Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate RR42_RS21345 RR42_RS21345 acetylornithine deacetylase
Query= curated2:Q89BP2 (388 letters) >FitnessBrowser__Cup4G11:RR42_RS21345 Length = 449 Score = 77.0 bits (188), Expect = 1e-18 Identities = 102/408 (25%), Positives = 168/408 (41%), Gaps = 60/408 (14%) Query: 10 DLIRCPSVTPADAGALGVLENALNAAGFTCHRV-----------TFSEPGTADVD--NLY 56 + + PS + + A+ +E AL G R+ FS P D NL Sbjct: 41 EFVAAPSPSGQEQPAVAFMEGALRELGLEPERIYLRSETLKDLPLFSPPCCPDGGRYNLL 100 Query: 57 AR---IGSEGPHITFAGHTDVVPAGDESAWSVGAFSGEVKDGFLHGRGAVDMKGGIACSV 113 A G + F GH DVVP G ES W ++ V+DG+L GRGA DMK GI C++ Sbjct: 101 ATHRPATKGGRSVLFNGHLDVVPTGPESMWRQSPYAPFVEDGWLFGRGAGDMKAGIICTL 160 Query: 114 AAVLEHLAANGGKPRGDGTGSISFLITGDEEDVSING---TIKLLKWAAERGE--TFDHC 168 AA + L G +P G++ F +EE+ NG T+ L A G+ +FD Sbjct: 161 AA-YKALKDLGVQP----AGAVGFNAVLEEENTG-NGALATVAALASAVGAGKLASFDTV 214 Query: 169 VLGEPSNVETLGDTIKVGRRGSQSGTLYVDGVQGHVAYPHRASNPV-------PDISRLI 221 V+ EP LG+ + + G + + G H AY NPV D+ +L Sbjct: 215 VIPEP-----LGENLMSAQMGVFWMFVELTGRPAHAAYMTTGVNPVEAGIEVMADLRKLE 269 Query: 222 VAISDEPLDHGSAQFQASNLEFTSVDV-GNKANNVIPGEARAKFNIRY----NDNHTQAS 276 + + A + F + G + N+ +P I + + +A Sbjct: 270 AEWNLPENRPAVYRDHAHPINFNLGQIQGGEWNSSVPCTCTLGIRIGFFPTMSVTDAKAR 329 Query: 277 LRELVETRLAKACGNRIKARIVWEPSNSNVFVTKPGPFTDLAVSAIE-------EITGRK 329 ++ V L + N + I +E ++ PG DL V +++ ++ G + Sbjct: 330 VQACVRGTLERLASN-LTLDIRYEGFHA------PGCEFDLDVPSMQALGEAHRKVNGEE 382 Query: 330 PELSTSGGTSDARF--ISSYCPVIEFGLVGQTMHQVDERVPVKDLEKL 375 + T+DAR + PV +G + +H +DE V ++ + ++ Sbjct: 383 VRREATTATTDARHFRLMLETPVTCYGPQARNIHGIDESVSIQSMVRV 430 Lambda K H 0.316 0.135 0.397 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: 421 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 388 Length of database: 449 Length adjustment: 32 Effective length of query: 356 Effective length of database: 417 Effective search space: 148452 Effective search space used: 148452 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 (21.6 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