Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate BWI76_RS14620 BWI76_RS14620 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase
Query= SwissProt::Q9JYL2 (381 letters) >FitnessBrowser__Koxy:BWI76_RS14620 Length = 370 Score = 114 bits (285), Expect = 4e-30 Identities = 86/279 (30%), Positives = 131/279 (46%), Gaps = 16/279 (5%) Query: 4 TQSLELAKELISRPSVTP--DDRDCQKLLAERLHKIGFAAEELHFGDTKN---IWLRRGT 58 T +LELA++L+ ++ P + DC + A+ L+ GFA FG++++ WL T Sbjct: 2 TTTLELARQLLGFNTINPPGSEADCMRYFADWLNANGFAVSLSSFGESRSNLIAWLPGAT 61 Query: 59 KAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVA 118 + F GH D VP G +W PF DGRLYGRG++DMK +IA F AC + Sbjct: 62 PGKPLAFTGHLDTVPLGNA-RWRYDPFGSQMEDGRLYGRGSSDMKAAIAAFAVACVQQRE 120 Query: 119 KHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNG 178 +G++ LLIT EE DG + + A + IVGEPTA + G Sbjct: 121 TILAGRGAV-LLITGGEE-TGCDGARAL--IASAPLPEVGALIVGEPTA-----NYPVIG 171 Query: 179 RRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNI 238 +G+L +GK H A P L IN ++ A AL ++ + + + I Sbjct: 172 HKGALWLRCETRGKTAHGAMPELGINAIYLAADALAKIQHFSPGAPHPLMKQPTVNVGRI 231 Query: 239 NGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAIL 277 GG N +P + R + + A ++QR+ +L Sbjct: 232 EGGLN-INSVPDRTRFDVDIRSAPDLQHATIRQRLTTLL 269 Lambda K H 0.317 0.135 0.400 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: 345 Number of extensions: 20 Number of successful extensions: 4 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: 381 Length of database: 370 Length adjustment: 30 Effective length of query: 351 Effective length of database: 340 Effective search space: 119340 Effective search space used: 119340 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