Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_086509625.1 BZY95_RS09090 aspartate aminotransferase family protein
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >NCBI__GCF_002151265.1:WP_086509625.1 Length = 446 Score = 278 bits (712), Expect = 2e-79 Identities = 157/426 (36%), Positives = 236/426 (55%), Gaps = 21/426 (4%) Query: 22 PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81 P++ +Q K + PRII A+G Y D++G +I DG++GLW G+ R E+ +A ++Q++ Sbjct: 22 PYTGNRQFK-RDPRIIVGAEGSYFTDADGRRIFDGLSGLWTCGAGHCRPEITEAVTRQLQ 80 Query: 82 ELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQ 141 +L Y + FQ HP ELA I + P+G++HVF+TGSGSE DT L++ R YW KG+ Sbjct: 81 QLDY-SPAFQFGHPKAFELAHRIRGLMPQGLDHVFYTGSGSESADTALKIARAYWRKKGK 139 Query: 142 PNKKVIISRINGYHGSTVAGASLGGM---TYMHEQGDLPIPGIVHIPQPYWFGEGGDMTP 198 P K ++ R GYHG G SLGG+ + QG H+P Sbjct: 140 PTKTKLVGRAKGYHGVNFGGISLGGIGANRVLFGQGI----DADHLPHTLLAENAFTKGM 195 Query: 199 EEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFV 258 E G A +L E I + A I EP+ G+ GVI PP Y R++EI ++DIL + Sbjct: 196 PERGAERAEELLELIALHDASNIAAVIVEPLAGSAGVIPPPKGYLQRLREICDQHDILLI 255 Query: 259 ADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGG--- 315 DEVI GFGR G G++ +G+ PD++ +AK LT+G +PMG +IV+ E+ E G Sbjct: 256 FDEVITGFGRMGSMTGAEEFGVVPDILNVAKQLTNGAVPMGAVIVQGEIYHTFMEHGGPD 315 Query: 316 ---DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGE 372 + HG+TYSGHPVA A AL + +L +++I+ VR E +P ++ L L + + Sbjct: 316 YMLELPHGYTYSGHPVACAAALAALDVLENDRLIQRVR-EMSPVFEEALHGLKGTRYISD 374 Query: 373 VRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKA 432 +R GL GA+++ AR + C++ G +R GDT+ + P ++ + Sbjct: 375 IRNYGLAGALQIEPYPGEPARRPFE-----IAMKCWNKGFYVRYGGDTIQLGLPFIVERD 429 Query: 433 EIDELV 438 EID LV Sbjct: 430 EIDRLV 435 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: 601 Number of extensions: 30 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: 446 Length adjustment: 33 Effective length of query: 421 Effective length of database: 413 Effective search space: 173873 Effective search space used: 173873 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