Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_106711603.1 CU102_RS13315 succinyl-diaminopimelate desuccinylase
Query= BRENDA::Q9KQ52 (377 letters) >NCBI__GCF_003010955.1:WP_106711603.1 Length = 398 Score = 283 bits (723), Expect = 8e-81 Identities = 161/393 (40%), Positives = 224/393 (56%), Gaps = 22/393 (5%) Query: 1 MTDS--PVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFE-----DTTNFW 53 MT S PV LA +LI+ S+TPA+ G + L LGF +E VF D N + Sbjct: 1 MTSSIDPVQNLA-QLIACPSITPAEGGALSALQAMLAPLGFSVERPVFSEAGTPDVENLY 59 Query: 54 ARRGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAV 113 ARR P +FAGHTDVVP G W PPF + +G ++GRGA DMKG +AC + AV Sbjct: 60 ARRSGNGPHLMFAGHTDVVPVGDEGAWTVPPFSAEIRNGEMYGRGAVDMKGGIACFVAAV 119 Query: 114 ERFIAEHPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGD 173 R + ++ +GS+ F+IT DEEGP INGT +++E AR E D IVGEP++ +GD Sbjct: 120 ARHLEKNGALKGSVSFVITGDEEGPSINGTGKLLEWAKARGEKWDAAIVGEPTNPDKLGD 179 Query: 174 VVKNGRRGSITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSF 233 ++K GRRGS++G + V G QGH AYPHLA+NPV + + L +DEG F PT+ Sbjct: 180 MIKIGRRGSLSGTVVVHGVQGHAAYPHLADNPVRGLVTLVDSLLYPVFDEGTKDFQPTNL 239 Query: 234 QIPNLQAGTGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLD------------AHG 281 ++ + G A NVIP FN RF+ T E + +H+ LD + Sbjct: 240 EVTTIDVGNPAVNVIPATATATFNVRFNDTWTGETLMAEIHNRLDQASRRHKLRPGKSEP 299 Query: 282 LDYDVKW-TLSGQPFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVV 340 ++YD+ W FLT +L+ + +++E+V P L T+GGTSD RFI VV Sbjct: 300 VNYDLNWRNRVSHVFLTHEEKLIGTLSSSIEKVTGNRPQLSTSGGTSDARFIKDY-CPVV 358 Query: 341 ELGPVNATIHKVNECVRIADLEKLTDMYQKTLN 373 E G V T+H V+E V +ADLE LT +Y++ ++ Sbjct: 359 EFGLVGKTMHMVDERVALADLETLTQVYERFIS 391 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: 468 Number of extensions: 31 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: 398 Length adjustment: 30 Effective length of query: 347 Effective length of database: 368 Effective search space: 127696 Effective search space used: 127696 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_106711603.1 CU102_RS13315 (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.2898748.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-128 414.7 0.0 2e-128 414.4 0.0 1.0 1 NCBI__GCF_003010955.1:WP_106711603.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106711603.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.4 0.0 2e-128 2e-128 5 369 .. 11 392 .. 8 393 .. 0.97 Alignments for each domain: == domain 1 score: 414.4 bits; conditional E-value: 2e-128 TIGR01246 5 akeLisrksvtPndagaqeliaerLkklgfeieilefe.....dtknlwatrgteepvlvfaGhtDvvPaGel 72 + +Li +s+tP++ ga++ +++ L lgf++e+ f d++nl+a+r + p+l+faGhtDvvP+G++ NCBI__GCF_003010955.1:WP_106711603.1 11 LAQLIACPSITPAEGGALSALQAMLAPLGFSVERPVFSeagtpDVENLYARRSGNGPHLMFAGHTDVVPVGDE 83 578*****************************99877533344899*************************** PP TIGR01246 73 ekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetl 145 +W+ +pf++e+r+G +ygrGa+Dmkg++a+fv+a+ r+++kn kGs+s++it Deeg +i+Gt k++e+ NCBI__GCF_003010955.1:WP_106711603.1 84 GAWTVPPFSAEIRNGEMYGRGAVDMKGGIACFVAAVARHLEKNGALKGSVSFVITGDEEGPSINGTGKLLEWA 156 ************************************************************************* PP TIGR01246 146 kerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDe 218 k+r e+ d a+vgeP+ +klGD+ikiGrrGs++g++ ++G+qGh aYPh+a+nPv +v ++ l+ +De NCBI__GCF_003010955.1:WP_106711603.1 157 KARGEKWDAAIVGEPTNPDKLGDMIKIGRRGSLSGTVVVHGVQGHAAYPHLADNPVRGLVTLVDSLLYPVFDE 229 ************************************************************************* PP TIGR01246 219 GneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkh............kldY 279 G++ f+p++l+++ i++g+ a nviP+ ++++fn+rf+ ++ e+l ++++ ld+ ++Y NCBI__GCF_003010955.1:WP_106711603.1 230 GTKDFQPTNLEVTTIDVGNPAVNVIPATATATFNVRFNDTWTGETLMAEIHNRLDQAsrrhklrpgksePVNY 302 *******************************************************988999999999988*** PP TIGR01246 280 elewk.lsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneav 351 +l+w+ + ++ flt+e+kli ++ ++ie+v++++p+lstsGGtsDarfi+++ + vve+Glv +t+h v+e+v NCBI__GCF_003010955.1:WP_106711603.1 303 DLNWRnRVSHVFLTHEEKLIGTLSSSIEKVTGNRPQLSTSGGTSDARFIKDY-CPVVEFGLVGKTMHMVDERV 374 ****7257999*****************************************.******************** PP TIGR01246 352 kiedleklsevyekllee 369 ++dle l++vye+++++ NCBI__GCF_003010955.1:WP_106711603.1 375 ALADLETLTQVYERFISD 392 **************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (370 nodes) Target sequences: 1 (398 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 27.74 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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