Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_012282524.1 HM1_RS06545 acetylornithine transaminase
Query= curated2:P59317 (406 letters) >NCBI__GCF_000019165.1:WP_012282524.1 Length = 432 Score = 359 bits (922), Expect = e-104 Identities = 174/379 (45%), Positives = 250/379 (65%), Gaps = 6/379 (1%) Query: 29 VKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVFTNEPALR 88 VKGQG+R+WD G+EY+DF G+AV +LGHCHP +V+AL+ Q TL H+SN++ EP ++ Sbjct: 26 VKGQGARLWDADGREYLDFLAGLAVNSLGHCHPKVVDALQQQAATLLHVSNLYWIEPQVQ 85 Query: 89 LGRKLIEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFT 148 L + L+E +FA++V F NSG EANE A KLAR YA K +II +FHGR+L T Sbjct: 86 LAQVLVENSFADKVFFCNSGAEANEGAIKLARKYAKKTWGSDKYEIITMEKSFHGRTLAT 145 Query: 149 VSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVTAATPEF 208 V+ QPKY + P P +VPF DL A++ + HTCA++VEP+QGEGGV A P F Sbjct: 146 VTATAQPKYQKDYEPLPQGFRYVPFGDLKALERAISPHTCAILVEPVQGEGGVNLAEPSF 205 Query: 209 LQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLT 268 QGL +L ++ LL+FDEVQCG+GRTG LFA+ HYGVTP I+T AKAL GG P+ A+L Sbjct: 206 WQGLAKLAAANKLLLIFDEVQCGLGRTGKLFAHEHYGVTPHIMTLAKALAGGAPMGALLA 265 Query: 269 TAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAKRQHFVDHLQKIDQQ 328 T ++A+AF PG H ST+GGNPL A A A D++ +++ + +F+ HL+++ ++ Sbjct: 266 TDDVANAFQPGDHASTFGGNPLVAAAAVAVMDVLLNDGLMDNCREMAAYFMGHLRRLQEK 325 Query: 329 YDVFSDIRGMGLLIGAEL-KPQYKGRARDFLYAGAEEGVMVLNAGPDVMRFAPSLVVEDA 387 Y +++RG+GL++ EL +P D + E+G+++ +V+RF P L++ A Sbjct: 326 YPFITEVRGLGLMVACELDRP-----GADIVANCLEKGLIINCTAGNVLRFLPPLIINKA 380 Query: 388 DIDEGMHRFAHAVAKVVGA 406 D+DE + +A VV A Sbjct: 381 DVDEAVAVLEEVLASVVAA 399 Lambda K H 0.322 0.138 0.416 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: 440 Number of extensions: 14 Number of successful extensions: 2 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: 432 Length adjustment: 32 Effective length of query: 374 Effective length of database: 400 Effective search space: 149600 Effective search space used: 149600 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 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