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 Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Korea:Ga0059261_4131 Length = 398 Score = 196 bits (497), Expect = 1e-54 Identities = 135/403 (33%), Positives = 195/403 (48%), Gaps = 44/403 (10%) Query: 24 PIFADRAENCRVWDVEGRE-YLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSH--TCFQV 80 PI DR E ++ V+G E YLD G+A GH HP +VAA+EAQ KL H F++ Sbjct: 13 PIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISNMFEM 72 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAF 134 E + FA +G+EAVE A+K+AR +R I F Sbjct: 73 PGQNALAE------RLTTASFADTVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVIGF 126 Query: 135 SGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKND 194 SGA+HGRT+ + G +PG V+ A+ P ++ D+ Sbjct: 127 SGAFHGRTYGAMNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSAT--------- 177 Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254 AA+V+EPVQGEGG A + F+ +LRA C HG++LI DEVQ+G GRTG LFA Sbjct: 178 ------AAVVVEPVQGEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAH 231 Query: 255 E-QMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLK 313 + PD+ AK++ GFP+ AE + PG G T GNP+A A+ Sbjct: 232 QWYPDATPDIMALAKALGSGFPVGACLATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFD 291 Query: 314 VFEQENLLQKANDLGQKLKDGLLAIAEKHP-EIGDVRGLGAMIAIELFEDGDHNKPDAKL 372 + L A ++ Q L+ GL +A HP I ++RG G ++ + L + Sbjct: 292 EIAKPETLTHAREVAQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPN---------- 341 Query: 373 TAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415 +A AR++ L++ G N +R+L PLT+ A+ Q L+ Sbjct: 342 NRAFMAAAREQRLLVAGGGD--NCVRLLPPLTLTVAEADQILD 382 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: 441 Number of extensions: 32 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: 398 Length adjustment: 31 Effective length of query: 395 Effective length of database: 367 Effective search space: 144965 Effective search space used: 144965 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 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