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_076478048.1 BW971_RS07615 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_900156495.1:WP_076478048.1 Length = 462 Score = 207 bits (527), Expect = 5e-58 Identities = 140/417 (33%), Positives = 217/417 (52%), Gaps = 30/417 (7%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 +I P+ + VWD +GR LDF+ + N GH HP+V+AA++ Q KL Q Sbjct: 43 EISPMGITASAGSYVWDGDGRRLLDFSSMLVNTNIGHQHPRVIAAIQRQAAKLCTVAPQY 102 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 A + E ++ ++ PGD K G++A E+AV++AR T R + +YHG Sbjct: 103 -ANDVRSEAARLIAERTPGDL-DKIFFTNGGADANEHAVRMARLHTGRRKVLTRYRSYHG 160 Query: 141 RTHYTLALTGKVN--PYSAGMGLMPGHVYRALYPCPLHGISEDD----AIASIHRIFKND 194 T + LTG P G + LY H +E+ A+ + + + + Sbjct: 161 GTDTAINLTGDPRRWPNDHGDSGVVHFFGPFLYRSRFHAETEEQECARALDHLDEVIRME 220 Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254 P IAAIV+E + G G P +++ +R LCD +GI+ IADEV +G GR+GT F++ Sbjct: 221 G-PSTIAAIVLETIPGTAGIMIPPPGYLRGVRELCDRYGIVYIADEVMAGFGRSGTWFSV 279 Query: 255 EQMGVAPDLTTFAKSIAGGF-PLAGVTGRAEVMDAV----APGGLGGTYAGNPIACVAAL 309 + +GV PDL TFAK + G+ PL GV A + PGGL TY+G+P+A AA+ Sbjct: 280 DLVGVTPDLLTFAKGVNSGYVPLGGVAISAAIAATFDHRPYPGGL--TYSGHPLATAAAV 337 Query: 310 EVLKVFEQENLLQKANDLG-QKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKP 368 + E+++ A+ +G + + GL +A++HP +G+VRG G A+EL D +P Sbjct: 338 ATITAMADEDVVGNASRIGAEVIGPGLAELADRHPSVGEVRGCGVFWALELVRDRTTREP 397 Query: 369 DAKLTA------EIVARARDKGLILLSCGPYYNVLRILV--PLTIEDAQIRQGLEII 417 A A ++VA R GL+ P+ NV RI V P T+ ++R+GL ++ Sbjct: 398 LAPYGASSAAMNDVVAACRSGGLL-----PFANVNRIHVVPPCTVTAEEVREGLTVL 449 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: 564 Number of extensions: 29 Number of successful extensions: 6 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: 462 Length adjustment: 32 Effective length of query: 394 Effective length of database: 430 Effective search space: 169420 Effective search space used: 169420 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 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