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_012501411.1 CPAR_RS00790 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000020505.1:WP_012501411.1 Length = 431 Score = 155 bits (393), Expect = 2e-42 Identities = 116/351 (33%), Positives = 169/351 (48%), Gaps = 27/351 (7%) Query: 1 MNSNKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIA 51 + + EL ++ + IP GV PI+ + + + DV+G YLD+ G Sbjct: 4 LTRSAELFEKAKKFIPGGVNSPVRAFKSVGGTPIYMAKGQGAYMTDVDGNTYLDYVGSWG 63 Query: 52 VLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTG 111 G +HP++ AA+E L+ + + + E +E+ E++ Q VP + +V +G Sbjct: 64 PFILGSMHPRLTAAIEYTLRNIGTSFGTPIEIE--IEIAELLCQIVPS--LEMVRMVNSG 119 Query: 112 SEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALY 171 +EA +AV++AR T + I F G YHG L G + G PG V + Sbjct: 120 TEATMSAVRLARGYTGKDKIIKFEGCYHGHGDSFLIKAGS-GVLTLGDPDSPG-VTKGTA 177 Query: 172 PCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDE 231 L+ D I S+ I + +AAI+IEPV G G + F+ LR LCD Sbjct: 178 NDTLNATYND--IESVKAIVNENKG--QVAAIIIEPVAGNTGVIPAKKEFLVALRELCDA 233 Query: 232 HGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAP 291 GI+LI DEV G R A E GV PDLTT K I GG P+ G+ ++M+ +AP Sbjct: 234 EGIVLIFDEVMCGF-RVALGGAQELYGVTPDLTTMGKIIGGGLPVGAFGGKRKIMENIAP 292 Query: 292 GG---LGGTYAGNPIACVAALEVLKVFEQEN----LLQKANDLGQKLKDGL 335 G GT +GNP+A A LE LK+ +EN L +KA L KD + Sbjct: 293 LGSVYQAGTLSGNPLALTAGLETLKILMEENPYPELERKAAFLEAGFKDNM 343 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: 428 Number of extensions: 24 Number of successful extensions: 5 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: 431 Length adjustment: 32 Effective length of query: 394 Effective length of database: 399 Effective search space: 157206 Effective search space used: 157206 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