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_028999256.1 H537_RS0120050 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000430725.1:WP_028999256.1 Length = 434 Score = 546 bits (1406), Expect = e-160 Identities = 267/427 (62%), Positives = 325/427 (76%), Gaps = 1/427 (0%) Query: 1 MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP 60 +N+N LM RR A+P G+GQ H IF RAEN VWDVEGR Y+DFAGGIAVLNTGH HP Sbjct: 7 LNTNAHLMARRRAALPAGMGQAHEIFVQRAENAEVWDVEGRRYIDFAGGIAVLNTGHRHP 66 Query: 61 KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK 120 +VAAV+ QL++ +HTCFQVLAYEPY+EL E +N PGDFAKK+ +TTG+EAVENAVK Sbjct: 67 ALVAAVQEQLQRFTHTCFQVLAYEPYVELAERLNAMAPGDFAKKSFFLTTGAEAVENAVK 126 Query: 121 IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE 180 IARA TKRS IAF GA+HGRT +ALTGKV PY G G MP ++ A +PCPLHG+S Sbjct: 127 IARAYTKRSAVIAFGGAFHGRTLLGMALTGKVVPYKVGFGPMPAEIFHAKFPCPLHGVSV 186 Query: 181 DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE 240 +DA+AS+ +FK D P +AAI++EPVQGEGGFY + PAF++ LR +CD HGI+LIADE Sbjct: 187 EDAVASVEALFKYDVEPARVAAIILEPVQGEGGFYVAPPAFVRALRDICDRHGIVLIADE 246 Query: 241 VQSGAGRTGTLFAMEQM-GVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYA 299 VQ+GAGRTGT A EQ GV PDL T AKS+ GG PL+ V GRAE+MDA PGGLGGTYA Sbjct: 247 VQTGAGRTGTFLACEQWDGVVPDLITMAKSLGGGMPLSAVIGRAEIMDAPGPGGLGGTYA 306 Query: 300 GNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIEL 359 GNP+AC AAL VL FE+E+LL ++ +G++L GL AIA +H IG+VRGLGAM+A+EL Sbjct: 307 GNPLACAAALAVLDAFEREDLLARSRAVGERLVAGLQAIAARHSVIGEVRGLGAMVAVEL 366 Query: 360 FEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 FEDG+ +P A LT ++V A + GLILLSCG + NV+RILVPLT DA + +GL II Sbjct: 367 FEDGNVKRPAAALTQKVVKAAAEAGLILLSCGTHANVVRILVPLTASDAVLDEGLTIIGS 426 Query: 420 CFDEAKQ 426 FD Q Sbjct: 427 VFDHLAQ 433 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: 612 Number of extensions: 18 Number of successful extensions: 2 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: 434 Length adjustment: 32 Effective length of query: 394 Effective length of database: 402 Effective search space: 158388 Effective search space used: 158388 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