Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4179 Length = 459 Score = 189 bits (481), Expect = 1e-52 Identities = 126/350 (36%), Positives = 176/350 (50%), Gaps = 32/350 (9%) Query: 22 GVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLM-AM 80 GV HDL I + + A +WD EG +ID GG V N GH + V+ AVK Q + Sbjct: 48 GVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLDLYTHTC 107 Query: 81 PQTLPTPMRGEFYRTLTAILPPEL-NRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRG 139 Q + E L + P + + +G EA E A+K ARA+T R +A G Sbjct: 108 FQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPGVIAFTGG 167 Query: 140 FSGRTMGSLSVTWE-PKYREPFLPL---------------------VEPVEFIPYNDVEA 177 + GRT +L +T + Y+ F P + VE I ND+E Sbjct: 168 YHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQALHSVELIFKNDIEP 227 Query: 178 LKRAVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKR 237 E AA I+EPVQGEGG A PEF+ + + G LLI DE+QTG GRTG Sbjct: 228 ------ERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTW 281 Query: 238 FAFEHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAA 297 FA E + + PD++T AK+L GG PL V R +V + GG G T+ G+P+A AA +A Sbjct: 282 FASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAV 341 Query: 298 IRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKE 345 I + +L R+ ++G + L+ + + P I +VRG+G MV +EL E Sbjct: 342 IEAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFE 391 Lambda K H 0.319 0.137 0.402 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: 413 Number of extensions: 19 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: 395 Length of database: 459 Length adjustment: 32 Effective length of query: 363 Effective length of database: 427 Effective search space: 155001 Effective search space used: 155001 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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