Align acetylornithine aminotransferase (EC 2.6.1.11); succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_011032001.1 MM_RS00255 aspartate aminotransferase family protein
Query= reanno::Marino:GFF3099 (404 letters) >NCBI__GCF_000007065.1:WP_011032001.1 Length = 475 Score = 201 bits (510), Expect = 5e-56 Identities = 137/408 (33%), Positives = 216/408 (52%), Gaps = 35/408 (8%) Query: 21 PGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NVM 79 P ++ R +GS + D +G+E+ID GIAV G+S+P + A+ Q EK+ H Sbjct: 73 PYPLVVDRAKGSVVRDIDGKEYIDFVAGIAVMNAGYSNPEVQAAISAQLEKMVHCGYGDF 132 Query: 80 TNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSF 139 EP L+LAK L DL+ +VF+ NSGAE+ EAA KL+ W+ ++ ISF N+F Sbjct: 133 FAEPPLKLAKKLRDLSGYSKVFYCNSGAESIEAAMKLS---LWK---TKRQNFISFYNAF 186 Query: 140 HGRTLFTVSVG-GQPKYLEGFEPAPGGIH-------HAEFN------DLESVKKL----- 180 HGRTL +S+ + ++ E F P +H N +E K++ Sbjct: 187 HGRTLGALSLTCSKVRHKEHF-PTIRTVHTDYAYCYRCPLNLDYPSCGIECAKQIENLVF 245 Query: 181 ---ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHF 237 +S E T A+ VEPIQGEGG + F + +R +C +ND LLV DEVQ+G R+G F Sbjct: 246 RRELSPEDTAAVFVEPIQGEGGYIVPPVEFHKEVRRICTDNDVLLVADEVQTGCFRTGPF 305 Query: 238 YAYQMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRV 297 A + + V DI AK LG G P+ AML ++ G H +T+GGN L+ A A Sbjct: 306 LAMENFEVRADITCLAKALGSGLPIGAMLADNEL-MDWPPGVHSNTFGGNLLSSAAALAS 364 Query: 298 VDTVSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQG----KA 353 ++ + + V+ +R + ++ E + +VRG GL+ G + + + + Sbjct: 365 LEFLEKENTENHVREMGAHIRHRLRELQENFPCIGDVRGLGLMTGVEIVKPDKSIDPVRR 424 Query: 354 KDFLNAGLEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKK 401 + ++GV++L G +VIR +P L++ + + +L L++FE A+KK Sbjct: 425 DKIIREAFKDGVLLLPCGDSVIRFSPPLVMTDEEADLGLDKFEKALKK 472 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: 439 Number of extensions: 22 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 404 Length of database: 475 Length adjustment: 32 Effective length of query: 372 Effective length of database: 443 Effective search space: 164796 Effective search space used: 164796 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 Apr 10 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