Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_003562266.1 RLEG_RS23740 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000023185.1:WP_003562266.1 Length = 444 Score = 163 bits (412), Expect = 1e-44 Identities = 123/420 (29%), Positives = 195/420 (46%), Gaps = 36/420 (8%) Query: 30 AENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLEL 89 AE D++G + LD G+ N GH K+ AVE QL L + + + + Sbjct: 35 AEGMYYTDIDGHQVLDGTAGLWCCNAGHGRKKIAQAVERQLATLDYAPTFQMGHPIAFDF 94 Query: 90 CEIMNQKVPGDFAKKT---LLVTTGSEAVENAVKIARAATK------RSGTIAFSGAYHG 140 + PG K +GSE+V+ A+KIA A + R+ I YHG Sbjct: 95 AAKLAANAPGGPDAKLDRIFFTGSGSESVDTALKIAIAYQRAIGQGTRTRIIGREKGYHG 154 Query: 141 RTHYTLALTGKVNPYSAGMGLMPGHVYRAL--------YPCPLHGISEDDAIASIHRIFK 192 +++ G VN + H+ L P HG+ D + + ++ Sbjct: 155 VGFGGISVGGLVNNRRVFPQIPADHMRHTLDIGRNAFSKGLPAHGVELADDLERLVQLH- 213 Query: 193 NDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLF 252 E IAA+++EP+ G G + ++++LRA D+HGI+LI DEV +G GR GT F Sbjct: 214 ---GAETIAAVIVEPMSGSAGVVLPAKGYLEKLRATADKHGILLIFDEVITGFGRLGTPF 270 Query: 253 AMEQMGVAPDLTTFAKSIAGG-FPLAGVTGRAEVMDAVAPGG-------LGGTYAGNPIA 304 A + GV PDL T AK I G P+ V V D + G G TY+G+P+A Sbjct: 271 ATDYFGVVPDLITTAKGITNGTIPMGAVFASRRVYDGLMVGPDNAIELFHGYTYSGHPVA 330 Query: 305 CVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGD 364 C A L L+++E+E LL +A++L + ++ L ++ P++ D+R LG + A+EL Sbjct: 331 CAAGLATLEIYEEEGLLTRASELAEYWQEALHSL-NGLPQVVDIRNLGLVGAVEL---AP 386 Query: 365 HNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDEA 424 + +I +KGL++ G +++ + PL IE QI + I+ A Sbjct: 387 RDGAPGTRAYDIFVDCFEKGLLIRVTG---DIIALSPPLIIEKDQIDTIVAILGDALKRA 443 Lambda K H 0.320 0.137 0.401 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: 519 Number of extensions: 29 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: 426 Length of database: 444 Length adjustment: 32 Effective length of query: 394 Effective length of database: 412 Effective search space: 162328 Effective search space used: 162328 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 10 2024. The underlying query database was built on Apr 09 2024.
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