Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate GFF769 PGA1_c07830 acetylornithine deacetylase ArgE
Query= curated2:B2FIC0 (375 letters) >FitnessBrowser__Phaeo:GFF769 Length = 384 Score = 118 bits (296), Expect = 2e-31 Identities = 122/394 (30%), Positives = 181/394 (45%), Gaps = 34/394 (8%) Query: 1 MSAVLDLTCELIARPSVTPD-DAGCQALLAARLKQAGFQCDHL--RLGDVDNLWATHGLG 57 M + +LIA P+V+ D + A LA RL+ G + D + G NL+AT G Sbjct: 2 MEQTTRILSDLIAYPTVSADSNLEMIAYLANRLEDCGARVDVMFDAGGQKANLFATLGPD 61 Query: 58 APV-LVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGSVAAFVVAAEQFVA 116 +VL GH+DVVP ++ WTSDPFT DG LYGRG DMKG +AA + A +F Sbjct: 62 TDGGIVLSGHSDVVPVTDQD-WTSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKFAE 120 Query: 117 DHPDHPGTLAVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCITGEPSSTATLGDLLRVG 176 P + T DEE I G H+ + RG + + GEP+S + G Sbjct: 121 QISRRP--IHFAFTYDEEVGCI-GAGHLVQALRERGLKPRLALIGEPTSMRVV-----EG 172 Query: 177 RRGSLSAKLRVQGVQGHVAYPEKARNPIHQAAPALAELCARRWD-------DGYESFPPT 229 +G R QG++GH + P + N + AA ++ L R D D P T Sbjct: 173 HKGCHEYSTRFQGLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQRTPPDSRFDPPWT 232 Query: 230 SLQISNIHAGTGANNVIPGELDVDFNIRYNPHWDAPKLEAEI------TALLERHGL--Q 281 +L I ++ G+ A+NVI + VD+ +R DA ++ + T L + + Sbjct: 233 TLNIGALNGGS-AHNVIASKAQVDWEMRPVQPSDADHVKDTMARYCRDTLLPAMQAIYPE 291 Query: 282 YTLKWHRSGE-PFYTPEGTLRAIARAVLAEHIGRAPEESTGGGTSDARFIAPLGAQCIEV 340 +++ GE TP T + AR ++A+ +G E GT +A LG + Sbjct: 292 ASIETEVVGEVAGLTP--TTQNEARELMADLLGSNAAELVPFGT-EAGLFQELGMDVVVC 348 Query: 341 GPVN-ASIHQVDENVRVDDLEALPGLYQRLVERL 373 GP + A H+ DE + +D L + RL RL Sbjct: 349 GPGSIAQAHKADEYLSLDQLSQCLTVLNRLAGRL 382 Lambda K H 0.319 0.137 0.421 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: 382 Number of extensions: 27 Number of successful extensions: 3 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: 375 Length of database: 384 Length adjustment: 30 Effective length of query: 345 Effective length of database: 354 Effective search space: 122130 Effective search space used: 122130 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 (21.7 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