Align 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_092344171.1 BLU87_RS01565 aspartate aminotransferase family protein
Query= curated2:P63505 (449 letters) >NCBI__GCF_900107645.1:WP_092344171.1 Length = 460 Score = 249 bits (636), Expect = 1e-70 Identities = 154/441 (34%), Positives = 240/441 (54%), Gaps = 15/441 (3%) Query: 15 PGPASQALTHRRAAAVSSGVGVT--LPVFVARAGGGIVEDVDGNRLIDLGSGIAVTTIGN 72 PGP SQ + +A SS + +P+ +A+ G +EDVDGN ID+ SG V +G+ Sbjct: 23 PGPKSQEILKYQADNESSAISYAKGMPMAMAKGKGATIEDVDGNIYIDMFSGAGVMALGH 82 Query: 73 SSPRVVDAVRTQVAEFTHTCFMVTPYEGYVAVAEQLNRITPGSGPKRSVLFNSGAEAVEN 132 S P V+ A + + THT + +P + + + +I P + +G++AVE Sbjct: 83 SHPDVLKASHEAIEDITHTLDIPSPIRQ--RMVKSMKKILPKELTRVFFGGPTGSDAVEQ 140 Query: 133 AVKIARSYTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYRAPLSYPYRD 192 A+K+A+ TG+ V+AF+ +YHG T + +ALT + ++ G GP +P + P Y YR+ Sbjct: 141 AIKLAKFNTGRYGVIAFEGSYHGMTGMALALTCDAH-HRQGLGPLSPGVQFLPYPYEYRN 199 Query: 193 --GLLDKQLATNGELAAARAIGVIDKQVGANNLAALVIEPIQGEGGFIVPAEGFLPALLD 250 G D+ L R + D G AA+++E +QGEGG I+PA FL + + Sbjct: 200 PFGCPDEDLQLQAAENLERVLS--DSHSGYLKPAAVILESVQGEGGTIIPAPIFLQRVRE 257 Query: 251 WCRKNHVVFIADEVQTGFARTGAMFACEHEGPDGLEPDLICTAKGIAD-GLPLSAVTGRA 309 C K+ +V I DE+Q G RTG MFA EH G+ PD++ +K + G P+SA+ R Sbjct: 258 ICTKHDIVMICDEIQAGLGRTGKMFAFEHA---GIVPDIVTMSKALGGIGFPISAIAYRE 314 Query: 310 EIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERARQIERLVTDRLTTLQAVDD 369 E+ P G GTF GN +A AA A + ++ +G+IE A + +L L+A Sbjct: 315 ELNTWP-TGLTIGTFRGNMIAFAAGSAALEWMQDNGVIEHAAGLGEKCMVKLKELEAQSA 373 Query: 370 RIGDVRGRGAMIAVELVKSGTTEPDAGLTERLATA-AHAAGVIILTCGMFGNIIRLLPPL 428 +G+ RG G M+A+E+VK + AG +L AH GV+I G GN+ RLLPPL Sbjct: 374 IVGESRGLGMMLAIEMVKDKESREPAGDYAKLVRKHAHLRGVMIEVGGHHGNVARLLPPL 433 Query: 429 TIGDELLSEGLDIVCAILADL 449 I ++L +G++I+ ++ D+ Sbjct: 434 IITEDLAMKGIEIIAGVIKDI 454 Lambda K H 0.319 0.137 0.397 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: 536 Number of extensions: 28 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: 449 Length of database: 460 Length adjustment: 33 Effective length of query: 416 Effective length of database: 427 Effective search space: 177632 Effective search space used: 177632 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