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_011937064.1 GURA_RS00600 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000016745.1:WP_011937064.1 Length = 438 Score = 397 bits (1019), Expect = e-115 Identities = 201/428 (46%), Positives = 275/428 (64%), Gaps = 9/428 (2%) Query: 4 NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63 N+ELMQ ++Q +P+GV + P F +A + DV+GRE +DFAGGI V N GH HPKVV Sbjct: 5 NEELMQLKNQHVPQGVANLSPAFISKARGAIMVDVDGRELIDFAGGIGVNNVGHCHPKVV 64 Query: 64 AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123 AA++ Q +K HTCF V YEPY+EL +N+ PGDFAK T+ +G+EA ENA+KIAR Sbjct: 65 AAIKDQAEKYIHTCFHVALYEPYVELAARLNELAPGDFAKMTMFANSGAEADENAIKIAR 124 Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRA----LYPCPLHGIS 179 ATKR IAF +HGRT T+ LT KV PY G G YR Y CP G++ Sbjct: 125 YATKRPAVIAFENGFHGRTLMTMTLTSKVKPYKLGYGPFAPETYRIPYAYCYRCPF-GMT 183 Query: 180 EDDAIAS----IHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIM 235 AS + F N A E AAI+ EP+QGEGGF P + +L+A+C ++GI+ Sbjct: 184 YPACKASCADYLEEFFINHVAAEQTAAIIAEPIQGEGGFITPPPEYFAKLQAICQKYGIL 243 Query: 236 LIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLG 295 LI DE+Q+G GRTG +FA++ G+ PDL T AKS+AGG PL+ +TGRAE+M+ GGLG Sbjct: 244 LIIDEIQTGMGRTGKIFAIDHWGIKPDLITTAKSLAGGMPLSAITGRAELMNMSHAGGLG 303 Query: 296 GTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMI 355 GTY GNPI+C AAL VL++ ++ LL KA++LG KL + + H IG+VRG G M+ Sbjct: 304 GTYGGNPISCRAALAVLEILLEDGLLNKADELGAKLTARFEELQKTHEIIGEVRGKGPML 363 Query: 356 AIELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415 A+EL D + +P ++ +KGL++LSCG + NV+R+L+PL I D ++ +G+ Sbjct: 364 ALELVRDRETKEPAGAEAKKLTKLCFEKGLVILSCGNHGNVIRVLMPLVITDEELGRGIA 423 Query: 416 IISQCFDE 423 I+ + E Sbjct: 424 ILDESLHE 431 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: 564 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: 438 Length adjustment: 32 Effective length of query: 394 Effective length of database: 406 Effective search space: 159964 Effective search space used: 159964 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