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_025272511.1 HALAL_RS0102620 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000527155.1:WP_025272511.1 Length = 417 Score = 293 bits (750), Expect = 7e-84 Identities = 159/404 (39%), Positives = 229/404 (56%), Gaps = 8/404 (1%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 Q P+ AD E ++D +GR YLDF GI V +TGH HP VV A + Q+ KL H + Sbjct: 10 QATPVVADHGEGVYLYDADGRRYLDFTAGIGVTSTGHCHPHVVQAAQEQVGKLIHGQYTT 69 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 + ++P LEL + +P +GSEAVE A++++R AT R + F G +HG Sbjct: 70 VMHQPLLELTRRLGDVLPAGL-DSLFFSNSGSEAVEAALRLSRQATGRPNIVVFQGGFHG 128 Query: 141 RTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLH-----GISEDDAIASIHRIFKNDA 195 RT T LT +SAG+ + V+ A +P + + A+ + +F Sbjct: 129 RTVATATLTTSGTRFSAGISPLMSGVHMAPFPYAYRYGWDESTATEFALRELDYLFATVT 188 Query: 196 APEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAME 255 +P + AA IEPV GEGG+ ++P F+ LR DEHGI+L+ DE+Q+G GRTG + + Sbjct: 189 SPAETAAFFIEPVLGEGGYVPANPEFLAGLRQRADEHGILLVLDEIQTGFGRTGKFWGHD 248 Query: 256 QMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVF 315 GV PD+ AK +A GFPL+G+ E+M PG GGTY GN +AC AA+ L V Sbjct: 249 HFGVHPDVVLIAKGLASGFPLSGMATSEELMSQAWPGSQGGTYGGNAVACAAAVATLDVI 308 Query: 316 EQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAE 375 ++E L+ A D G++L +G I EK P IGDVRGLG M+ E F D +PD Sbjct: 309 QREGLVDNAADRGRQLLEGARHIGEKTPLIGDVRGLGLMVGSE-FTTPD-GQPDTATAQA 366 Query: 376 IVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 A +GL+LL+CG + NV+R++ PL ++ AQ+ + L+I S+ Sbjct: 367 AQKEAAARGLMLLTCGAHMNVVRMIPPLVVDAAQVDEALDIWSE 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: 454 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: 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 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