Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate AZOBR_RS18740 AZOBR_RS18740 succinyl-diaminopimelate desuccinylase
Query= curated2:B6IPH8 (386 letters) >FitnessBrowser__azobra:AZOBR_RS18740 Length = 427 Score = 132 bits (332), Expect = 2e-35 Identities = 124/397 (31%), Positives = 182/397 (45%), Gaps = 45/397 (11%) Query: 6 IALARDLIRCPSVTPADAGALDRVQSV---LEGLGFTCHRLPFQ-EPG-TERVD--NLYA 58 +AL RDLIR P+V P D + + L G GF + PG ++R N+ A Sbjct: 21 VALTRDLIRIPTVNPPGDVYTDCAEFLGRRLAGRGFAVEYVRADGAPGDSDRYPRTNVIA 80 Query: 59 RLGDKGPNFC--FAGHTDVVPAGDAAAWTVDPFGGEIIDGRLYGRGAADMKGGVAAFIAA 116 R+ + P C F GH DVVPAG WTVDPF G + DGR+YGRGA DMKGG+AA I A Sbjct: 81 RVEGREPGPCVHFNGHIDVVPAGQG--WTVDPFEGVVKDGRVYGRGACDMKGGIAASIIA 138 Query: 117 VGSFLERNGPPAGSISLLITGDEEGPAVNGTRKVLDWMAAAGERIDACLVGEPTNPRALG 176 V + LE P G++ + T DEE G + + R+D ++ EP N Sbjct: 139 VEAILEAGIPFPGALEISGTVDEESGGYGGVGHLATLGYFSRPRVDHVIIPEPLNV---- 194 Query: 177 DMIKVGRRGSLTATLTALGAQGHTAYPHLADNPLPRLAEALHLLAS----------SPLD 226 D + +G RG A + G H + P L + + + LH + + + + Sbjct: 195 DRVCIGHRGVWWAEIETKGRVAHGSMPFLGNCAVRHMGAVLHRIETELIPRLAAKRTAMP 254 Query: 227 MGTPHFQPSTLALTSIDVGNP------ASNVIPARGTARFNIRFNDLHTPESLEAHIRDV 280 + + STL + +I G P S ++P R + R+ PE + A I + Sbjct: 255 VVPEGARQSTLNINAIHGGQPEDHGGLPSPMVPDRCRMVIDRRYLIEEDPEEVRAEIVGI 314 Query: 281 LEEV-----GGAWELALQTSGVAFLTPPGA-LSDIVAAAVEAHTGRTPELSTSGGTSDAR 334 LE++ G +EL + + LT A + V AA+E GR S GT D + Sbjct: 315 LEDLRRERPGFDYELREVLAFLPTLTDADAPVVRAVGAAIETVLGRPAAQVVSPGTYDQK 374 Query: 335 FI------KDHCPVVEFGLVGASMHKVDENVAVADLL 365 I KD C G++ + H+ DE V + D++ Sbjct: 375 HIARVGHLKD-CIAYGPGILDLA-HQPDEYVGIDDMV 409 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: 516 Number of extensions: 36 Number of successful extensions: 5 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: 427 Length adjustment: 31 Effective length of query: 355 Effective length of database: 396 Effective search space: 140580 Effective search space used: 140580 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 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