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_037572372.1 BS73_RS14180 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000744815.1:WP_037572372.1 Length = 451 Score = 360 bits (925), Expect = e-104 Identities = 191/424 (45%), Positives = 258/424 (60%), Gaps = 6/424 (1%) Query: 4 NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63 ++EL R++ A+ GVG P++ RA + D +G +DF GIAV N G+ VV Sbjct: 26 SQELHARKAAAVAAGVGTTLPVYVTRAGGGVIEDADGNSLIDFGSGIAVTNVGNSAEAVV 85 Query: 64 AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123 A QL +HTCF V YE Y+ + E +N+ PGD K+T L +G+EAVENAVKIAR Sbjct: 86 ARATEQLAAFTHTCFMVAPYEGYVAVAEQLNELTPGDHEKRTALFNSGAEAVENAVKIAR 145 Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGIS---- 179 A TKR + F YHGRT+ T+ALT K PY G G VYRA P ++ Sbjct: 146 AYTKRQAVVVFDHGYHGRTNLTMALTAKNMPYKNGFGPFAPEVYRAPLAYPFRWLTGPEN 205 Query: 180 -EDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIA 238 ++A A + E+IAAI+IEP+QGEGGF + F+ +L HGI+ +A Sbjct: 206 CAEEAAAQAIDLMSKQIGGENIAAIIIEPIQGEGGFIEPARGFLTKLVEYARAHGIVFVA 265 Query: 239 DEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTY 298 DE+Q+G RTG FA E G+ PDL T AK IAGG PLA VTGRAE+MDAV GGLGGTY Sbjct: 266 DEIQTGFCRTGQWFACEDEGIVPDLITTAKGIAGGLPLAAVTGRAEIMDAVHGGGLGGTY 325 Query: 299 AGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIE 358 GNP+AC AA+ ++ + ++L KA +G+ + L +I EKH +GDVRG GAMIA+E Sbjct: 326 GGNPVACAAAIGAIETMKSQDLNAKARKIGETMLPRLRSIQEKHAVVGDVRGRGAMIAVE 385 Query: 359 LFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIIS 418 L + G +PD + TA I ++GL++L+ G Y NVLR L PL I + + +GL+I+ Sbjct: 386 LVKPGT-KEPDPETTAAIAKACHNEGLLVLTAGTYGNVLRFLPPLVIPEHLLTEGLDILE 444 Query: 419 QCFD 422 + F+ Sbjct: 445 RAFE 448 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: 582 Number of extensions: 29 Number of successful extensions: 3 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: 451 Length adjustment: 32 Effective length of query: 394 Effective length of database: 419 Effective search space: 165086 Effective search space used: 165086 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