Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate Ac3H11_336 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
Query= BRENDA::B7WZA5 (303 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_336 Length = 342 Score = 540 bits (1390), Expect = e-158 Identities = 265/303 (87%), Positives = 280/303 (92%) Query: 1 MTPQDLKDVMSSGLLSFPVTDFDAQGNFNAKGYAARLEWLAPYGASALFAAGGTGEYFSL 60 MTPQDLK +M SGLLSFP+TDFDAQGNF K Y RLEWLAPYGASALFAAGGTGEYFSL Sbjct: 40 MTPQDLKTIMGSGLLSFPITDFDAQGNFRPKTYIERLEWLAPYGASALFAAGGTGEYFSL 99 Query: 61 YGEEYGQIIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ 120 G EY ++IKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ Sbjct: 100 SGPEYSEVIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ 159 Query: 121 EGLIAHVEQVCKSVKFGVIVYNRDRTRFTPESLAILAERCPNLVGFKDGMGNIETMSSIF 180 EGLIAHV QVC SVKFGVIVYNRDRT+ T ESLAILAERCPNL+GFKDG+GNIETMSSI+ Sbjct: 160 EGLIAHVAQVCNSVKFGVIVYNRDRTKLTAESLAILAERCPNLIGFKDGVGNIETMSSIY 219 Query: 181 MKMGDRFAYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPRTAMAFYEAVRTDDMATQHK 240 MKMGDRF+YLGGLPTAEVYAAAYKALGTPVYSSAVFNFIP+TAM FY+AV DD+ATQHK Sbjct: 220 MKMGDRFSYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPKTAMEFYKAVAADDIATQHK 279 Query: 241 LLKEFFMPYLKIRNRVEGYGVSIIKAGAKLVGHDAGPVRAPLTDLKPAEMEELKVLIDKL 300 LLKEFFMPYL IRNRVEGYGVSIIKAGA++VGHD GPVRAPLTDLKP E+EEL LI KL Sbjct: 280 LLKEFFMPYLAIRNRVEGYGVSIIKAGARIVGHDGGPVRAPLTDLKPHEVEELAALIKKL 339 Query: 301 GPQ 303 GPQ Sbjct: 340 GPQ 342 Lambda K H 0.320 0.138 0.405 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: 10 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: 303 Length of database: 342 Length adjustment: 28 Effective length of query: 275 Effective length of database: 314 Effective search space: 86350 Effective search space used: 86350 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate Ac3H11_336 (5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))
to HMM TIGR03249 (kdgD: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))
# 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.carbon/TIGR03249.hmm # target sequence database: /tmp/gapView.22984.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03249 [M=299] Accession: TIGR03249 Description: KdgD: 5-dehydro-4-deoxyglucarate dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-133 430.4 0.0 1.8e-133 430.2 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_336 5-dehydro-4-deoxyglucarate dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_336 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.2 0.0 1.8e-133 1.8e-133 1 298 [. 42 339 .. 42 340 .. 1.00 Alignments for each domain: == domain 1 score: 430.2 bits; conditional E-value: 1.8e-133 TIGR03249 1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaev 63 pq+lk+ +gsGllsfP+t+fda+g+++++++ e++e+l++++++alf+agGtGe+fsl+ e+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_336 42 PQDLKTIMGSGLLSFPITDFDAQGNFRPKTYIERLEWLAPYGASALFAAGGTGEYFSLSGPEY 104 89************************************************************* PP TIGR03249 64 eqvvevaveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvk 126 ++v++ av++++gkvP++ag+Gg +++ai a++ae+ Ga+G+lllP+yl+ea qeGl+a+v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_336 105 SEVIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQEGLIAHVA 167 *************************************************************** PP TIGR03249 127 aviesvdlgvivyqrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrllylg 189 +v++sv++gvivy+rd ++l+a++l+ laer+pnl+GfkdG+G+ie++ +i+ k+Gdr+ ylg lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_336 168 QVCNSVKFGVIVYNRDRTKLTAESLAILAERCPNLIGFKDGVGNIETMSSIYMKMGDRFSYLG 230 *************************************************************** PP TIGR03249 190 GlPtaevtalaylalGvtsyssaifnfiPkiarkfyealrkgdeatvkeilkevilPiveirn 252 GlPtaev+a+ay+alG +yssa+fnfiPk+a++fy+a++ +d at +++lke+++P+++irn lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_336 231 GLPTAEVYAAAYKALGTPVYSSAVFNFIPKTAMEFYKAVAADDIATQHKLLKEFFMPYLAIRN 293 *************************************************************** PP TIGR03249 253 rkkGyavslikaGlevvGrdvgpvraPlvdlekeelaeleellkka 298 r +Gy vs+ikaG+++vG+d gpvraPl+dl+ +e++el++l+kk+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_336 294 RVEGYGVSIIKAGARIVGHDGGPVRAPLTDLKPHEVEELAALIKKL 339 ********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (342 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: 12.26 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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