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_037574082.1 BS73_RS18925 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000744815.1:WP_037574082.1 Length = 453 Score = 222 bits (565), Expect = 2e-62 Identities = 141/422 (33%), Positives = 214/422 (50%), Gaps = 35/422 (8%) Query: 22 IHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVL 81 I P+ AE WD +G YLDF G+ N G+ HPKVVAA++ Q KL T Sbjct: 33 IDPLPVAGAEGSYFWDFDGNRYLDFTSGLVNANIGYQHPKVVAAIQEQAGKLV-TFAPAF 91 Query: 82 AYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGR 141 A E E ++ ++ PGD K G+EA ENA+++AR T R ++ +YHG Sbjct: 92 ALESRSEAARLIAERTPGDL-NKIFFTNGGAEANENAIRLARQYTGRHKVLSTYRSYHGA 150 Query: 142 THYTLALTGKVNPYSAGMGLMPGHVYRALYP--CPLHGISEDDAIASIHRIFKNDAA--- 196 T + LTG + +G+ + YP P H SE + + A Sbjct: 151 TANAIMLTGDPRRWQNEIGVGGVSHFWGPYPYRSPFHSTSEQQECERALQHLEETIAFEG 210 Query: 197 PEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQ 256 P +AA+++E + G G P ++ +R +CD +GI+ I DEV +G GRTG FA + Sbjct: 211 PGTVAAVILETIVGTAGVLVPPPGYLAGVREICDRYGIVFILDEVMAGFGRTGEWFAADH 270 Query: 257 MGVAPDLTTFAKSIAGGF-PLAGVTGRAEVM----DAVAPGGLGGTYAGNPIACVAALEV 311 GV PDL TFAK + G+ PL GV + + PGGL TY+G+P+AC +A+ Sbjct: 271 WGVTPDLLTFAKGVNSGYVPLGGVAISERIAAIFDERPFPGGL--TYSGHPLACASAVAT 328 Query: 312 LKVFEQENLLQKANDLGQK-LKDGLLAIAEKHPEIGDVRGLGAMIAIELFE--------- 361 + +E +++ A LG+ L GL +AE+HP +G+VRGLG A++L + Sbjct: 329 INAMAEEGIVEHARALGENVLGPGLRELAERHPSVGEVRGLGVFWALDLVKSKETREALV 388 Query: 362 ----DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 G+ NKP AE+ A + +GL ++ N L ++ P T +A+ ++GL I+ Sbjct: 389 PYNPSGEQNKP----IAELAAACKQRGLWPMT---NMNRLHVVPPCTTSEAEAKEGLAIL 441 Query: 418 SQ 419 + Sbjct: 442 DE 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: 527 Number of extensions: 29 Number of successful extensions: 6 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: 453 Length adjustment: 32 Effective length of query: 394 Effective length of database: 421 Effective search space: 165874 Effective search space used: 165874 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 Jul 26 2024. The underlying query database was built on Jul 25 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