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 GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Marino:GFF3099 Length = 404 Score = 216 bits (550), Expect = 1e-60 Identities = 136/402 (33%), Positives = 208/402 (51%), Gaps = 36/402 (8%) Query: 20 GQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQ 79 G I P+ R E R+WD EGRE++D GGIAV GH HP +V A+ Q +K+ H Sbjct: 22 GSIIPV---RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-N 77 Query: 80 VLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATKRSGTIA 133 V+ EP L L + + FA++ +G+EA E A K+AR +++ I+ Sbjct: 78 VMTNEPALRLAKTLCDLT---FAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIIS 134 Query: 134 FSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKN 193 F ++HGRT +T+++ G+ Y G PG ++ A E + + S+ ++ Sbjct: 135 FKNSFHGRTLFTVSVGGQPK-YLEGFEPAPGGIHHA----------EFNDLESVKKLISK 183 Query: 194 DAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFA 253 E AIV+EP+QGEGG AF+Q LR LCDE+ +L+ DEVQSG GR+G +A Sbjct: 184 ----EKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYA 239 Query: 254 MEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLK 313 + GV PD+ + AK + GGFP+A + A+V ++ G G TY GN +AC A V+ Sbjct: 240 YQMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVD 299 Query: 314 VFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLT 373 Q +L+ KL+ G++ I E++ +VRG G ++ L E D Sbjct: 300 TVSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKD---- 355 Query: 374 AEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415 + ++G+++L G NV+R+ L I + I LE Sbjct: 356 --FLNAGLEEGVMVLVAGA--NVIRLAPSLIIPEPDIELALE 393 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: 516 Number of extensions: 20 Number of successful extensions: 4 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: 404 Length adjustment: 31 Effective length of query: 395 Effective length of database: 373 Effective search space: 147335 Effective search space used: 147335 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