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_066608605.1 V473_RS18720 diaminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_001046645.1:WP_066608605.1 Length = 436 Score = 181 bits (459), Expect = 4e-50 Identities = 134/418 (32%), Positives = 206/418 (49%), Gaps = 19/418 (4%) Query: 7 LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAV 66 + +RR A+ R + P ++A+ + D +G YLDF G + LN GH HP + A+ Sbjct: 18 IYERRESAV-RSYARAMPRQFNQAQGVWMHDNQGGRYLDFLSGCSTLNYGHNHPVLKNAL 76 Query: 67 EAQLKKLSHTCFQVLAYEPYLELCEIMNQKV--PGDFAKKTLLV-TTGSEAVENAVKIAR 123 + T L + + + + P D + + TG+ AVE A+K+AR Sbjct: 77 VDYIVNDGITHGLDLHTDAKADFLAALEDVILTPRDLDYRAMFTGPTGTNAVEAAIKLAR 136 Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA 183 T R IAF+ +HG T LA TG G G+ HV Y HG D A Sbjct: 137 KITGRELVIAFTNGFHGMTLGALACTGNAAK-RGGAGVPLNHVSHEPYD-GYHGPGVDTA 194 Query: 184 IASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQS 243 R+ + + AAI++E VQGEGG A+SP +++++ + HG ++I D++Q+ Sbjct: 195 EQLERRLSDPSSGLDAPAAILVETVQGEGGLNAASPRWLRQIADIAKRHGALMIIDDIQA 254 Query: 244 GAGRTGTLFAMEQMGVAPDLTTFAKSIAG-GFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302 G GRTG F+ E MG PD+ T AKS++G G P A R E +D +PG GT+ GN Sbjct: 255 GCGRTGNFFSFEGMGFTPDIVTMAKSLSGMGLPFALTLFRPE-LDQWSPGEHNGTFRGNN 313 Query: 303 IACVAALEVLKVFEQE-NLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFE 361 A V A L+ F + N Q G L+ L A+A +H +RG G M I++ Sbjct: 314 HAFVTATATLRHFWSDGNFQQDIARRGALLERRLAAMATEHGL--SIRGRGMMRGIDV-- 369 Query: 362 DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 ++ I A +GLI+ + G + ++++L PL I+D+ + GL+I+ Q Sbjct: 370 ------GSGEIAQTITAACFAQGLIIETSGAHDEIVKVLAPLVIDDSVLSAGLDILEQ 421 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: 475 Number of extensions: 23 Number of successful extensions: 5 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: 436 Length adjustment: 32 Effective length of query: 394 Effective length of database: 404 Effective search space: 159176 Effective search space used: 159176 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 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