFQVINAGGDFNHGFTYSGHPVAAAVALENLRILREEKIVERVKAQTAPYLQRRLREL 366 Query: 365 NDHPLVGEVRGVGLLGAIELVQDKATRARYVG-KGVGMICRQFCFDNGLIMRAVGDTMII 423 DHPLVGEVRGVG+LGAIELV++KATR RY + VGMICR CF+NGLIMRAVGDTMII Sbjct: 367 ADHPLVGEVRGVGMLGAIELVKNKATRERYPSERAVGMICRGHCFNNGLIMRAVGDTMII 426 Query: 424 APPLVITKAEIDELVTKARKCLDLT 448 +PPLVI++AEIDEL+ KAR+CLDLT Sbjct: 427 SPPLVISEAEIDELLAKARRCLDLT 451 Lambda K H 0.320 0.140 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: 838 Number of extensions: 32 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: 454 Length of database: 457 Length adjustment: 33 Effective length of query: 421 Effective length of database: 424 Effective search space: 178504 Effective search space used: 178504 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