Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate 201612 SO2471 succinyl-diaminopimelate desuccinylase (NCBI ptt file)
Query= BRENDA::Q9KQ52 (377 letters) >FitnessBrowser__MR1:201612 Length = 384 Score = 521 bits (1341), Expect = e-152 Identities = 253/372 (68%), Positives = 293/372 (78%) Query: 5 PVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFV 64 PV L K LI+R SVTP D GCQ LM ERL A+GF IE+MVFEDTTN WARRG P+F Sbjct: 12 PVTELTKALIARPSVTPLDEGCQTLMAERLAAIGFNIEAMVFEDTTNMWARRGNTGPVFC 71 Query: 65 FAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQ 124 FAGHTDVVP G LS+WHTPPFEPT+IDG+L+GRGAADMKGSLA M+VA ERF+A+HP+H Sbjct: 72 FAGHTDVVPTGDLSRWHTPPFEPTIIDGYLYGRGAADMKGSLAAMVVATERFVAKHPNHP 131 Query: 125 GSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGSIT 184 GSI FLITSDEEGPFINGT RV++TL ARNE I +VGEPSSTL +GDVVKNGRRGS+T Sbjct: 132 GSIAFLITSDEEGPFINGTTRVIDTLEARNEKITWALVGEPSSTLKLGDVVKNGRRGSLT 191 Query: 185 GDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAGTGA 244 +L VKG QGHVAYPHLA+NP+HKA P LAEL+ T WD GNA+FPPTS QI N+ GTGA Sbjct: 192 ANLTVKGVQGHVAYPHLADNPIHKAAPFLAELSQTHWDNGNAFFPPTSMQIANINGGTGA 251 Query: 245 SNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGELLA 304 SNVIPG +V FNFR+STE+T E + RV ++L AH LDYD++WT +G PFLT G LL Sbjct: 252 SNVIPGALEVMFNFRYSTEVTAEILIERVETLLTAHELDYDIRWTFNGLPFLTGEGPLLD 311 Query: 305 AVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKL 364 A A+ +V TTGGTSDGRFIA GA+V+ELGPVNATIHKVNECV++ DLE+L Sbjct: 312 ATRHAIRQVTGYDTDPQTTGGTSDGRFIAPTGAKVLELGPVNATIHKVNECVKVDDLEQL 371 Query: 365 TDMYQKTLNHLL 376 Y+ L LL Sbjct: 372 ALCYEVILEQLL 383 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: 533 Number of extensions: 16 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: 377 Length of database: 384 Length adjustment: 30 Effective length of query: 347 Effective length of database: 354 Effective search space: 122838 Effective search space used: 122838 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 201612 SO2471 (succinyl-diaminopimelate desuccinylase (NCBI ptt file))
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.2133.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-173 562.4 0.0 2.4e-173 562.3 0.0 1.0 1 lcl|FitnessBrowser__MR1:201612 SO2471 succinyl-diaminopimelate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201612 SO2471 succinyl-diaminopimelate desuccinylase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 562.3 0.0 2.4e-173 2.4e-173 1 370 [] 13 382 .. 13 382 .. 1.00 Alignments for each domain: == domain 1 score: 562.3 bits; conditional E-value: 2.4e-173 TIGR01246 1 vlelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWssdp 79 v+el+k Li r+svtP d+g+q l+aerL ++gf+ie + fedt+n+wa+rg pv++faGhtDvvP+G+l++W+++p lcl|FitnessBrowser__MR1:201612 13 VTELTKALIARPSVTPLDEGCQTLMAERLAAIGFNIEAMVFEDTTNMWARRGNTGPVFCFAGHTDVVPTGDLSRWHTPP 91 589**************************************************************************** PP TIGR01246 80 fepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidyavvg 158 fep+++dG+lygrGaaDmkgslaa+vva+erfv+k+++h Gs+++litsDeeg +i+Gt++v++tl++r+e+i++a+vg lcl|FitnessBrowser__MR1:201612 92 FEPTIIDGYLYGRGAADMKGSLAAMVVATERFVAKHPNHPGSIAFLITSDEEGPFINGTTRVIDTLEARNEKITWALVG 170 ******************************************************************************* PP TIGR01246 159 ePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqianieagt 237 ePss+ klGDv+k+GrrGs+t++l++kG+qGhvaYPh+a+nP+hka+p+l+el ++++D+Gn+ffpp+s+qiani++gt lcl|FitnessBrowser__MR1:201612 171 EPSSTLKLGDVVKNGRRGSLTANLTVKGVQGHVAYPHLADNPIHKAAPFLAELSQTHWDNGNAFFPPTSMQIANINGGT 249 ******************************************************************************* PP TIGR01246 238 gasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpels 316 gasnviPg+l+v+fn+r+s+ev++e l ++ve++l +h+ldY+++w++ g pflt eg l+++ ++ai++v++ ++ + lcl|FitnessBrowser__MR1:201612 250 GASNVIPGALEVMFNFRYSTEVTAEILIERVETLLTAHELDYDIRWTFNGLPFLTGEGPLLDATRHAIRQVTGYDTDPQ 328 ******************************************************************************* PP TIGR01246 317 tsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370 t+GGtsD+rfia ga+v+elG+vn+tihkvne+vk++dle+l+ ye +le+l lcl|FitnessBrowser__MR1:201612 329 TTGGTSDGRFIAPTGAKVLELGPVNATIHKVNECVKVDDLEQLALCYEVILEQL 382 **************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (370 nodes) Target sequences: 1 (384 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.26 // [ok]
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