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 Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 Length = 430 Score = 435 bits (1119), Expect = e-126 Identities = 209/417 (50%), Positives = 283/417 (67%) Query: 1 MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP 60 ++ L+++R Q +PRG+ HP+ DRA+ +WDV+G+ YLDF GGI VLN GH HP Sbjct: 5 VDETPHLLRQRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHP 64 Query: 61 KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK 120 KVVAAV+AQL+K+SH CFQV+AY+PYL+L + + + + G + K T+G+EAVENAVK Sbjct: 65 KVVAAVQAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFTSGAEAVENAVK 124 Query: 121 IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE 180 IARA T RS IAF G +HGRT LTG PY G V+ YP G++ Sbjct: 125 IARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTS 184 Query: 181 DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE 240 D A+ ++ + APE +AAI+IEPVQG+GGF ++ F+Q LRAL +HGI+LI DE Sbjct: 185 DMALKALDELLATQVAPERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVLILDE 244 Query: 241 VQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG 300 +Q+G GRTG F + G+ PDL T AKS+AGG PL+GV G+AE+MDA PGGLGGTY G Sbjct: 245 IQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGG 304 Query: 301 NPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELF 360 N ++C AAL V++ +EQE LL + LG++L++GLL + ++P IGDVRG G M+AIEL Sbjct: 305 NALSCAAALAVIEAYEQEQLLARGEALGERLREGLLRLQARYPRIGDVRGSGFMLAIELI 364 Query: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 +D D PDA L ++ AR GL+++ CG Y NVLR L PL +AQ+ + L+I+ Sbjct: 365 KDDDARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQVDEALQIL 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: 566 Number of extensions: 20 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