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_055068649.1 M72_RS13930 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_001406815.1:WP_055068649.1 Length = 424 Score = 140 bits (353), Expect = 7e-38 Identities = 124/419 (29%), Positives = 198/419 (47%), Gaps = 48/419 (11%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAY 83 P F A+ + DV+G E +D+ GH +V+ V+A C + L + Sbjct: 35 PRFIQSAKGSHITDVDGNEMIDYVCSWGPGILGHADSRVIEKVKA-------ACEEGLTF 87 Query: 84 ----EPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYH 139 E +E+ E++ Q VP + + LV++G+EA +A+++AR TKR I F G YH Sbjct: 88 GAPTEREVEMAELLAQLVPS--MEVSRLVSSGTEATMSAIRVARGYTKRDKIIKFRGCYH 145 Query: 140 GRTHYTLALTGKVN-----PYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKND 194 G + L G P SAG+ P R ++E ++ S+ +F + Sbjct: 146 GHSDGLLVKAGSAALTTSVPDSAGV---PADFTRHTL------VAEYNSPDSVKALF--E 194 Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254 A P++IAAI++EPV G + F++ LR + +G + I DEV +G R A Sbjct: 195 AYPDEIAAIIVEPVAANMGVVPPADGFLEFLREITKHYGALFIFDEVITGF-RLALGGAQ 253 Query: 255 EQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGG---LGGTYAGNPIACVAALEV 311 E + PDL+TF K I GG P+ GR ++M V+P G GT +GNPIA A L Sbjct: 254 EYFHITPDLSTFGKIIGGGMPVGAYGGREDIMRMVSPDGPVYQAGTLSGNPIATAAGLAT 313 Query: 312 LKVFEQENLLQKANDLGQKLKD--GLLAIAEKHPEIG--DVRGLGAMIAIELFEDGDHNK 367 L++ E + D+ +L++ +LA A +H V +G++++I F D Sbjct: 314 LRILEAD------TDIYMRLQENTAMLADAVRHAAGNRVHVNQIGSLMSI-FFTGEDVTD 366 Query: 368 PDAKLTAEIVARARDKGLILLSCGPYY---NVLRILVPLTIEDAQIRQGLEIISQCFDE 423 D+ TA+ A A G +L G Y + V DA I++ + ++ + F E Sbjct: 367 YDSATTADTKAYADYFG-FMLDHGIYVAPSQFESMFVSDAHTDADIQKTIHVMQEYFAE 424 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: 415 Number of extensions: 28 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: 424 Length adjustment: 32 Effective length of query: 394 Effective length of database: 392 Effective search space: 154448 Effective search space used: 154448 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