Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_012673760.1 SULAZ_RS04620 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:P59317 (406 letters) >NCBI__GCF_000021545.1:WP_012673760.1 Length = 427 Score = 139 bits (350), Expect = 2e-37 Identities = 103/332 (31%), Positives = 158/332 (47%), Gaps = 33/332 (9%) Query: 30 KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVFTNEPALRL 89 +G+GSRIWD G EY+D+ LGH H +VNA+K + S E + + Sbjct: 40 RGKGSRIWDVDGNEYIDYVLSWGPLILGHAHDQVVNAIKQVAN--YGTSFGAPTELEIEM 97 Query: 90 GRKLIEAT-FAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGR---- 144 + +++A E V F+NSGTEA +A +LAR Y + KI+ F +HG Sbjct: 98 AKAVVDAVKSVEMVRFVNSGTEATMSAIRLARGYT------KRKKIVKFDGCYHGHGDSL 151 Query: 145 ------SLFTVSVGGQPKYSDGFGPKPADI-IHVPFNDLHAV----KAVMDDHTCAVVVE 193 + T+ + G P G + A++ I +P+ND+ AV K +D C V++E Sbjct: 152 LVSAGSGVATLGIPGTP----GIPEELANLTIVLPYNDIEAVEEAFKRYGEDIAC-VIIE 206 Query: 194 PIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTS 253 P+ G GV A + E+ Q LR++ ++ ALL+FDEV G R A YG+ PD+ T Sbjct: 207 PVAGNMGVVAPSKEYHQRLRDITRKYGALLIFDEVMTGF-RLAYGGAQELYGIDPDLTTF 265 Query: 254 AKALGGGFPVSAMLTTAEI---ASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEG 310 K +GGG PV A EI + P T GNPLA A ++ Sbjct: 266 GKVIGGGLPVGAYGGKREIMEYVAPVGPVYQAGTLSGNPLAMAAGLRQLQLLKELNPYRE 325 Query: 311 IQAKRQHFVDHLQKIDQQYDVFSDIRGMGLLI 342 + K + + ++I Q++ + +G +I Sbjct: 326 LDEKGRFLEEGFKQIAQEFSAAIQVNRVGSMI 357 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: 419 Number of extensions: 20 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: 427 Length adjustment: 31 Effective length of query: 375 Effective length of database: 396 Effective search space: 148500 Effective search space used: 148500 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