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_010531860.1 ON01_RS14825 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000224785.1:WP_010531860.1 Length = 433 Score = 377 bits (967), Expect = e-109 Identities = 184/424 (43%), Positives = 268/424 (63%), Gaps = 7/424 (1%) Query: 5 KELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVA 64 K L ++R IP+GV + A V D++ E++DFAG I LN GH HPKV Sbjct: 9 KALQEKRENYIPKGVSNGNSNIVKDAIGATVTDIDNNEWIDFAGAIGTLNVGHTHPKVTT 68 Query: 65 AVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124 AV+ Q K H F V+ YE Y+ L E + Q PG F K+ LL+ +G+EA+ENA+K++R Sbjct: 69 AVKEQADKFLHPGFNVMMYEGYINLAEKLCQITPGHFNKQALLLNSGAEAIENAIKVSRK 128 Query: 125 ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE---- 180 T + ++F +HGRT+ T+ +T KV PY G G +Y+A YP H S+ Sbjct: 129 YTGKQAVVSFERGFHGRTNLTMGMTSKVKPYKFGFGPFAPDIYQAPYPYLYHKPSQLTDD 188 Query: 181 ---DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLI 237 D I F + APE++A +V+EPVQGEGGF F+Q ++ C++HGI+ + Sbjct: 189 EYVDQVIRDFEDFFVSSVAPENVACVVMEPVQGEGGFIIPPKRFVQYVKEFCEKHGIVFV 248 Query: 238 ADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGT 297 ADE+Q+G GRTG LFA++ V PDL T +KS+A G PL+GV G+ E+++A PG LGGT Sbjct: 249 ADEIQTGFGRTGKLFAVDHFDVEPDLMTVSKSMAAGLPLSGVVGKKEILNAANPGELGGT 308 Query: 298 YAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAI 357 YAGNP+AC AAL V+ V E+ENL +KA+ +G+K++ L + +K+ +G++R LGAM+A+ Sbjct: 309 YAGNPVACSAALAVIDVMEEENLPEKADVIGRKIEGKLQELQKKYEFVGEIRRLGAMVAV 368 Query: 358 ELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 E+ ED + +PD + T++I A A GL+LLS G N++R L PL I D ++ +GL+I+ Sbjct: 369 EIVEDRESKRPDKQKTSDITANANQNGLLLLSAGINSNIVRFLAPLVITDEELEKGLDIL 428 Query: 418 SQCF 421 Q F Sbjct: 429 EQTF 432 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: 454 Number of extensions: 23 Number of successful extensions: 2 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: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 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 Jul 26 2024. The underlying query database was built on Jul 25 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