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_028312237.1 H566_RS0116110 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000482785.1:WP_028312237.1 Length = 426 Score = 170 bits (430), Expect = 9e-47 Identities = 118/357 (33%), Positives = 169/357 (47%), Gaps = 34/357 (9%) Query: 1 MNSNKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIA 51 M+ N EL R ++IP GV P F +R R+WD +GREY+D+ G Sbjct: 1 MSRNDELFARAQRSIPGGVNSPVRAFRQVGGTPRFFERGAGARLWDADGREYIDYVGSWG 60 Query: 52 VLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTG 111 + GH HP VVAAV+ +H E + + E + + +P +K V++G Sbjct: 61 PMILGHAHPTVVAAVQ---DAAAHGLGYGAPTEAEIVIAEEVMKLMPS--LEKIRFVSSG 115 Query: 112 SEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGK-----VNPYSAGMGLMPGHV 166 +EA +A+++AR AT R+ + F G YHG L G NP SAG +P Sbjct: 116 TEAAMSAIRLARGATGRTRIVKFDGCYHGHADSLLVKAGSGLLTFGNPTSAG---VPADF 172 Query: 167 YRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLR 226 + I+E DA + +IA +++EP+ G F +P + RLR Sbjct: 173 AAHTIVLDYNDIAEIDACF--------EKFGHEIACVIVEPIAGNMNFVRGTPEWHARLR 224 Query: 227 ALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVM 286 LC +HG +LI DEV +G R A G+ PDLT K I GG P+A G AEVM Sbjct: 225 ELCTQHGSVLIWDEVMTGF-RVALGGAQSLYGIRPDLTVLGKVIGGGMPVAAFGGSAEVM 283 Query: 287 DAVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAE 340 +AP G GT +GNP+A A L L++ ++ + + KL G A AE Sbjct: 284 KFLAPEGPVYQAGTLSGNPVAVAAGLATLRLIQEPGFHDRLGEQTAKLMAGFQAAAE 340 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: 503 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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 10 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