Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate HSERO_RS23725 HSERO_RS23725 peptidase M20
Query= curated2:Q5NM04 (376 letters) >FitnessBrowser__HerbieS:HSERO_RS23725 Length = 414 Score = 74.7 bits (182), Expect = 4e-18 Identities = 98/403 (24%), Positives = 167/403 (41%), Gaps = 43/403 (10%) Query: 6 DPVDLAARLIACKSVTPSDDGAMNIMADALKSAGF----TVHLLTKGQAPD---GPVTNL 58 + V + +LI + TP + A + A A AG+ H++ Q D +TNL Sbjct: 20 EEVGVLQQLIRIPTDTPPGNNAPHADAVAELVAGWGWAAEKHVVPAQQVADYGMQSITNL 79 Query: 59 IAIR--GEGYPHLAYAGHSDVVPAGQGWSSDPFTPTIKDGYLVGRGAVDMKSSVAAFIAA 116 I R G+G P LA H DVVP G+GW+ DP+ I DG + GR A KS A+++ A Sbjct: 80 IVRRPYGDGGPTLALNAHGDVVPPGEGWTHDPYGGEIADGRIYGRAAAVSKSDFASYLFA 139 Query: 117 ASRY----TEHKGTLSLLITGDEEGPATFGTPAIIEWLNEQSI-KPDYCLVGEPTSVERL 171 +G + L T DEE FG WL EQ + +PDY L Sbjct: 140 TRALEAVGASLRGGVELHFTYDEE----FGGLLGPGWLLEQKLTRPDYVLAA------GF 189 Query: 172 GDTVKNGRRGSVNMWIEVEGIQGHVAYPDRACNPIPVLARIISDLESWV-----LDKGDQ 226 V + I V G H + P+ + + I++ + + + Sbjct: 190 SYNVVTAHNACLQFEITVHGRATHGSMPETGHDALQAATAILNAIYGALPGLKEIRSAIP 249 Query: 227 WFQPSNLEVTSIECDNKATNVIPALAKAQLNIRFNALHKGAELVDSLKK----RVAAIDP 282 + V I+ TNV+P +++ R +++ ++K VA + Sbjct: 250 GITHPTMIVGRID-GGTNTNVVPGKVVLKMDRRMIPEEDPSQVEAGVRKLIEDAVAGLPG 308 Query: 283 -KARVKAAISGEAFVTEEG--VLTDTISAAIAKNTGITPSLSTSGGTSDARFLTKL-CPV 338 + ++ + A G L +++ + G T + + S +DAR + PV Sbjct: 309 IRVEIRRLLLARALRPLPGHEKLVESLLRNAREVMGETLTTNGSALYTDARLYGEQGIPV 368 Query: 339 VEFG-----LVNATMHKVDEKASVEDIRQLSRIDEDIIKSFLG 376 V FG L+ + + DE +++D+R+ +++ ++ FLG Sbjct: 369 VLFGAGPRTLMESNAKQADENLALDDLRKATKVVALMLLDFLG 411 Lambda K H 0.316 0.133 0.389 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: 354 Number of extensions: 15 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: 2 Length of query: 376 Length of database: 414 Length adjustment: 31 Effective length of query: 345 Effective length of database: 383 Effective search space: 132135 Effective search space used: 132135 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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