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_054255500.1 BN2503_RS04745 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_001298675.1:WP_054255500.1 Length = 436 Score = 155 bits (393), Expect = 2e-42 Identities = 121/391 (30%), Positives = 176/391 (45%), Gaps = 37/391 (9%) Query: 4 NKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIAVLN 54 N L +R IP GV P F RA+ +WD G+ ++D+ G + Sbjct: 8 NLSLFERAKALIPGGVNSPVRAFRAVGGTPRFIARAQGAYMWDANGQRFIDYIGSWGPMI 67 Query: 55 TGHLHPKVVAAVE-AQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSE 113 GH HP V+ AV+ A L+ S E +EL E + + VP + LV++G+E Sbjct: 68 LGHGHPAVLEAVQKAALEGFSFGA----PTEREVELAEEIIRHVPS--MEMIRLVSSGTE 121 Query: 114 AVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMP-GHVYRALYP 172 A +A+++AR AT RS I F+G YHG L AG GL GH A P Sbjct: 122 AGMSAIRLARGATGRSKIIKFNGCYHGHADSLLV--------KAGSGLATFGHATSAGVP 173 Query: 173 CPLHG---ISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALC 229 + + E + +A + F +++A +++EP+ G F +S FM+R R LC Sbjct: 174 AEVVQHTLVLEYNDVAQLEEAFALHG--KEVACVIMEPIAGNMNFVRASVPFMRRARELC 231 Query: 230 DEHGIMLIADEVQS----GAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEV 285 +HG +L+ DEV + G G L+A + G APDLT K I GG PLA G + Sbjct: 232 TQHGALLVIDEVMTGFRVGLGSAQGLYAQQIPGFAPDLTVLGKVIGGGMPLAAFGGPRAI 291 Query: 286 MDAVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKH 342 M+ +AP G GT +GNP+A L L+ + ++ + L DGL A+ Sbjct: 292 MEQLAPLGPVYQAGTLSGNPVATACGLATLREIAKPGFYEQLAARTRALIDGLAGAAQAE 351 Query: 343 PEIGDVRGLGAMIAIELFEDGDHNKPDAKLT 373 G M L N P+ T Sbjct: 352 GVAFCADSEGGMFGFFLLPQLPQNYPEVLKT 382 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: 483 Number of extensions: 23 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: 436 Length adjustment: 32 Effective length of query: 394 Effective length of database: 404 Effective search space: 159176 Effective search space used: 159176 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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