Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_038218171.1 Q392_RS30065 aspartate aminotransferase family protein
Query= SwissProt::P40732 (405 letters) >NCBI__GCF_000745855.1:WP_038218171.1 Length = 441 Score = 184 bits (468), Expect = 3e-51 Identities = 134/424 (31%), Positives = 198/424 (46%), Gaps = 47/424 (11%) Query: 29 VKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHT-SNVFTNEPAL 87 V G + D QG+ Y+D +GG AV++LGH HP ++ A+ +Q + L + ++ FT E A Sbjct: 17 VSASGMFIRDAQGRAYLDASGGAAVSSLGHGHPDVIAAMHAQIDRLAYAHTSFFTTEVAE 76 Query: 88 RLGRKLIDAT--FAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145 +L +L+ ++ G+EA E A K+AR Y P +T IA ++HG + Sbjct: 77 QLADELVRTAPEGTSHAYLVSGGSEAVEAALKMARQYFVETGQPQRTHFIARRQSYHGNT 136 Query: 146 LFTVSVGGQPKYSDGFGPKPADIIHV----PFNDLH------------------AVKAVM 183 L ++VGG + F P HV P+ + A+ A Sbjct: 137 LGALAVGGNAWRREPFAPILVPATHVSPCYPYREQREGENAQQYGQRLADELEQAILAQG 196 Query: 184 DDHTCAVVVEPIQGE-GGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYM 242 D A V E + G GV P + K +R++CD H LL+ DEV CGMGRTG L+A Sbjct: 197 ADRVIAFVAETVGGATAGVLTPVPGYFKAVREVCDRHGVLLILDEVMCGMGRTGTLYACE 256 Query: 243 HYGVTPDILTSAKALGGGF-PVSAMLTTQEIASAFHVGS----HGSTYGGNPLACAVAGA 297 GV PD++T AK LGGG+ PV A+L + I A GS HG TY G+P+ACA A A Sbjct: 257 QEGVAPDLVTVAKGLGGGYQPVGAVLAQRRIVEAMSSGSGFFQHGHTYLGHPVACAAALA 316 Query: 298 AFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRA--- 354 +I+ +L + + + F + L+ DIRG G G EL + G+ Sbjct: 317 VQRVIHRDGLLARVRERGEVFGRLLREALGAHPHVGDIRGRGFFWGVELVAERAGKTPFD 376 Query: 355 ------RDFLYAGAEAGVMVLNAG-------ADVMRFAPSLVVEEADIHEGMQRFAQAVG 401 A G++V G D + AP + EAD+ + + A A+ Sbjct: 377 PARRLHARVKQAAMAQGLLVYPMGGTVDGRQGDHVLLAPPFIASEADLAQIARLLATALD 436 Query: 402 KVVA 405 +A Sbjct: 437 AALA 440 Lambda K H 0.322 0.137 0.412 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: 515 Number of extensions: 26 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: 405 Length of database: 441 Length adjustment: 32 Effective length of query: 373 Effective length of database: 409 Effective search space: 152557 Effective search space used: 152557 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 Jul 25 2024. The underlying query database was built on Jul 25 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