Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 372 bits (956), Expect = e-108 Identities = 191/391 (48%), Positives = 256/391 (65%), Gaps = 3/391 (0%) Query: 18 LPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHI 77 LP+Y P E + G+G+R+WD +G++YVD GIAV ALGH P LV+AL TQ LWH Sbjct: 19 LPVYRPREVVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHS 78 Query: 78 SNVFTNEPALRLGRKLIEAT-FAERVVFMNSGTEANETAFKLARHYACVR-HSPFKTKII 135 SNVF EP L L +L++A+ FAERV NSGTEANE A KL R +A + +P + I+ Sbjct: 79 SNVFYTEPPLHLAEELVQASGFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVIL 138 Query: 136 AFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVM-DDHTCAVVVEP 194 F +FHGR+L V+ QPKY + + P P ++ FND+ ++A AV++EP Sbjct: 139 TFRGSFHGRTLAAVTATAQPKYQENYEPLPGGFRYLDFNDVAGLEAAFAQGDVAAVMLEP 198 Query: 195 IQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSA 254 +QGEGGV A+P F++ RELCD H+ALLV DE+QCGMGRTG LFA+ GVTPDI+T A Sbjct: 199 VQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQDGVTPDIVTLA 258 Query: 255 KALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAK 314 KALG GFPI AML ++A G+HG+T+GGNP+A AVA A + + E++ + + Sbjct: 259 KALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLASAELMANVAKQ 318 Query: 315 RQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVMVLNAGPD 374 Q D L ID + +F+++RG GL++GA L YKGRA + L A G++VL AGPD Sbjct: 319 AQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKGRAGEVLDHAAAHGLLVLQAGPD 378 Query: 375 VMRFAPSLVVEDADIDEGMQRFAHAVAKVVG 405 V+RF P L + DAD+ EG+ R A+A VG Sbjct: 379 VLRFVPPLNITDADLAEGLARLRAALADFVG 409 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: 488 Number of extensions: 20 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: 406 Length of database: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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 09 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