Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate PfGW456L13_5045 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1110 (303 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 Length = 303 Score = 591 bits (1524), Expect = e-174 Identities = 299/303 (98%), Positives = 302/303 (99%) Query: 1 MNPQELKSILSSGLLSFPVTDFNAQGDFHRAGYIKRLEWLAPYGASALFAAGGTGEFFSL 60 MNPQELKSILSSGLLSFPVTDFNAQGDF+RAGYIKRLEWLAPYGASALFAAGGTGEFFSL Sbjct: 1 MNPQELKSILSSGLLSFPVTDFNAQGDFNRAGYIKRLEWLAPYGASALFAAGGTGEFFSL 60 Query: 61 AASEYSEIIKTAVDTCATSVPILAGVGGATRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120 AASEYS+IIKTAVDTCATSVPILAGVGG+TRQAIEYAQEAERLGAKGLLLLPHYLTEASQ Sbjct: 61 AASEYSQIIKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120 Query: 121 DGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180 DGVAAHVEAVCKSV IGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR Sbjct: 121 DGVAAHVEAVCKSVNIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180 Query: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAREDHATVGK 240 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAREDHATVGK Sbjct: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAREDHATVGK 240 Query: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGPVRAPLTDLTGEEYEMLAALIDKQ 300 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGPVRAPLTDLTGEEYEMLAALIDKQ Sbjct: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGPVRAPLTDLTGEEYEMLAALIDKQ 300 Query: 301 GAQ 303 GAQ Sbjct: 301 GAQ 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: 486 Number of extensions: 7 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 PfGW456L13_5045 (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.26568.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-137 442.1 0.0 4.7e-137 442.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 5-dehydro-4-deoxyglucarate dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 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 ! 442.0 0.0 4.7e-137 4.7e-137 1 298 [. 3 300 .. 3 301 .. 0.99 Alignments for each domain: == domain 1 score: 442.0 bits; conditional E-value: 4.7e-137 TIGR03249 1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGef 55 pqelk ++sGllsfPvt+f+a+g+++ a + +++e+l++++++alf+agGtGef lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 3 PQELKSILSSGLLSFPVTDFNAQGDFNRAGYIKRLEWLAPYGASALFAAGGTGEF 57 89***************************************************** PP TIGR03249 56 fsltkaeveqvvevaveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllP 110 fsl +e++q+++ av++++ vP+lagvGg++++aie+a++ae+ Ga+GllllP lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 58 FSLAASEYSQIIKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLP 112 ******************************************************* PP TIGR03249 111 pylieaeqeGlaayvkaviesvdlgvivyqrdnavleadtlerlaerlpnlvGfk 165 +yl+ea+q+G+aa+v+av++sv++gv+vy+r+ + l+a+ lerlaer+pnl+G+k lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 113 HYLTEASQDGVAAHVEAVCKSVNIGVVVYNRNVCRLTAPLLERLAERCPNLIGYK 167 ******************************************************* PP TIGR03249 166 dGiGdiekvieitqklGdrllylgGlPtaevtalaylalGvtsyssaifnfiPki 220 dG+Gdie +++i+++lGdr+ ylgGlPtaev+a+ay+alGv +yssa+fnfiPk+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 168 DGLGDIELMVSIRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKT 222 ******************************************************* PP TIGR03249 221 arkfyealrkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrdvgp 275 a++fy+a++++d+atv +i+++++lP++ irnrk+Gyavs++kaG+++ G d+gp lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 223 AMDFYHAIAREDHATVGKIIDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGP 277 ******************************************************* PP TIGR03249 276 vraPlvdlekeelaeleellkka 298 vraPl+dl+ ee++ l++l++k+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5045 278 VRAPLTDLTGEEYEMLAALIDKQ 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: 8.73 // [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