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 HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__HerbieS:HSERO_RS05420 Length = 426 Score = 469 bits (1206), Expect = e-137 Identities = 231/417 (55%), Positives = 303/417 (72%), Gaps = 1/417 (0%) Query: 3 SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62 +N+EL QR++ A PRGVG + +A+RA N +WDVEGR ++DFA GIAVLNTGH HPK+ Sbjct: 6 NNQELQQRKNAATPRGVGVMCDFYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKL 65 Query: 63 VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122 + A+ AQ+ K +HT +Q++ Y Y+EL E +N+ PG++ KKT +TG+EAVENA+KIA Sbjct: 66 LDAMRAQMDKFTHTAYQIVPYASYVELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIA 125 Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182 RA T R G IAF+G +HGRT +ALTGKV PY G G PG V+ A YP LHGI+ +D Sbjct: 126 RAHTGRPGVIAFAGGFHGRTMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITSED 185 Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242 A+ ++ +FK+D + +AAI++EPVQGEGGFYA+ FM+ LRALCDEHGI+LIADEVQ Sbjct: 186 ALEAVKGLFKSDIEAKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQ 245 Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302 SG GRTG LFAME V PDL T AKS+AGG PL+ V GRAE+MDA APGGLGGTYAGNP Sbjct: 246 SGYGRTGKLFAMEHYDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNP 305 Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362 +A +AL VL V E+E L+ + LG KL++ L + P+I +VRG+GAM+A+E F D Sbjct: 306 LAIASALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVE-FAD 364 Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 KPDA+ T ++ A + GL+LL+CG Y NV+R L PLTI D + + L I+++ Sbjct: 365 PATGKPDAEYTKKVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILAK 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: 609 Number of extensions: 24 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: 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 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