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_022948199.1 H035_RS0106595 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000421465.1:WP_022948199.1 Length = 415 Score = 279 bits (714), Expect = 1e-79 Identities = 152/406 (37%), Positives = 227/406 (55%), Gaps = 8/406 (1%) Query: 19 VGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCF 78 + Q + +R E ++D G +YLDF GI V TGH HP VVAA + Q+ L H + Sbjct: 8 LAQSSSVLVERGEGAYLYDAAGTKYLDFTSGIGVTATGHCHPTVVAAAQKQVATLVHAQY 67 Query: 79 QVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAY 138 + + LEL + + +++P + +GSEAVE+AV++AR AT R+ IAF G + Sbjct: 68 TTVKHPRMLELTDRLYERLPAEL-DAIAFWNSGSEAVESAVRLARQATGRANIIAFQGGF 126 Query: 139 HGRTHYTLALTGKVNPYSAGMG-LMPGHVYRALYPCPLHGISEDDA----IASIHRIFKN 193 HGRT +LT G +M G VY +G SE++ + + +F Sbjct: 127 HGRTMGAASLTTSTPKVRTGFHPMMAGVVYAPFPHTYRYGWSEEETTRFCLQELDHLFVT 186 Query: 194 DAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFA 253 +AP D AAI++EPVQGE G+Y ++ FMQ LR CD HGI+LI DE+Q+G GRTG ++ Sbjct: 187 QSAPSDTAAIIVEPVQGEYGYYPATEGFMQGLRERCDRHGIVLICDEIQAGYGRTGQFWS 246 Query: 254 MEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLK 313 E V PD+ AK +A G+PL+ + A++M PG GGTY N +AC AAL L Sbjct: 247 HEHFDVRPDILITAKGLASGYPLSAIAASADLMKQGFPGSQGGTYGANAVACAAALATLD 306 Query: 314 VFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLT 373 VFEQENLL + G L+ L + + I ++RG+G M+ +E+ + D +P + Sbjct: 307 VFEQENLLANVRENGAYLRQQLERLQSAYRFIDEIRGMGLMLGMEIVD--DKKQPSGERA 364 Query: 374 AEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 A+++ + GL++L CG + V+R L PL + QI + + + Q Sbjct: 365 AQLLKESEAAGLLMLRCGTHGQVVRWLPPLIVTREQIDEAVGLFEQ 410 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: 436 Number of extensions: 17 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: 415 Length adjustment: 32 Effective length of query: 394 Effective length of database: 383 Effective search space: 150902 Effective search space used: 150902 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