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_011779097.1 MVAN_RS09350 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000015305.1:WP_011779097.1 Length = 450 Score = 333 bits (853), Expect = 8e-96 Identities = 178/421 (42%), Positives = 242/421 (57%), Gaps = 6/421 (1%) Query: 6 ELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAA 65 EL RRS A+P G+ ++ A DV+G ++D GIAV G+ P VV Sbjct: 28 ELAARRSAALPAGLASAAGVYVAAAGGGVAVDVDGNSFIDLGSGIAVTTVGNSAPAVVER 87 Query: 66 VEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAA 125 AQL + +HTCF YEPY+E+ E +N+ PG K+T L TGSEAVENAVK ARAA Sbjct: 88 ATAQLARYTHTCFLATPYEPYIEVAETLNRLTPGSHDKRTALFNTGSEAVENAVKYARAA 147 Query: 126 TKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGIS-----E 180 T RS + F A+HGR+ T+ +T K PY G G VYRA P S Sbjct: 148 TGRSAVVVFDHAFHGRSLLTMTMTAKNQPYKHGFGPFAPEVYRAPMAYPYRWPSGPQHCA 207 Query: 181 DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE 240 ++A A ++ + +A +V+EP+QGEGGF + F++ + C E GI+L+ADE Sbjct: 208 EEAFAHFAQLVDAQIGADAVACVVVEPIQGEGGFIVPADGFLRAVAEFCRERGILLVADE 267 Query: 241 VQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG 300 VQ+G RTG FA E G+ PDL T AK +AGG PLA VTGRA+VMDA PGG+GGTY+G Sbjct: 268 VQTGIARTGAWFACEHDGIVPDLITTAKGLAGGLPLAAVTGRADVMDAAHPGGIGGTYSG 327 Query: 301 NPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELF 360 NP+AC AAL V + E L+++A +G+ + L IA IG++RG GAMIA EL Sbjct: 328 NPVACAAALGVFEEIESGRLVERARTIGEAMVTALEDIAAGTDVIGEIRGRGAMIAAELV 387 Query: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQC 420 G +P+ A I G++ L+ G + NV+R L PL+I D + + +++ Sbjct: 388 VPGT-REPNRDAVAAISRHCHLNGVLTLTAGTFGNVMRFLPPLSISDELLTEAFDVVRDG 446 Query: 421 F 421 F Sbjct: 447 F 447 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: 582 Number of extensions: 21 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: 450 Length adjustment: 32 Effective length of query: 394 Effective length of database: 418 Effective search space: 164692 Effective search space used: 164692 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 Jul 25 2024. The underlying query database was built on Jul 25 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