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_017599103.1 D471_RS0113530 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000341125.1:WP_017599103.1 Length = 418 Score = 290 bits (741), Expect = 7e-83 Identities = 160/409 (39%), Positives = 230/409 (56%), Gaps = 8/409 (1%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 Q P+ A R E ++D + R YLDF GI V +TGH HP+VVAA + Q+ L H + Sbjct: 10 QATPVLAARGEGAYLYDEDDRRYLDFTAGIGVTSTGHCHPRVVAAAQEQVATLIHGQYTT 69 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 + + P L L E + +P + + V +GSEAVE A+++AR AT R I F G++HG Sbjct: 70 VMHRPLLRLTERLGDVLP-EGVDRLFYVNSGSEAVEAALRLARQATGRQNAIVFQGSFHG 128 Query: 141 RTHYTLALTGKVNPYSAGMG-LMPGHVYRALYPCPLHGISEDDAIASIHRIFKND----A 195 RT +LT AG+G L+PG V G++E+DA+A R F + Sbjct: 129 RTMGAASLTTSGVKIRAGIGPLVPGVVVSPFPYAYRLGMAEEDAVAHALREFDYQLTTVS 188 Query: 196 APEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAME 255 +P+D AA+ IEPV GEGG+ +F++ LR D+HG +L+ DEVQ+G GRTGT + E Sbjct: 189 SPKDTAAVFIEPVLGEGGYVPVPDSFLRGLRERADQHGFLLVLDEVQTGFGRTGTFWGHE 248 Query: 256 QMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVF 315 GV PD+ AK +A GFPL+ + +M PG GGTY GN +AC AA+ L V Sbjct: 249 PSGVRPDIVITAKGLASGFPLSAIAAPESIMAKAWPGSQGGTYGGNAVACAAAIATLDVI 308 Query: 316 EQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAE 375 ++E L++ + +G++L+ GL +A HP IGDVRG G M+A E PD Sbjct: 309 QEEGLVENSARMGERLRQGLEKVAGAHPVIGDVRGRGLMLANEF--TAPDGSPDGATALR 366 Query: 376 IVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDEA 424 A GL+LL+CGP NV+R++ PL + Q+ + + + +EA Sbjct: 367 AQQAAAGNGLLLLTCGPAGNVVRMIPPLVVNGEQVDTAVSLWAASVEEA 415 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: 477 Number of extensions: 25 Number of successful extensions: 4 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: 418 Length adjustment: 32 Effective length of query: 394 Effective length of database: 386 Effective search space: 152084 Effective search space used: 152084 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 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