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 AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__azobra:AZOBR_RS19630 Length = 428 Score = 475 bits (1223), Expect = e-138 Identities = 232/423 (54%), Positives = 305/423 (72%), Gaps = 2/423 (0%) Query: 3 SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62 SN+ RR+ A+PRG+ P++ DRAEN +WDVEG ++DFAGGIAVLNTGH HPK+ Sbjct: 2 SNQSFQDRRNAAVPRGLANAMPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKI 61 Query: 63 VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122 + AV+AQL + +HTC V YE ++ L E +N VPG KKT TTG+EAVENAVKIA Sbjct: 62 IEAVKAQLDRFTHTCAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIA 121 Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182 RA T R G IAFSGA+HGRT +ALTGKV PY G G P VY A +P G+S D Sbjct: 122 RAHTGRPGVIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQD 181 Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242 ++ ++ ++FK+D +AAI++EPVQGEGGF + P F+Q LR +CDE+GI+LI DE+Q Sbjct: 182 SLKALEQLFKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQ 241 Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302 +G RTG +FA+E GV PDL T AKS+AGGFPL+ VTG+AE+MDA PGG+GGTYAG+P Sbjct: 242 TGFARTGKMFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSP 301 Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKH--PEIGDVRGLGAMIAIELF 360 +A AAL VL V E+E L+Q++NDLG+++ +A+++ IGDVR LG MIA+EL Sbjct: 302 LATTAALAVLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELV 361 Query: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQC 420 +D +P A+LT +VA+A +KGL+LLSCG Y NV+RILVPLT DA + +GL+II + Sbjct: 362 KDRGTKEPAAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERS 421 Query: 421 FDE 423 +E Sbjct: 422 LEE 424 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: 533 Number of extensions: 19 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: 428 Length adjustment: 32 Effective length of query: 394 Effective length of database: 396 Effective search space: 156024 Effective search space used: 156024 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 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