Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate AO356_26715 AO356_26715 4-aminobutyrate aminotransferase
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26715 Length = 430 Score = 219 bits (558), Expect = 1e-61 Identities = 127/402 (31%), Positives = 221/402 (54%), Gaps = 33/402 (8%) Query: 28 RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NVMTNEPALR 86 R +G+ +WD +G ++D GGI V +GH+HP +V A+ Q +K+ H V+ +P L Sbjct: 33 RAQGAEVWDVDGARYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKVSHACFQVVAYKPYLD 92 Query: 87 LAKTLCDLTFAERVFFA---NSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRT 143 L K LC+L ++ + A SGAEA E A K+AR + + +ISF+ FHGRT Sbjct: 93 LVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHT------NRPAVISFRGGFHGRT 146 Query: 144 LFTVSVGGQPK-YLEGFEPAPGGIHHAEFND----------LESVKKL----ISKEKTCA 188 L ++ G + Y + F P + H + + L+++ +L ++ ++ A Sbjct: 147 LLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSSEMALQALNELLATQVAPDRVAA 206 Query: 189 IVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPD 248 I++EP+QG+GG + FLQ LR L +++ +L+ DE+Q+G GR+G ++ +Q G+ PD Sbjct: 207 IIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFGRTGKWFGFQHAGIQPD 266 Query: 249 ILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILK 308 +++ AK L GG P++ ++ A + + G G TYGGNAL+CA A V+D Q ++L+ Sbjct: 267 LVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCAAALAVIDAYEQEQLLE 326 Query: 309 GVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKD------FLNAGLE 362 + ++LR+G++ + R+ +VRG G +L L + + ++ D ++ Sbjct: 327 RGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIKDDEARSPDAELTQQLIDQARV 386 Query: 363 EGVMVLVAGA--NVIRLAPSLIIPEPDIELALERFEAAVKKL 402 ++V+ G NV+R L+ E I+ AL EAA+ ++ Sbjct: 387 GRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAALLRV 428 Lambda K H 0.318 0.137 0.406 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: 450 Number of extensions: 20 Number of successful extensions: 5 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: 404 Length of database: 430 Length adjustment: 31 Effective length of query: 373 Effective length of database: 399 Effective search space: 148827 Effective search space used: 148827 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: 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