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_028311050.1 H566_RS0108125 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000482785.1:WP_028311050.1 Length = 435 Score = 459 bits (1181), Expect = e-134 Identities = 224/425 (52%), Positives = 300/425 (70%), Gaps = 3/425 (0%) Query: 3 SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62 +N + + RR+ A+PRGVGQ HP+ A RA N VWDVEG+ Y+DF GIAV+NTGH +P+V Sbjct: 7 TNADQLARRAAALPRGVGQAHPVVAQRALNAEVWDVEGKRYIDFVAGIAVVNTGHNNPRV 66 Query: 63 VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122 +AAV+ Q++ +HTCFQVLAY+ Y+ L E +N ++PG AKK+ + +G+EAVENA+K+A Sbjct: 67 LAAVQEQMQHFTHTCFQVLAYDGYITLAEKLNARMPGPGAKKSFFMNSGAEAVENAIKVA 126 Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182 RAAT R G IAF+G +HGRT +TL LTGKV+PY G G VY A +P PLHG+S +D Sbjct: 127 RAATGRPGIIAFNGGFHGRTMFTLGLTGKVDPYKIGFGPFSADVYHAPFPNPLHGLSAED 186 Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242 A+ + +FK D +AA +IEPVQGEGG+ + F++ LR + D HGI++IADE+Q Sbjct: 187 ALKGVEALFKFDIEASRVAAFIIEPVQGEGGYLPAPAPFLRGLREIADRHGILIIADEIQ 246 Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302 SG RTG + +E GVAPD+ T AK + GGFP+A V GRAEVMDA APGGLGGTY GNP Sbjct: 247 SGVCRTGKFYGIEHSGVAPDIITMAKGLGGGFPIAAVVGRAEVMDAAAPGGLGGTYGGNP 306 Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE-IGDVRGLGAMIAIEL-F 360 ++C AAL VL + E E L +K G+ + L IA HP+ + +VRGLGAM+AIE Sbjct: 307 LSCAAALAVLDIVEDEQLNEKVQATGRTMLAKLDEIAAAHPDRVAEVRGLGAMLAIEFGT 366 Query: 361 EDGD-HNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 D D H PD L IVA AR +GL++LSCGPY NV+R++ PLT+ +A + +GL++++ Sbjct: 367 RDADGHWTPDGALVKAIVAEARARGLLILSCGPYGNVIRLMPPLTVGEAVLAEGLDLLAA 426 Query: 420 CFDEA 424 D A Sbjct: 427 SVDAA 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: 584 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: 435 Length adjustment: 32 Effective length of query: 394 Effective length of database: 403 Effective search space: 158782 Effective search space used: 158782 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 Apr 09 2024. The underlying query database was built on Apr 09 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