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_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_900105005.1:WP_090271605.1 Length = 417 Score = 284 bits (726), Expect = 4e-81 Identities = 155/407 (38%), Positives = 235/407 (57%), Gaps = 22/407 (5%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 Q + A+R E C + +G+ YLDF GI V +TGH HP VVAA Q+ KL H + Sbjct: 10 QSSKVCAERGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTT 69 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 + ++P L+L E + K+P D GSEAVE A+++AR AT+R+ I F+G +HG Sbjct: 70 VTHQPMLDLAERLVGKMP-DGIDSVAFSNAGSEAVEMALRLARHATRRANVIVFNGGFHG 128 Query: 141 RTHYTLALT-------GKVNPYSAGMGLMP-GHVYRALYPCPLHGISEDDA----IASIH 188 RT ++T +P AG+ + P H +R +G SE++A +A + Sbjct: 129 RTMGAASMTTSGTKVRNAYHPMMAGVVVAPFPHSWR-------YGWSEEEATRFCLAELD 181 Query: 189 RIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRT 248 I K APED AA+VIEPVQGE G+Y + AFMQ L C +HGI+L+ DE+Q+G GR+ Sbjct: 182 HILKTQTAPEDTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRS 241 Query: 249 GTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAA 308 G ++ + G+ PD+ AK +A GFPL+ + +M G GGTY N ++C AA Sbjct: 242 GKFWSHQHFGITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAA 301 Query: 309 LEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKP 368 L L+V + ENL+ A GQ+L D L + +++P++ D+RG G M+ +E+ + D KP Sbjct: 302 LATLRVMDNENLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPD--KP 359 Query: 369 DAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415 A L A + + ++GL+LL CG ++R L PL + +A++ ++ Sbjct: 360 LADLAASLTTASEEEGLLLLRCGTDSQIIRWLPPLVVSEAEVDDAVQ 406 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: 410 Number of extensions: 20 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: 417 Length adjustment: 32 Effective length of query: 394 Effective length of database: 385 Effective search space: 151690 Effective search space used: 151690 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