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_011188057.1 DP_RS04140 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000025945.1:WP_011188057.1 Length = 430 Score = 156 bits (395), Expect = 1e-42 Identities = 108/351 (30%), Positives = 174/351 (49%), Gaps = 30/351 (8%) Query: 4 NKELMQRRSQAIPRGVGQ---------IHPIFADRAENCRVWDVEGREYLDFAGGIAVLN 54 +K+L + IP GV P+F +RAE ++D +G++YLDF + Sbjct: 6 SKKLFAEAKKVIPGGVNSPVRACLSVGCDPLFIERAEGSYIYDADGQKYLDFVNSWGPMI 65 Query: 55 TGHLHPKVVAAVE-AQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSE 113 GH HP ++ A++ A + S+ ++L ++ + VP +K V++G+E Sbjct: 66 MGHAHPDIIKAIQDAAVYGTSYGA----PTSSEVDLASMVVEAVPS--IEKVRFVSSGTE 119 Query: 114 AVENAVKIARAATKRSGTIAFSGAYHGRTHYTL--ALTGKVNPYSAGMGLMPGHVYRALY 171 A +AV++AR T ++ + F G YHG L A +G + G +P + + Sbjct: 120 ATMSAVRLARGYTGKNVIVKFDGCYHGHADSFLVKAGSGVLTLGIPGSPGVPEDIVKNTI 179 Query: 172 PCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDE 231 P + + +A+ + R A +IA +++EPV G G +P F+Q+LR + E Sbjct: 180 SIPYNSV---EALETTLR-----DADLNIACVIVEPVAGNMGCVPPAPGFLQKLREITAE 231 Query: 232 HGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAP 291 GI+LI DEV +G R A + GV PDLT K I GG P+ G+A++M++VAP Sbjct: 232 EGIVLIFDEVITGF-RLSYGGAQQYYGVTPDLTCLGKIIGGGLPVGAYGGKADIMNSVAP 290 Query: 292 GG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIA 339 G GT +GNP+A A LK+ +Q+ + N DGLL +A Sbjct: 291 DGPVYQAGTLSGNPLAMAAGKAALKLLQQDGFYEDLNQKSAAYADGLLEVA 341 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: 433 Number of extensions: 24 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: 430 Length adjustment: 32 Effective length of query: 394 Effective length of database: 398 Effective search space: 156812 Effective search space used: 156812 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