Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_084076256.1 BUB04_RS06460 aspartate aminotransferase family protein
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >NCBI__GCF_900129305.1:WP_084076256.1 Length = 449 Score = 267 bits (682), Expect = 6e-76 Identities = 158/433 (36%), Positives = 244/433 (56%), Gaps = 17/433 (3%) Query: 19 HLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASK 78 H+ ++ LK+ P ++ +GVY+WD G + +DG G V+IG+G E+ +A + Sbjct: 5 HMKDHIFYRNLKKTYP-VVDRGEGVYIWDKNGKRYIDGSGGACVVSIGHGVPEILEAMKE 63 Query: 79 QMRELPYYNLFFQTAHPPVLELAKAISDIAPE-GMNHVFFTGSGSEGNDTMLRMVRHYWA 137 Q R + + + T+ LE A+ + +AP+ +N V+F GSE +T +++VR YW Sbjct: 64 QARRICFAHGSHFTSEA-ALECAERLVRMAPDPALNRVYFLSGGSEAVETAVKVVRQYWR 122 Query: 138 IKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMT 197 G+P+K +ISR +HG+T +LGG T + HI Y + Sbjct: 123 EVGKPDKYKVISRWTSFHGNTTGALALGGHTGRRKHYHPLFLHTPHIEPAYCYRCPFGRE 182 Query: 198 PEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGA-GGVIIPPDSYWPRIKEILAKYDIL 256 PE + A+QLE I G D V AFIAEP+ GA G ++P D YW RI+EI Y + Sbjct: 183 PEACSLECADQLERTIKYEGPDAVAAFIAEPVVGATAGALVPRDGYWQRIREICNAYQVK 242 Query: 257 FVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEG-G 315 +ADEV+ G GRTG+ F D + + PD++ AKGL+SGY P+G +IV++E+ + + G G Sbjct: 243 LIADEVMTGVGRTGQNFCLDHWKVVPDVIVTAKGLSSGYTPLGAVIVKEEIHDAIRSGSG 302 Query: 316 DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAE-TAPYLQKRLRELNDHPLVGEVR 374 F HG TY +P++AA+ +R L E+ ++ R+E L ++L+ L +HP VG+VR Sbjct: 303 AFVHGHTYCQNPLSAAIGAAVLRYLEEQNLV--ARSERMGKVLLEKLQVLLEHPTVGDVR 360 Query: 375 GVGLLGAIELVQDKATRARY-VGKGVGMICRQFCFDNGLIM--------RAVGDTMIIAP 425 G+GL +ELV+DK T+A + + Q F GLI GD +++AP Sbjct: 361 GLGLFAGVELVRDKKTKATFDPSLKINARVAQEAFRRGLITYPGSGGADGIHGDHILLAP 420 Query: 426 PLVITKAEIDELV 438 P VIT+++ID+LV Sbjct: 421 PFVITESQIDDLV 433 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: 590 Number of extensions: 35 Number of successful extensions: 7 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: 449 Length adjustment: 33 Effective length of query: 421 Effective length of database: 416 Effective search space: 175136 Effective search space used: 175136 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 Apr 09 2024. 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