Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate AO356_07185 AO356_07185 5-dehydro-4-deoxyglucarate dehydratase
Query= reanno::WCS417:GFF826 (303 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07185 Length = 303 Score = 566 bits (1459), Expect = e-166 Identities = 285/303 (94%), Positives = 293/303 (96%) Query: 1 MNPQELKSILSHGLLSFPVTDFNAQGDFHQAGYIKRLEWLAPYGATALFAAGGTGEFFSL 60 MNPQELKSILS GLLSFPVTDF AQGDF++ Y+KRLEWLAPYGA+ALFAAGGTGEFFSL Sbjct: 1 MNPQELKSILSSGLLSFPVTDFTAQGDFNRDSYVKRLEWLAPYGASALFAAGGTGEFFSL 60 Query: 61 AASEYSQVVKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120 AASEYSQV+KTAVDTCATSVPILAGVGG+TRQAIEYAQEAERLGAKGLLLLPHYLTEASQ Sbjct: 61 AASEYSQVIKTAVDTCATSVPILAGVGGATRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120 Query: 121 DGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180 DGVAAHVEAVCKSVKIGVVVYNRNVCRL A LE+LAERCPNLIGYKDGLGDIELMVSIR Sbjct: 121 DGVAAHVEAVCKSVKIGVVVYNRNVCRLNATQLEQLAERCPNLIGYKDGLGDIELMVSIR 180 Query: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAKDDHATVSK 240 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIA+DDH TV K Sbjct: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIARDDHETVGK 240 Query: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ 300 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ Sbjct: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ 300 Query: 301 GAQ 303 G Q Sbjct: 301 GKQ 303 Lambda K H 0.320 0.137 0.399 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: 415 Number of extensions: 8 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: 303 Length adjustment: 27 Effective length of query: 276 Effective length of database: 276 Effective search space: 76176 Effective search space used: 76176 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 AO356_07185 AO356_07185 (5-dehydro-4-deoxyglucarate dehydratase)
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.13792.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-137 442.4 0.0 3.9e-137 442.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07185 AO356_07185 5-dehydro-4-deoxyglu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07185 AO356_07185 5-dehydro-4-deoxyglucarate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.2 0.0 3.9e-137 3.9e-137 1 298 [. 3 300 .. 3 301 .. 0.99 Alignments for each domain: == domain 1 score: 442.2 bits; conditional E-value: 3.9e-137 TIGR03249 1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaev 63 pqelk ++sGllsfPvt+f a+g+++ +++ +++e+l++++++alf+agGtGeffsl +e+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07185 3 PQELKSILSSGLLSFPVTDFTAQGDFNRDSYVKRLEWLAPYGASALFAAGGTGEFFSLAASEY 65 89************************************************************* PP TIGR03249 64 eqvvevaveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvk 126 +qv++ av++++ vP+lagvGg++++aie+a++ae+ Ga+GllllP+yl+ea+q+G+aa+v+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07185 66 SQVIKTAVDTCATSVPILAGVGGATRQAIEYAQEAERLGAKGLLLLPHYLTEASQDGVAAHVE 128 *************************************************************** PP TIGR03249 127 aviesvdlgvivyqrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrllylg 189 av++sv++gv+vy+r+ + l+a +le+laer+pnl+G+kdG+Gdie +++i+++lGdr+ ylg lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07185 129 AVCKSVKIGVVVYNRNVCRLNATQLEQLAERCPNLIGYKDGLGDIELMVSIRRRLGDRFSYLG 191 *************************************************************** PP TIGR03249 190 GlPtaevtalaylalGvtsyssaifnfiPkiarkfyealrkgdeatvkeilkevilPiveirn 252 GlPtaev+a+ay+alGv +yssa+fnfiPk+a++fy+a++++d++tv +i+++++lP++ irn lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07185 192 GLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIARDDHETVGKIIDDFFLPYLDIRN 254 *************************************************************** PP TIGR03249 253 rkkGyavslikaGlevvGrdvgpvraPlvdlekeelaeleellkka 298 rk+Gyavs++kaG+++vG d+gpvr+Pl+dl ee++ l++l++k+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07185 255 RKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ 300 ******************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (303 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.75 // [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