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_106717846.1 CU100_RS17540 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_003010935.1:WP_106717846.1 Length = 427 Score = 410 bits (1054), Expect = e-119 Identities = 197/418 (47%), Positives = 276/418 (66%), Gaps = 2/418 (0%) Query: 5 KELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVA 64 ++L++RR + I RG+ HPI A +A+ +WDVEGR YLDF GGI VLN GH HP+VV Sbjct: 9 QDLLERRDRNIARGIATAHPILASKAKGTELWDVEGRRYLDFVGGIGVLNVGHNHPRVVD 68 Query: 65 AVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124 AV+ Q++ LSH CFQVL YEPY+ L E +N + D+ K+ T+G+EAVEN+VKIAR Sbjct: 69 AVKRQIETLSHACFQVLGYEPYVALAEKLNTLIGKDY--KSAFFTSGAEAVENSVKIARG 126 Query: 125 ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAI 184 T R IAF G +HGRT ++LTG PY G ++ YP G++ DA+ Sbjct: 127 YTNRPAVIAFRGGFHGRTLLGVSLTGMSQPYKQNFGPFAPEIFHIPYPNAYRGVTTADAL 186 Query: 185 ASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSG 244 A++ +F D APE +AAI+IEPVQG+GGF+ + F+ LR + ++HGI+LI DE+Q+G Sbjct: 187 AALAEVFATDVAPERVAAIIIEPVQGDGGFHPAPVNFVAALREITNKHGIVLILDEIQTG 246 Query: 245 AGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIA 304 GRTG +F + G+ PDL T AKS+AGG PL+ V G+AE+MDA PGGLGGTY GN +A Sbjct: 247 FGRTGEMFGFQHSGIEPDLVTIAKSLAGGLPLSAVVGKAEIMDAPTPGGLGGTYGGNALA 306 Query: 305 CVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGD 364 C AAL V++ FE++++L+ +L+ GL+A+ ++H IGDVRGLG M+AIE+ D Sbjct: 307 CAAALAVIETFERDDILRNGRQRAAQLRKGLIALQQRHAFIGDVRGLGFMLAIEIVSDRA 366 Query: 365 HNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422 PDA T ++ AR GL+L+ CG + N +R L PL +A+I + L + + + Sbjct: 367 TKAPDADRTQHVLDEARKGGLLLIKCGIHRNTVRFLAPLVATEAEIDEALAALGEALE 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: 25 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: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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