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_012991510.1 THAL_RS02335 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000025605.1:WP_012991510.1 Length = 424 Score = 157 bits (396), Expect = 8e-43 Identities = 112/371 (30%), Positives = 180/371 (48%), Gaps = 32/371 (8%) Query: 3 SNKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIAVL 53 +N+ELM+R + +P GV PI A+ CR+WDVEG+EY+DF L Sbjct: 2 TNRELMERAKKLMPGGVSSPVRAFKAVGGEPIVVREAKGCRLWDVEGKEYIDFLMSWGPL 61 Query: 54 NTGHLHPKVVAAVEAQLKK-LSH--TCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTT 110 GH HP VV+ VE QL + +S+ TC++ + L E++ VP + V++ Sbjct: 62 ILGHAHPYVVSEVERQLSRGMSYGLTCYE------EIRLAELVVSSVPS--VEMVRFVSS 113 Query: 111 GSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYT-LALTGKVNPYSAGMGLMPGHVYRA 169 G+EA +A+++AR T R + F G YHG HY L ++ + G+ PG Sbjct: 114 GTEATMSAIRLARGYTGRKFVVKFEGCYHG--HYDGLLVSAGSGVATLGIPGTPGVPEEI 171 Query: 170 LYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALC 229 + ++ DA+ S + EDIA +++EPV G G S F++ LR + Sbjct: 172 AGLTLVLPYNDTDAVLSTFERY-----GEDIACVIVEPVAGNMGVVLPSEGFLEVLREVT 226 Query: 230 DEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAV 289 ++G +LI DEV + R A E + PD+T K + GG PL G+ E+M V Sbjct: 227 RKYGAVLIFDEVITNF-RLSVGGAQEYYAIDPDITCMGKILGGGMPLGAYGGKKEIMSHV 285 Query: 290 APGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIG 346 AP G GT +GNP++ V L+ + Q + ++L +G+ + ++ Sbjct: 286 APEGKVYQAGTLSGNPVSVVCGRATLEELLRLKPYQLLEERTRRLAEGISTVLKEKGIPH 345 Query: 347 DVRGLGAMIAI 357 + +G+M + Sbjct: 346 TINRIGSMFTV 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: 432 Number of extensions: 22 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: 424 Length adjustment: 32 Effective length of query: 394 Effective length of database: 392 Effective search space: 154448 Effective search space used: 154448 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 10 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