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_014518834.1 CA_RS02090 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000008765.1:WP_014518834.1 Length = 426 Score = 299 bits (765), Expect = 1e-85 Identities = 171/423 (40%), Positives = 249/423 (58%), Gaps = 18/423 (4%) Query: 7 LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAV 66 L +R + IP G+ + R E ++ +GR+ LDFA G+AV N GH +P V+ A Sbjct: 4 LYERSLKVIPPVAGRATKLGVVRGEGAYLYTEDGRKVLDFASGVAVCNLGHNNPAVIKAA 63 Query: 67 EAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLV--TTGSEAVENAVKIARA 124 + Q+ KL H V+ YE Y++L E K+ KT++ +G+EA E A+K+A+ Sbjct: 64 KEQMDKLIHGGHNVVYYESYVKLAE----KIVELTGNKTMVYFSNSGAEANEGAIKLAKY 119 Query: 125 ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGM-GLMPGHVYRALYP----CPLHGIS 179 TKR I+F G++HGRT T ++TG + Y GL+P VY A YP CP Sbjct: 120 ITKRQAIISFKGSFHGRTLATTSITGSSSKYRKNYEGLLPS-VYFAEYPYCFRCPYKQNK 178 Query: 180 ED---DAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIML 236 E + I+ +FK PE +AAI++EPVQGEGG+ F++ +R +CD++GI L Sbjct: 179 ESCNMECISQFEDMFKKLIEPESVAAIIMEPVQGEGGYIVPPKKFLKAVREICDKYGICL 238 Query: 237 IADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG 296 I DEVQ G GRTG +FA E V PD+ T AK+IA GFPL+ V G+ E+M+ G GG Sbjct: 239 IFDEVQCGFGRTGKIFAHENFEVEPDIFTCAKAIASGFPLSAVIGKKELMEKWPAGAHGG 298 Query: 297 TYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIA 356 T+ GNP+AC A+L +K E +L AN++G LK+ LL + +K+ IGD+RG+G MI Sbjct: 299 TFGGNPVACAASLATIKELE-SGVLDNANNMGNYLKEELLKLKDKYACIGDIRGIGLMIG 357 Query: 357 IELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416 +E + ++N PD + I A + LILL CG +NVLR + PLT+E ++I + I Sbjct: 358 MEFCK--ENNNPDGDIVTFIREVAVNNNLILLGCGTEHNVLRFIAPLTVEKSEIDMAISI 415 Query: 417 ISQ 419 + + Sbjct: 416 VEK 418 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: 475 Number of extensions: 26 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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 25 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