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_028583531.1 G494_RS0104195 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000429965.1:WP_028583531.1 Length = 429 Score = 154 bits (389), Expect = 5e-42 Identities = 117/369 (31%), Positives = 170/369 (46%), Gaps = 42/369 (11%) Query: 7 LMQRRSQAIPRGVGQ---------IHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGH 57 L + Q IP GV P+F +A C V DV+G E++DF G + TGH Sbjct: 9 LFPQAQQVIPGGVNSPVRACRSVGCDPLFIQKAAGCTVTDVDGNEFIDFVGSWGPMITGH 68 Query: 58 LHPKVVAAVEAQLKKLSHTCFQVLAYEPY-LELCEIMNQKVPGDFAKKTLLVTTGSEAVE 116 P+V+ A+ + L T F A P +EL E++ VP +K V +G+EA Sbjct: 69 AQPEVIEAI--RKTALDGTSFG--APTPLEVELAELVCDSVPS--LEKIRFVNSGTEATM 122 Query: 117 NAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLH 176 +AV++AR T R+ + F G YHG L G G + + P Sbjct: 123 SAVRLARGYTGRNVVVKFDGCYHGHADSFLVKAGS------------GVITLGIPGSP-- 168 Query: 177 GISEDDAIASIHRIFKNDAAPE--------DIAAIVIEPVQGEGGFYASSPAFMQRLRAL 228 G+ ED ++ + N+A E DIA +++EPV G G +F+++LR L Sbjct: 169 GVPEDIVKNTLSIPYNNEAILEQTLRDPQLDIACVILEPVAGNMGVVVPEMSFLKKLREL 228 Query: 229 CDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDA 288 E GI+LI DEV +G R A E+ G+ PDLT K I GG P+ G+ E+MD Sbjct: 229 TRELGIVLIFDEVITGF-RLALGGAQERFGIIPDLTCLGKIIGGGLPVGAYGGKQEIMDQ 287 Query: 289 VAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEI 345 +AP G GT +GNP+A A L ++K+ + Q + L I P Sbjct: 288 IAPDGPVYQAGTLSGNPLAMAAGLAMVKILRRPGFYQALEEKSDWYAGQLEQIIAASPLE 347 Query: 346 GDVRGLGAM 354 V +G+M Sbjct: 348 VVVNRIGSM 356 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: 418 Number of extensions: 23 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: 429 Length adjustment: 32 Effective length of query: 394 Effective length of database: 397 Effective search space: 156418 Effective search space used: 156418 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 Apr 09 2024. The underlying query database was built on Apr 09 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