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_066600058.1 V473_RS02290 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_001046645.1:WP_066600058.1 Length = 398 Score = 207 bits (526), Expect = 6e-58 Identities = 145/398 (36%), Positives = 194/398 (48%), Gaps = 38/398 (9%) Query: 29 RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88 R E C + G YLDFA GIAV GH HP++V A+ Q L H L P E Sbjct: 19 RGEGCYLIGERGERYLDFASGIAVNLLGHGHPRLVKAIADQAATLMHV--SNLYGMPLGE 76 Query: 89 LCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAFSGAYHGRT 142 + + V FA +G+EAVE A+K AR R I+F A+HGRT Sbjct: 77 --QFAQKLVDNSFADTVFFTNSGAEAVECAIKTARRYHYANGQAHRHKIISFDNAFHGRT 134 Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAA 202 T++ T + L+PG P + + D A+A I ++ A Sbjct: 135 LGTISATSQPKMRDGFEPLLPGFTV-----VPFNDL--DAALAQID---------DNTAG 178 Query: 203 IVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPD 262 ++EPVQGEGG S+ AF++ LR CD HG++LI DEVQ G RTGT FA EQ GV PD Sbjct: 179 FLLEPVQGEGGVTPSTQAFLKGLREACDAHGLLLILDEVQCGYARTGTFFAHEQYGVTPD 238 Query: 263 LTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQ 322 + AK I GFPL E + G G TY GNP+A + VL+ + L Sbjct: 239 IMAVAKGIGAGFPLGACLATEEAAKGMVFGTHGSTYGGNPLAMAVGIAVLEEVLADGFLD 298 Query: 323 KANDLGQKLKDGLLAIAEKHPEI-GDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARAR 381 + +G +L+ L + H + DVRG+G M+ ++L DA V R Sbjct: 299 RVTAMGARLRSALEQLIPNHDGMFEDVRGMGLMLGVKL--------KDAHDARAFVGHLR 350 Query: 382 D-KGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIIS 418 D GL+ +S G NVLRIL PL IE++ I + +E IS Sbjct: 351 DHHGLLAVSAG--QNVLRILPPLVIEESHIAECIEKIS 386 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: 468 Number of extensions: 18 Number of successful extensions: 6 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: 398 Length adjustment: 31 Effective length of query: 395 Effective length of database: 367 Effective search space: 144965 Effective search space used: 144965 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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