Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_057509166.1 ABB28_RS13775 aspartate aminotransferase family protein
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_001431535.1:WP_057509166.1 Length = 408 Score = 356 bits (914), Expect = e-103 Identities = 184/392 (46%), Positives = 249/392 (63%), Gaps = 3/392 (0%) Query: 18 LPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHI 77 LP+Y P + + +GQG+R+WD QG+EY+D A GIAV LGH P L AL Q LWH Sbjct: 16 LPVYKPRQVVLERGQGARVWDSQGREYIDLAAGIAVCGLGHNDPDLTAALVEQAGKLWHT 75 Query: 78 SNVFTNEPALRLGRKLIEAT-FAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIA 136 SNVF + P L L +L++A+ FAERV NSG EANE A K+ R +A + P ++I Sbjct: 76 SNVFYSAPPLHLAEELVKASRFAERVFLCNSGAEANEVAIKMVRKWASSQGRPADRRVIV 135 Query: 137 -FHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFND-LHAVKAVMDDHTCAVVVEP 194 F +FHGR+L V+ QPKY +G+ P P +V FND + A+ AV++EP Sbjct: 136 TFRGSFHGRTLAAVTATAQPKYQEGYEPLPQGFRYVDFNDEVQLETAMAAGDVAAVMLEP 195 Query: 195 IQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSA 254 +QGEGGV A P FL+ +RELCDQH ALLV DE+Q GMGRTG LFA+ GV PD++T A Sbjct: 196 VQGEGGVMPARPGFLKRVRELCDQHGALLVLDEIQAGMGRTGTLFAHWQDGVVPDMVTLA 255 Query: 255 KALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAK 314 KALGGGFPI AML ++A G+HG+T+GGNPLA AVA A + + E+ + + Sbjct: 256 KALGGGFPIGAMLAGPKVAETMQFGAHGTTFGGNPLAAAVARVALRKLASDEIAANVDRQ 315 Query: 315 RQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVMVLNAGPD 374 + + ++I+ ++ VF +RG GL++GA L + G+A L AE G++ L AGPD Sbjct: 316 SRALREGFERINAEFGVFGQVRGRGLMLGAVLSKDHLGQAGVILDHAAEHGLLTLQAGPD 375 Query: 375 VMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406 V+RF PSL + D +I EG++R AVA + A Sbjct: 376 VLRFVPSLNITDEEIAEGLKRLRAAVASYIAA 407 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: 470 Number of extensions: 15 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: 408 Length adjustment: 31 Effective length of query: 375 Effective length of database: 377 Effective search space: 141375 Effective search space used: 141375 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