Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_011603976.1 FRAAL_RS12310 hypothetical protein
Query= curated2:B6IPH8 (386 letters) >NCBI__GCF_000058485.1:WP_011603976.1 Length = 434 Score = 68.9 bits (167), Expect = 3e-16 Identities = 121/433 (27%), Positives = 156/433 (36%), Gaps = 85/433 (19%) Query: 2 APDP----IALARDLIRCPSVTPADAGALDR-----VQSVLEGLGFTCHRLPFQEPGTER 52 APD + L RDL+R SV +R V + L +G L EPG Sbjct: 3 APDAEGEVVELCRDLLRFESVNRGGGDGHERPIAEYVATKLAEVGIEPTILE-SEPGRTS 61 Query: 53 VDNLYARLGDKGPNFCFAGHTDVVPAGDAAAWTVDPFGGEIIDGRLYGRGAADMKGGVAA 112 V GH DVVPA DA+ W V PF GE +DG L+GRGA DMK VA Sbjct: 62 VIGRIEGADPSRAPLLIHGHLDVVPA-DASQWRVAPFSGEEVDGCLWGRGAVDMKDMVAM 120 Query: 113 FIAAVGSFLERNGPPAGSISLLITGDEEGPAVNGTRKVLDWMAAAGERIDA-C--LVGEP 169 +A V P + + DEE G R W+ + A C +GE Sbjct: 121 TLAVVRDLARSGRKPPRDLVVAFLADEEAGGGLGAR----WLVEHHPELFADCTEAIGEV 176 Query: 170 TN-PRALGD-----MIKVGRRGSLTATLTALGAQGHTAYPHLADNPLPRLAEALHLLA-- 221 + D +I+ +G LTA G GH + DN + L EA+ L Sbjct: 177 GGFSYTVSDDLRLYLIETAEKGLAWMKLTATGRAGHGSMIS-DDNAVTALCEAVARLGRH 235 Query: 222 SSPLDMGTP---------------HFQPSTLALTSIDVG--------------NPAS--- 249 PL + TP F+ L T +G NP Sbjct: 236 EFPLVL-TPTVRVFLNELGDALGIEFELDDLQATVSKLGPVARMIGATLRNTVNPTQLQA 294 Query: 250 ----NVIPARGTARFNIRFNDLHTPESLEAHIRDVLEEVG----GAWELALQTSGVAFLT 301 NVIP TA + RF P E +R + E +G W + F Sbjct: 295 GEKVNVIPGEATAYVDGRF----LPGQEEEFVRQLDEILGPDIRREWVVHHDAVETGF-- 348 Query: 302 PPGALSDIVAAAVEAH--TGRTPELSTSGGTSDARFIKDHCPVVEFG--LVGASM----- 352 GAL + + AA+ A R SGGT F + F L+ A + Sbjct: 349 -DGALVEAMGAALRAEDPIARAVPYMLSGGTDAKSFSRLGIRCFGFSPLLLPADLDFSGM 407 Query: 353 -HKVDENVAVADL 364 H VDE V V L Sbjct: 408 FHGVDERVPVESL 420 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: 473 Number of extensions: 24 Number of successful extensions: 1 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: 434 Length adjustment: 31 Effective length of query: 355 Effective length of database: 403 Effective search space: 143065 Effective search space used: 143065 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 Apr 10 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