Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_106710100.1 CU102_RS05900 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase family protein
Query= curated2:B6IPH8 (386 letters) >NCBI__GCF_003010955.1:WP_106710100.1 Length = 423 Score = 103 bits (257), Expect = 9e-27 Identities = 113/418 (27%), Positives = 175/418 (41%), Gaps = 49/418 (11%) Query: 4 DPIALARDLIRCPSVTP---ADAGALDRVQSVLEGLGFTCHRLPFQ-EPG-TERVD--NL 56 D IAL R+LIR P++ P A + + L+ +GF + + PG T+R N+ Sbjct: 15 DLIALTRELIRFPTINPPGEAYTPCAEYLAHRLQKIGFETQLIRGEGTPGDTDRYPRTNV 74 Query: 57 YARLGDK--GPNFCFAGHTDVVPAGDAAAWTVDPFGGEIIDGRLYGRGAADMKGGVAAFI 114 AR + G F H DVV G+ WTVDPF G + DG++YGRGA DMKGG+AA I Sbjct: 75 VARFDGRRHGQTVHFNSHIDVVDTGEG--WTVDPFEGVVKDGKIYGRGACDMKGGLAASI 132 Query: 115 AAVGSFLERNGPPAGSISLLITGDEEGPAVNGTRKVLDWMAAAGERIDACLVGEPTNPRA 174 A +FLE G+I + T DEE G + + R+D ++ EP N Sbjct: 133 IAAEAFLEVYPDFTGAIEISGTVDEESGGFGGVAYLASKGFFSKPRVDHVIIPEPLNK-- 190 Query: 175 LGDMIKVGRRGSLTATLTALGAQGHTAYPHLADNPLPRLAEALHLL----------ASSP 224 D I +G RG A + G H + P L D + + L + Sbjct: 191 --DRICLGHRGVWWAEIETKGEIAHGSMPFLGDCAVRHMGAVLDAFEKELFPLLDRKQTR 248 Query: 225 LDMGTPHFQPSTLALTSIDVGN-------PASNVIPARGTARFNIRFNDLHTPESLEAHI 277 + + + ST+ + SI G P+ NV P + RF ++ + Sbjct: 249 MPVVPEGARRSTMNINSIHGGQTDDYSGLPSPNV-PDSCRLTIDRRFLLEEDVTEVKREV 307 Query: 278 RDVLEEVGGAWE---LALQTSGVAFLTP-----PGALSDIVAAAVEAHTGRTPELSTSGG 329 +L+ + WE + + P + VA + + GR PE S G Sbjct: 308 TSILDRL--QWERPKFHYNIRDIMEVQPLMTERDAPVVTAVAQGIRSVFGREPEYVISPG 365 Query: 330 TSDARFIK-----DHCPVVEFGLVGASMHKVDENVAVADLLELTAIYRTVLERWFAGA 382 + D + I C G++ + H+ DE V + D++E + L+ +G+ Sbjct: 366 SYDQKHIARIGLLHDCIAYGPGILDLA-HRPDEYVGIEDMIESAKVMALGLKVLLSGS 422 Lambda K H 0.318 0.136 0.413 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: 452 Number of extensions: 31 Number of successful extensions: 2 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: 386 Length of database: 423 Length adjustment: 31 Effective length of query: 355 Effective length of database: 392 Effective search space: 139160 Effective search space used: 139160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Jul 26 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