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_012050345.1 SWIT_RS21085 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000016765.1:WP_012050345.1 Length = 434 Score = 431 bits (1107), Expect = e-125 Identities = 216/419 (51%), Positives = 284/419 (67%), Gaps = 1/419 (0%) Query: 2 NSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPK 61 +SN L RR A+P+GV PIFA RAEN +WDVEGR Y+DFA GIAVLN GH HP+ Sbjct: 7 SSNDALWGRRLAAVPQGVATAAPIFAARAENAEIWDVEGRRYIDFASGIAVLNVGHRHPR 66 Query: 62 VVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKI 121 ++AAVE QL + +HT FQV+ YEPY+ L E +N P KT+ TTG+EA ENAVKI Sbjct: 67 IIAAVEEQLGRFTHTAFQVVGYEPYVRLAERLNALAPVVGPAKTIFFTTGAEATENAVKI 126 Query: 122 ARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISED 181 AR A+ RS IAF +HGRT A+TGKV PY G G +PG +Y +P HGI+ + Sbjct: 127 ARYASGRSAVIAFVNGFHGRTLLASAMTGKVLPYKKGFGPLPGDIYHIPFPSEAHGITVE 186 Query: 182 DAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEV 241 ++A++ + +D ++AAI++EPVQGEGGF+ + F++ LR+LCDEHGI LIADEV Sbjct: 187 HSLAALANVLSSDVEAANVAAIILEPVQGEGGFHVAPFEFLRALRSLCDEHGIALIADEV 246 Query: 242 QSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGN 301 Q+G GRTG LFA+E GV PDL T AKS+ GGFPL+ V G A ++D V PGGLGGTYAG+ Sbjct: 247 QTGIGRTGKLFAVEHAGVRPDLITVAKSLGGGFPLSAVVGNAALIDRVPPGGLGGTYAGS 306 Query: 302 PIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHP-EIGDVRGLGAMIAIELF 360 PIAC A L VL V EQ+ L +A +G+++ + L A+A + IG RGLGAMIA ++ Sbjct: 307 PIACAAGLAVLDVIEQDRLCDRAERMGRRITERLSAVAARRELPIGLPRGLGAMIAFDIR 366 Query: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 D +PD + RA + GLILL+CG + +R+L PLT DA + +GL+I++Q Sbjct: 367 AGLDDLRPDGAAAKRVCVRALELGLILLTCGQHGEAIRLLAPLTASDAVLDEGLDILAQ 425 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: 543 Number of extensions: 22 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 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