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_004321319.1 C665_RS15305 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000310185.1:WP_004321319.1 Length = 427 Score = 172 bits (435), Expect = 2e-47 Identities = 120/373 (32%), Positives = 180/373 (48%), Gaps = 38/373 (10%) Query: 4 NKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIAVLN 54 N+ L+QR ++IP GV P F RAE RVWD +G+EY+D+ G Sbjct: 5 NEALIQRAQRSIPGGVNSPVRAFRSVGGTPRFLARAEGARVWDADGKEYIDYVGSWGPAI 64 Query: 55 TGHLHPKVVAAV-EAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSE 113 GH HP ++ AV EA LK LS E +++ E++ +P + LV++G+E Sbjct: 65 AGHAHPAIIEAVREAALKGLSFGA----PTESEVDMAELICAMLPS--VEMVRLVSSGTE 118 Query: 114 AVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGK-----VNPYSAGMGLMPGHVYR 168 A +A+++AR T R + F G YHG L G NP S G +P + Sbjct: 119 ATMSAIRLARGFTGRDAIVKFEGCYHGHADSLLVKAGSGLLTFGNPSSGG---VPADFAK 175 Query: 169 ALYPCPLHGISED-DAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRA 227 H I D + + + +FK A ++IAAI++EPV G P F++ LR Sbjct: 176 -------HTIVLDYNDLQQVEDVFK--ARGDEIAAIIVEPVAGNMNLIKPQPGFLEGLRR 226 Query: 228 LCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMD 287 +C E+G +LI DEV +G R G G+ PDLTT K I GG P+ GR ++M+ Sbjct: 227 ICTEYGAVLIFDEVMTGF-RVGPQGVQGLYGITPDLTTLGKVIGGGMPVGAFGGRRDIME 285 Query: 288 AVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE 344 +AP G GT +G+P+A A + L++ + ++ Q+L GL A A+ Sbjct: 286 KIAPLGSVYQAGTLSGSPVAVAAGMVSLQLTREAGFYERLTASTQRLVAGLAAAAKDAGV 345 Query: 345 IGDVRGLGAMIAI 357 +G M + Sbjct: 346 TFSADSVGGMFGV 358 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: 478 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: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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