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_012116197.1 XAUT_RS21405 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000017645.1:WP_012116197.1 Length = 428 Score = 445 bits (1145), Expect = e-129 Identities = 219/416 (52%), Positives = 288/416 (69%), Gaps = 2/416 (0%) Query: 1 MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP 60 M+ N L RR++AIPRG+ +P+FA +AE VWD +G Y+DFAGGIAVLNTGH HP Sbjct: 1 MSENAALQARRTKAIPRGIATAYPVFAQKAEGSEVWDADGTRYIDFAGGIAVLNTGHRHP 60 Query: 61 KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK 120 +V+AAV AQL +HT FQ++ YEPY+ LCE +N P A K++L +TG+EAVENAVK Sbjct: 61 RVLAAVRAQLDAYTHTAFQIVPYEPYVALCERLNAIAPFTGAAKSILFSTGAEAVENAVK 120 Query: 121 IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE 180 IA+AAT R+G I+FSG +HGRT T+ALTGKV PY G+ P ++ +PC HG+S Sbjct: 121 IAKAATGRTGVISFSGGFHGRTALTMALTGKVLPYKKKFGISPPGIFHLPFPCADHGVSV 180 Query: 181 DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE 240 D + ++ +F+ D P+D+AAI+IEPVQGEGGF + + LR CD HGI+LIADE Sbjct: 181 ADTLKALDYLFRADIGPQDVAAIIIEPVQGEGGFLPAPTELLVALRQTCDAHGIVLIADE 240 Query: 241 VQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG 300 VQ+G RTG +F +E GV PDL T AKS+AGGFPL+GV GR +MDA PGGLGGTYAG Sbjct: 241 VQTGFARTGRMFGIEHSGVEPDLVTVAKSLAGGFPLSGVIGREAIMDAAEPGGLGGTYAG 300 Query: 301 NPIACVAALEVLKVFEQENLLQKANDLGQKLKDGL--LAIAEKHPEIGDVRGLGAMIAIE 358 NPIAC AAL VL V +E L+++AN +G ++KD L +A+ IG +RG GAM+A + Sbjct: 301 NPIACAAALAVLDVIAEEKLVERANAIGARIKDALTRMALRNDAVAIGSIRGPGAMVAFD 360 Query: 359 LFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGL 414 + + +PDA + A GLIL++CG Y N +R+L PLTI DA + +GL Sbjct: 361 VVKKRGTVEPDADAARRVTQAALADGLILITCGVYGNTIRLLNPLTIPDALLDEGL 416 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: 547 Number of extensions: 16 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