Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_057507751.1 ABB28_RS05895 aspartate aminotransferase family protein
Query= curated2:P59317 (406 letters) >NCBI__GCF_001431535.1:WP_057507751.1 Length = 450 Score = 162 bits (410), Expect = 2e-44 Identities = 134/436 (30%), Positives = 192/436 (44%), Gaps = 50/436 (11%) Query: 12 TFDEVILPIYAPAEF-----IPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNA 66 T D +P A A+F + V+ QG D +G++ +D G+ GH +V A Sbjct: 18 TLDAFWMPFTANAQFKGAPRLLVRAQGMYYEDVEGRQILDGTAGLWCCNAGHGRKKIVQA 77 Query: 67 LKTQGETLWHISNVFTNEPA-LRLGRKLIEATFA--ERVVFMNSGTEANETAFKLARHYA 123 + Q TL P L ++L A V F NSG+EA ++A K+ + Sbjct: 78 IAEQAGTLDFAPTFQMGSPLPFVLAQRLAALAPAGLNHVFFTNSGSEAVDSAMKIVLAHH 137 Query: 124 CVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPF---------- 173 R +T+ I A+HG +++GG P FG + H+P Sbjct: 138 RARGEGQRTRFIGREKAYHGVGFGGMAIGGLPNNRRQFGLQLGGSAHLPHTLDLQRNAFS 197 Query: 174 -----------NDLHAVKAVMDDHTCAVV-VEPIQGEGGVTAATPEFLQGLRELCDQHQA 221 + L + A+ D T A V VEPI G GV P +LQ LRE+CD H Sbjct: 198 QGLPRHGAELADALERLIALHDASTIAAVFVEPIAGSAGVILPAPGYLQRLREICDHHGI 257 Query: 222 LLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAK-ALGGGFPVSAMLTTAEIASAFHPGS 280 +LVFDEV G GR G FA +GVTPD++T AK A G P+ +L I S+ G Sbjct: 258 VLVFDEVITGFGRVGMPFAAQRFGVTPDLITFAKGASNGAVPLGGVLVGDAIHSSLQQGP 317 Query: 281 -------HGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAKRQHFVDHLQKIDQQYDVFS 333 HG TY G+PLACA A A D+ + E +H+ L + +V Sbjct: 318 TQAIDLFHGYTYSGHPLACAAALATLDVYAEERLFERAIELGEHWQRALHGLQGLPNVV- 376 Query: 334 DIRGMGLLIGAELKPQYK---GRARDFLYAGAEEGVMVLNAGPDVMRFAPSLVVEDADID 390 DIR GL+ EL P+ R + +G +++ D + +P L+VE A ID Sbjct: 377 DIRNFGLVGAVELAPRRDAPGSRGYEVFRRCFHDGNLLVRQTGDTIALSPPLIVEPAQID 436 Query: 391 EGMHRFAHAVAKVVGA 406 + +A V+GA Sbjct: 437 Q--------IADVLGA 444 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: 522 Number of extensions: 34 Number of successful extensions: 5 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: 450 Length adjustment: 32 Effective length of query: 374 Effective length of database: 418 Effective search space: 156332 Effective search space used: 156332 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: 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