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 Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 Length = 430 Score = 431 bits (1108), Expect = e-125 Identities = 212/421 (50%), Positives = 283/421 (67%), Gaps = 4/421 (0%) Query: 1 MNSNKE----LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTG 56 MNS E L+++R Q +PRG+ HP+ DRA+ +WDV+G+ YLDF GGI VLN G Sbjct: 1 MNSKVEETPSLLRQRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIG 60 Query: 57 HLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVE 116 H HPKVVAAV+AQL+K+SH CFQV+AY+PYL+L + + + + G A K T+G+EAVE Sbjct: 61 HNHPKVVAAVQAQLQKISHACFQVVAYKPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVE 120 Query: 117 NAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLH 176 NAVKIARA T RS IAF G +HGRT LTG PY G V+ YP Sbjct: 121 NAVKIARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYR 180 Query: 177 GISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIML 236 G++ A+ ++ + APE +AAI+IEPVQG+GGF ++ F+Q LRAL +HGI+L Sbjct: 181 GVTSAMALQALDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVL 240 Query: 237 IADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG 296 I DE+Q+G GRTG F + G+ PDL T AKS+AGG PL+GV G+AE+MDA PGGLGG Sbjct: 241 ILDEIQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGG 300 Query: 297 TYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIA 356 TY GN ++C AAL V++ +EQE LL + LG++L+ GLL + ++P+IGDVRG G M+A Sbjct: 301 TYGGNALSCAAALAVIEAYEQEQLLARGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLA 360 Query: 357 IELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416 IEL + + PDA L ++ AR GL+++ CG Y NVLR L PL +AQI + L+I Sbjct: 361 IELIKHDEARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQI 420 Query: 417 I 417 + Sbjct: 421 L 421 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: 564 Number of extensions: 22 Number of successful extensions: 1 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 Sep 17 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