Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_085770154.1 B1812_RS02270 succinyl-diaminopimelate desuccinylase
Query= BRENDA::Q9KQ52 (377 letters) >NCBI__GCF_002117405.1:WP_085770154.1 Length = 385 Score = 290 bits (742), Expect = 5e-83 Identities = 163/380 (42%), Positives = 229/380 (60%), Gaps = 8/380 (2%) Query: 1 MTDSPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFE-----DTTNFWAR 55 M+ SP +ALA++LI SVTPADAG D++ L A GF +F D N +A+ Sbjct: 1 MSLSPSVALARDLIRCPSVTPADAGALDVLQGFLTAAGFACTRKIFTEPGTPDVDNLFAK 60 Query: 56 RGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVER 115 G P VFAGHTDVVP G +W PF + G L GRGA+DMK ++A VA Sbjct: 61 IGQGPPHLVFAGHTDVVPPGDAKRWRHDPFAGEIESGRLWGRGASDMKSAVAAFAVAARD 120 Query: 116 FIAEHPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVV 175 F+A H +G+I FLIT DEEG INGT ++++ + E D CIVGEPSS LA+GD++ Sbjct: 121 FVAAHGSAKGAISFLITGDEEGASINGTAKLLDWAKEQGERFDHCIVGEPSSVLALGDMM 180 Query: 176 KNGRRGSITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQI 235 K GRRGS++G + ++G QGHVAYP A+NPV K +A L+ ++DEG+A+F ++ + Sbjct: 181 KIGRRGSLSGRVTIEGVQGHVAYPERADNPVPKMARLVAALSDHRFDEGSAHFGASNLEF 240 Query: 236 PNLQAGTGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSV-LDAHGLDYDVKWT-LSGQ 293 ++ G A NVIP FN RF+ T E ++ + S+ A G + +T + + Sbjct: 241 TSVDVGNPAVNVIPARATAAFNIRFNDLWTPERLENEIRSITAQAVGAAAQLDFTPCNAR 300 Query: 294 PFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVN 353 FLT+ G +A V AVEE + P L TTGGTSD RFI + +VVE G N +IHK++ Sbjct: 301 AFLTNPGAFVALVSRAVEEATGRKPELSTTGGTSDARFIVR-DCEVVEFGLTNESIHKID 359 Query: 354 ECVRIADLEKLTDMYQKTLN 373 E + D++ LT +Y++ L+ Sbjct: 360 ENAALDDIDGLTKVYRRILD 379 Lambda K H 0.318 0.135 0.403 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: 406 Number of extensions: 17 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: 377 Length of database: 385 Length adjustment: 30 Effective length of query: 347 Effective length of database: 355 Effective search space: 123185 Effective search space used: 123185 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_085770154.1 B1812_RS02270 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01246.hmm # target sequence database: /tmp/gapView.8053.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01246 [M=370] Accession: TIGR01246 Description: dapE_proteo: succinyl-diaminopimelate desuccinylase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-129 418.4 0.0 1.6e-129 418.1 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085770154.1 B1812_RS02270 succinyl-diaminopi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085770154.1 B1812_RS02270 succinyl-diaminopimelate desuccinylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 418.1 0.0 1.6e-129 1.6e-129 2 367 .. 7 378 .. 6 380 .. 0.97 Alignments for each domain: == domain 1 score: 418.1 bits; conditional E-value: 1.6e-129 TIGR01246 2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefe.....dtknlwatrgteepvlvfaGhtD 65 ++la++Li+ +svtP+daga+++++ L++ gf++ +++f d+ nl+a+ g++ p+lvfaGhtD lcl|NCBI__GCF_002117405.1:WP_085770154.1 7 VALARDLIRCPSVTPADAGALDVLQGFLTAAGFACTRKIFTepgtpDVDNLFAKIGQGPPHLVFAGHTD 75 5799*******************************9999854444489********************* PP TIGR01246 66 vvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegea 134 vvP G+ ++W+ dpf+ e+++G+l+grGa Dmk+++aaf vaa++fv+++ kG +s+lit Deeg + lcl|NCBI__GCF_002117405.1:WP_085770154.1 76 VVPPGDAKRWRHDPFAGEIESGRLWGRGASDMKSAVAAFAVAARDFVAAHGSAKGAISFLITGDEEGAS 144 ********************************************************************* PP TIGR01246 135 idGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhk 203 i+Gt k++++ ke+ e d+++vgePssv +lGD++kiGrrGs++g+++i+G+qGhvaYP++a+nPv+k lcl|NCBI__GCF_002117405.1:WP_085770154.1 145 INGTAKLLDWAKEQGERFDHCIVGEPSSVLALGDMMKIGRRGSLSGRVTIEGVQGHVAYPERADNPVPK 213 ********************************************************************* PP TIGR01246 204 avpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekil 272 +++++++l + ++DeG+++f +s+l+ + +++g+ a nviP+ ++++fn+rf+ ++ e+l++++++i lcl|NCBI__GCF_002117405.1:WP_085770154.1 214 MARLVAALSDHRFDEGSAHFGASNLEFTSVDVGNPAVNVIPARATAAFNIRFNDLWTPERLENEIRSIT 282 ********************************************************************9 PP TIGR01246 273 dkh.kldYelewk.lsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGl 339 + + +l+++ + +++flt+ g ++ v a+ee +++kpelst+GGtsDarfi + +evve+Gl lcl|NCBI__GCF_002117405.1:WP_085770154.1 283 AQAvGAAAQLDFTpCNARAFLTNPGAFVALVSRAVEEATGRKPELSTTGGTSDARFIVRD-CEVVEFGL 350 88668888999974789****************************************997.******** PP TIGR01246 340 vndtihkvneavkiedleklsevyekll 367 +n++ihk++e+ ++d++ l++vy+++l lcl|NCBI__GCF_002117405.1:WP_085770154.1 351 TNESIHKIDENAALDDIDGLTKVYRRIL 378 *************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (370 nodes) Target sequences: 1 (385 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.84 // [ok]
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