Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate GFF373 Psest_0374 5-dehydro-4-deoxyglucarate dehydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1110 (303 letters) >FitnessBrowser__psRCH2:GFF373 Length = 303 Score = 535 bits (1379), Expect = e-157 Identities = 270/303 (89%), Positives = 283/303 (93%) Query: 1 MNPQELKSILSSGLLSFPVTDFNAQGDFHRAGYIKRLEWLAPYGASALFAAGGTGEFFSL 60 MNPQELK+ILSSGLLSFPVTDF+AQGDFHRAGYIKRLEWL PYGASALFAAGGTGEFFSL Sbjct: 1 MNPQELKAILSSGLLSFPVTDFDAQGDFHRAGYIKRLEWLGPYGASALFAAGGTGEFFSL 60 Query: 61 AASEYSEIIKTAVDTCATSVPILAGVGGATRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120 EYSEIIKTAVDTCA +VPILAGVGG TR AI+ AQEAERLGAKGLLLLPHYLTEASQ Sbjct: 61 EPREYSEIIKTAVDTCAGTVPILAGVGGPTRLAIQMAQEAERLGAKGLLLLPHYLTEASQ 120 Query: 121 DGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180 +GVA HVE VCKSV IGVVVYNRNVCRLTAP LE+LAERCPNLIGYKDGLGDIELMVSIR Sbjct: 121 EGVALHVEQVCKSVNIGVVVYNRNVCRLTAPHLEQLAERCPNLIGYKDGLGDIELMVSIR 180 Query: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAREDHATVGK 240 RRLG+RFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFY AIAREDH TVGK Sbjct: 181 RRLGERFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYQAIAREDHETVGK 240 Query: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGPVRAPLTDLTGEEYEMLAALIDKQ 300 +IDDFFLPYLDIRNR GYAVSIVKAGA+I+GYDAGPVRAPLT+L +EYE LA LI+KQ Sbjct: 241 LIDDFFLPYLDIRNRCKGYAVSIVKAGARISGYDAGPVRAPLTELKPDEYERLAVLIEKQ 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: 456 Number of extensions: 13 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 GFF373 Psest_0374 (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.30617.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-134 433.5 0.0 2e-134 433.4 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF373 Psest_0374 5-dehydro-4-deoxygluc Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF373 Psest_0374 5-dehydro-4-deoxyglucarate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.4 0.0 2e-134 2e-134 1 298 [. 3 300 .. 3 301 .. 0.99 Alignments for each domain: == domain 1 score: 433.4 bits; conditional E-value: 2e-134 TIGR03249 1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqvvevaveaakg 76 pqelk+ ++sGllsfPvt+fda+g+++ a + +++e+l +++++alf+agGtGeffsl+++e++++++ av++++g lcl|FitnessBrowser__psRCH2:GFF373 3 PQELKAILSSGLLSFPVTDFDAQGDFHRAGYIKRLEWLGPYGASALFAAGGTGEFFSLEPREYSEIIKTAVDTCAG 78 89************************************************************************** PP TIGR03249 77 kvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesvdlgvivyqrdnavleadtle 152 vP+lagvGg ++ ai++a++ae+ Ga+GllllP+yl+ea+qeG+a +v++v++sv++gv+vy+r+ + l+a++le lcl|FitnessBrowser__psRCH2:GFF373 79 TVPILAGVGGPTRLAIQMAQEAERLGAKGLLLLPHYLTEASQEGVALHVEQVCKSVNIGVVVYNRNVCRLTAPHLE 154 **************************************************************************** PP TIGR03249 153 rlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevtalaylalGvtsyssaifnfiPkiarkfyeal 228 +laer+pnl+G+kdG+Gdie +++i+++lG+r+ ylgGlPtaev+a+ay+alGv +yssa+fnfiPk+a++fy+a+ lcl|FitnessBrowser__psRCH2:GFF373 155 QLAERCPNLIGYKDGLGDIELMVSIRRRLGERFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYQAI 230 **************************************************************************** PP TIGR03249 229 rkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrdvgpvraPlvdlekeelaeleellkka 298 +++d++tv +++++++lP++ irnr kGyavs++kaG+++ G d+gpvraPl++l+ +e+++l+ l++k+ lcl|FitnessBrowser__psRCH2:GFF373 231 AREDHETVGKLIDDFFLPYLDIRNRCKGYAVSIVKAGARISGYDAGPVRAPLTELKPDEYERLAVLIEKQ 300 *******************************************************************985 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.14 // [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