Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein
Query= SwissProt::P40732 (405 letters) >FitnessBrowser__Koxy:BWI76_RS11670 Length = 406 Score = 505 bits (1300), Expect = e-147 Identities = 242/399 (60%), Positives = 305/399 (76%) Query: 7 AITRATFDEVILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEA 66 +ITR+ FDE ++PVYAPA FIPV+G+GSR+WDQQGKEYIDFAGGIAV ALGH HP LV+A Sbjct: 4 SITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKA 63 Query: 67 LKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVR 126 L Q WHT N +TNEP LRL ++LIDATFA+RV F NSG EANE A KLAR YA R Sbjct: 64 LTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDR 123 Query: 127 HSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDH 186 K+ I+AF NAFHGR+LFTVS GGQP YS F P P I H +NDL + KA++DD+ Sbjct: 124 FGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDN 183 Query: 187 TCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGV 246 TCAV+VEP+QGEGGV A +FL+GLR+LCD H ALL+FDEVQ G+GRTG+L+AYMHYGV Sbjct: 184 TCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGV 243 Query: 247 TPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPE 306 TPD+L++AKALGGGFP+ A+L ++ AS VG+HG+TYGGNPLACAVAG F INT E Sbjct: 244 TPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTRE 303 Query: 307 VLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGV 366 VL G+ + Q F + L AI+ ++ +F +IRG+GLLIG LK +Y G+A+ AE G+ Sbjct: 304 VLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGL 363 Query: 367 MVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405 M+L AGA+V+RFAP+L++ E +++ G+ RF A + +A Sbjct: 364 MILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLA 402 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: 514 Number of extensions: 13 Number of successful extensions: 1 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: 406 Length adjustment: 31 Effective length of query: 374 Effective length of database: 375 Effective search space: 140250 Effective search space used: 140250 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