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 WP_015887459.1 NGR_RS06525 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000018545.1:WP_015887459.1 Length = 422 Score = 468 bits (1205), Expect = e-136 Identities = 237/419 (56%), Positives = 294/419 (70%), Gaps = 1/419 (0%) Query: 7 LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAV 66 L R++ AI RGVG I+ADRAEN +WD E Y+DFA GIAV+NTGH HPKV+AAV Sbjct: 4 LTDRKNAAISRGVGMTTQIYADRAENAEIWDKESNRYIDFAAGIAVVNTGHRHPKVIAAV 63 Query: 67 EAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAAT 126 +AQL + +HTC QV+ YE Y+ L E +N PG FAKKT+ VTTG+EAVENAVKIARAAT Sbjct: 64 KAQLDRFTHTCHQVVPYENYVHLAERLNALAPGKFAKKTIFVTTGAEAVENAVKIARAAT 123 Query: 127 KRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIAS 186 R IAF G +HGRT +ALTGKV PY G G MP V+ A +P LHG+S + ++A+ Sbjct: 124 GRQAVIAFGGGFHGRTFMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVSVEQSLAA 183 Query: 187 IHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAG 246 + ++F D P +AAI++EPVQGEGGFY + AFM+ LR +CD+HGI+LIADEVQ+G Sbjct: 184 LKKLFAADVDPGRVAAIILEPVQGEGGFYPAPTAFMKALREICDQHGILLIADEVQTGFA 243 Query: 247 RTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACV 306 RTG LFAME VAPDL T AKS+AGGFPLA VTGRAE+MDA PGGLGGTY GNPI Sbjct: 244 RTGKLFAMEHHDVAPDLMTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPIGIA 303 Query: 307 AALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHN 366 AA VL V E+E L ++AN LG +LK L I EK PEI D+RG G M A+E F D Sbjct: 304 AAHAVLDVIEEEQLCERANQLGNRLKQRLAQIREKAPEIVDIRGPGFMNAVE-FNDVKTK 362 Query: 367 KPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDEAK 425 P A+ ++ A +KGLILL+CG + NV+R L P+TI+D + L+I+ EA+ Sbjct: 363 LPSAEFANKVRLIALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDILEASILEAR 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: 575 Number of extensions: 17 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: 422 Length adjustment: 32 Effective length of query: 394 Effective length of database: 390 Effective search space: 153660 Effective search space used: 153660 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