Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_090447366.1 BLS63_RS19055 aspartate aminotransferase family protein
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >NCBI__GCF_900100495.1:WP_090447366.1 Length = 445 Score = 309 bits (792), Expect = 1e-88 Identities = 172/423 (40%), Positives = 247/423 (58%), Gaps = 12/423 (2%) Query: 22 PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81 PF+ +Q K K PR++ +A+G+Y ++G K+LDG AGLWC G+GR E+ +A SKQ+ Sbjct: 22 PFTANRQFKAK-PRLLESAEGMYFTSTDGRKVLDGTAGLWCCNAGHGRREITEAVSKQIA 80 Query: 82 ELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQ 141 +L + F Q HP ELA +++IAP G+N VFFT SGSE DT L++ Y GQ Sbjct: 81 KLDFAPTF-QMGHPLPFELASRLAEIAPAGLNKVFFTNSGSESADTALKIALAYQRAIGQ 139 Query: 142 PNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGG-DMTPEE 200 + +I R GYHG G ++GGM + +PG+ H+P E Sbjct: 140 GTRTRLIGRELGYHGVGFGGIAVGGMLNNRRAFPVMLPGVDHLPHTLDIARNAFSRGLPE 199 Query: 201 FGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVAD 260 FGI A++LE + G + + A I EP+ G+ GVI+PP Y R++EI K+ IL + D Sbjct: 200 FGIDKADELERLVALHGAENIAAVIVEPMSGSAGVILPPVGYLQRLREITRKHGILLIFD 259 Query: 261 EVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGGD---F 317 EVI GFGR G+ F + +G+ PD++T AKGLT+G IPMG ++V + + E +G D Sbjct: 260 EVITGFGRVGQAFAAQRWGVTPDILTCAKGLTNGAIPMGAVLVDETIFEAFMQGPDGIEL 319 Query: 318 NHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGEVRGVG 377 HG+TYSGHPVA A AL + I + + + + E Y Q L L D P V ++R +G Sbjct: 320 FHGYTYSGHPVACAAALATLDIYQRDGLFDSA-IELEGYWQDALHSLRDLPNVIDIRAIG 378 Query: 378 LLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKAEIDEL 437 L+G ++L A A VGK + Q CF N L++R GDT+ ++PPL++ A+ID L Sbjct: 379 LVGGVQL----APSAEGVGKRGYQVFEQ-CFHNDLMVRVTGDTLAMSPPLIVENAQIDSL 433 Query: 438 VTK 440 V K Sbjct: 434 VDK 436 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: 537 Number of extensions: 34 Number of successful extensions: 5 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: 445 Length adjustment: 33 Effective length of query: 421 Effective length of database: 412 Effective search space: 173452 Effective search space used: 173452 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