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 RR42_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Cup4G11:RR42_RS26240 Length = 420 Score = 480 bits (1236), Expect = e-140 Identities = 237/414 (57%), Positives = 307/414 (74%), Gaps = 2/414 (0%) Query: 4 NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63 N +L++R+ A PRGVG + +A+RAEN +WDVEG Y+DFA GIAVLNTGH HP++V Sbjct: 3 NADLVRRKDAATPRGVGVMCNFYAERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPRLV 62 Query: 64 AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123 A++AQ+++ +HT +Q++ Y Y+EL E +N + PG FAKKT TTG+EAVENA+KIAR Sbjct: 63 QAMQAQMERFTHTAYQIVPYASYIELAEKINARAPGAFAKKTAFFTTGAEAVENAIKIAR 122 Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA 183 AAT R G IAFSG +HGRT +ALTGKV PY G G PG V+ A YP LHG+S D+ Sbjct: 123 AATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGDVFHAPYPYGLHGVSVQDS 182 Query: 184 IASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQS 243 I ++H++FK D P+ +AAI+ EPVQGEGGF + F++ LRA+CDEHGI+L+ADEVQ+ Sbjct: 183 INALHQLFKADVDPKRVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEVQT 242 Query: 244 GAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPI 303 G GRTG LFAME V PDLTT AKS+AGG PL+ V GRAE+MDA APGGLGGTYAGNP+ Sbjct: 243 GFGRTGKLFAMEHYDVTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPL 302 Query: 304 ACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDG 363 A +AL VL V E E L+++ LGQ+L+D L + + PEIG+VRG+GAMIA+E F Sbjct: 303 AVASALAVLDVLESEKLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVE-FRKA 361 Query: 364 DHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 D +PD + T ++ RA ++GL+LLSCG Y NV+R L PLTI DA + +GL I+ Sbjct: 362 D-GRPDPEFTRQVQDRALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGLGIL 414 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: 593 Number of extensions: 25 Number of successful extensions: 2 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: 420 Length adjustment: 32 Effective length of query: 394 Effective length of database: 388 Effective search space: 152872 Effective search space used: 152872 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: 50 (23.9 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