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 200475 SO1300 glutamate-1-semialdehyde-2,1-aminomutase (NCBI ptt file)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__MR1:200475 Length = 430 Score = 162 bits (410), Expect = 2e-44 Identities = 116/385 (30%), Positives = 183/385 (47%), Gaps = 41/385 (10%) Query: 1 MNSNKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIA 51 M ++ L ++ + IP GV P+F ++A+ ++D +G+ Y+D+ G Sbjct: 1 MTRSEALFEQAKKTIPGGVNSPVRAFNGVGGSPLFIEKADGAYIYDADGKAYIDYVGSWG 60 Query: 52 VLNTGHLHPKVVAAVEAQLKKLSHTCFQVLA-YEPYLELCEIMNQKVPGDFAKKTLLVTT 110 + GH HPK+ AV A + H A E +++ E + VP ++ +V++ Sbjct: 61 PMILGHNHPKIREAVLAAV----HNGLSFGAPTELEVQMAEKVIAMVPS--IEQVRMVSS 114 Query: 111 GSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPG------ 164 G+EA +A+++AR T R + F G YHG L G + G PG Sbjct: 115 GTEATMSAIRLARGFTNRDKILKFEGCYHGHADCLLVKAGS-GALTLGQPSSPGIPEDFA 173 Query: 165 -HVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQ 223 H A+Y ++ D++ S+ + P +I+ I+IEPV G P F++ Sbjct: 174 KHTLTAVY-------NDLDSVRSLFEQY-----PTEISCIIIEPVAGNMNCIPPIPGFLE 221 Query: 224 RLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRA 283 LR+LCDE G +LI DEV +G R A GV PDLTT K I GG P+ GR Sbjct: 222 GLRSLCDEFGALLIIDEVMTGF-RVSKSGAQGHYGVTPDLTTLGKVIGGGMPVGAFGGRK 280 Query: 284 EVMDAVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAE 340 +VM +AP G GT +GNPIA A L ++ +E L + + +++ +G A A+ Sbjct: 281 DVMQFIAPTGPVYQAGTLSGNPIAMSAGLAQMEALCEEGLYEALSAKTKRIAEGFKAAAD 340 Query: 341 KHPEIGDVRGLGAMIAIELFEDGDH 365 KH + +G M F + +H Sbjct: 341 KHGIPMAINYVGGMFGF-FFTEQEH 364 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: 481 Number of extensions: 26 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