Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 Length = 430 Score = 240 bits (613), Expect = 5e-68 Identities = 142/404 (35%), Positives = 213/404 (52%), Gaps = 34/404 (8%) Query: 30 KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALR 88 + QGS +WD GK Y+DF GGI V +GH HP +V A++ Q + + H V +P L Sbjct: 33 RAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKISHACFQVVAYKPYLD 92 Query: 89 LGRKLIE---ATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145 L ++L E A + F SG EA E A K+AR + ++ +IAF FHGR+ Sbjct: 93 LAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHTN------RSAVIAFRGGFHGRT 146 Query: 146 LFTVSVGGQPK-YSDGFGPKPADIIHVPFNDLH-------AVKA--------VMDDHTCA 189 L ++ G + Y FGP ++ H P+ + + A++A V + A Sbjct: 147 LLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSAMALQALDELLATQVAPERVAA 206 Query: 190 VVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPD 249 +++EP+QG+GG +A EFLQGLR L +H +L+ DE+Q G GRTG F + H G+ PD Sbjct: 207 IIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFGRTGKWFGFQHAGIQPD 266 Query: 250 ILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLE 309 ++T AK+L GG P+S ++ AEI A PG G TYGGN L+CA A A + ++L Sbjct: 267 LVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEAYEQEQLLA 326 Query: 310 GIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARD------FLYAGAE 363 + +R L + +Y D+RG G ++ EL + R D + Sbjct: 327 RGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIKHDEARTPDADLNQRLIDEARA 386 Query: 364 AGVMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVG 405 G++V+ G +V+RF LV +A IDE +Q A+A+V+G Sbjct: 387 GGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALARVLG 430 Lambda K H 0.322 0.138 0.415 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: 504 Number of extensions: 25 Number of successful extensions: 6 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: 406 Length of database: 430 Length adjustment: 32 Effective length of query: 374 Effective length of database: 398 Effective search space: 148852 Effective search space used: 148852 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 (21.9 bits) S2: 50 (23.9 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