Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate SMa1440 SMa1440 5-dehydro-4-deoxyglucarate dehydratase
Query= BRENDA::Q8UB77 (303 letters) >FitnessBrowser__Smeli:SMa1440 Length = 301 Score = 401 bits (1030), Expect = e-116 Identities = 191/301 (63%), Positives = 236/301 (78%) Query: 1 MNPEQIKTALGSGLLSFPVTHFDAEGRFAADSYREHVEWLAGYKAPVLFAAGGTGEFFSL 60 M+PE+IK+ +GSGLLSFPVTHF ++ + +SYR HVEWL+G++A LFAAGGTGEFFSL Sbjct: 1 MSPEEIKSRVGSGLLSFPVTHFTSDYKLNLESYRRHVEWLSGFEAAALFAAGGTGEFFSL 60 Query: 61 KPDEIPTIVAAAKEVAGETAIVSGCGYGTEIAVDIARSVEKVGADGILLLPHYLIDAPQE 120 P+E+ + AAK+V+GE I++GCGYGT +AV+ A+ VE+ GADGILLLPHYL +APQE Sbjct: 61 SPNEVGQVTRAAKDVSGEVPIIAGCGYGTSLAVETAKIVEEAGADGILLLPHYLTEAPQE 120 Query: 121 GLYAHIKKVCQSVGIGVMVYNRDNSVLQADTLARLCDECPNLVGFKDGTGDIGLVRQITA 180 G+YAH+K VC S G+GV++YNR NSV ADT+ARL + CPNL+GFKDGTG + LVR +TA Sbjct: 121 GIYAHVKAVCDSTGLGVILYNRANSVANADTVARLAEACPNLIGFKDGTGKVDLVRHVTA 180 Query: 181 KMGDRLMYLGGMPTAELFAEAYLGAGFTTYSSAVFNFVPGLANEFYAALRAGERATCERI 240 K+GDRL Y+GGMPT ELFAE + G G TTYSSAVFNFVP LA FY A+RAG+RA E I Sbjct: 181 KLGDRLCYIGGMPTHELFAEGFNGVGVTTYSSAVFNFVPELAQRFYRAMRAGDRAVMEGI 240 Query: 241 LVDFFYPFMAIRNRAKGYAVSAVKAGVRLQGFNAGPVRAPLKDLTNEEIGMLEALIGTHK 300 L FF+PF A+R+R GY VS +KAGV L GF GPVR PL DLT EE +L+ LI + Sbjct: 241 LHTFFFPFAALRDRKAGYPVSIIKAGVELAGFAPGPVRPPLVDLTGEEREILQGLIEASR 300 Query: 301 R 301 R Sbjct: 301 R 301 Lambda K H 0.321 0.139 0.409 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: 398 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: 303 Length of database: 301 Length adjustment: 27 Effective length of query: 276 Effective length of database: 274 Effective search space: 75624 Effective search space used: 75624 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 SMa1440 SMa1440 (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.16431.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-125 402.9 0.0 4.3e-125 402.7 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMa1440 SMa1440 5-dehydro-4-deoxyglucara Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMa1440 SMa1440 5-dehydro-4-deoxyglucarate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.7 0.0 4.3e-125 4.3e-125 1 297 [. 3 298 .. 3 300 .. 0.99 Alignments for each domain: == domain 1 score: 402.7 bits; conditional E-value: 4.3e-125 TIGR03249 1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqvvevaveaakg 76 p e+k ++gsGllsfPvt+f +d++l+ +++r+++e+l + +++alf+agGtGeffsl+++ev qv ++a + ++g lcl|FitnessBrowser__Smeli:SMa1440 3 PEEIKSRVGSGLLSFPVTHFTSDYKLNLESYRRHVEWLSGFEAAALFAAGGTGEFFSLSPNEVGQVTRAA-KDVSG 77 7899***************************************************************999.8999* PP TIGR03249 77 kvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesvdlgvivyqrdnavleadtle 152 +vP++ag G+++s a+e+a++ e++GadG+lllP+yl+ea qeG++a+vkav++s+ lgvi+y+r+n+v +adt++ lcl|FitnessBrowser__Smeli:SMa1440 78 EVPIIAGCGYGTSLAVETAKIVEEAGADGILLLPHYLTEAPQEGIYAHVKAVCDSTGLGVILYNRANSVANADTVA 153 **************************************************************************** PP TIGR03249 153 rlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevtalaylalGvtsyssaifnfiPkiarkfyeal 228 rlae +pnl+GfkdG G+++ v ++t+klGdrl y+gG+Pt+e++a+ + +Gvt+yssa+fnf+P++a++fy+a+ lcl|FitnessBrowser__Smeli:SMa1440 154 RLAEACPNLIGFKDGTGKVDLVRHVTAKLGDRLCYIGGMPTHELFAEGFNGVGVTTYSSAVFNFVPELAQRFYRAM 229 **************************************************************************** PP TIGR03249 229 rkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrdvgpvraPlvdlekeelaeleellkk 297 r gd a+++ il+ +++P+ ++r rk+Gy vs+ikaG+e+ G gpvr+Plvdl+ ee + l+ l+++ lcl|FitnessBrowser__Smeli:SMa1440 230 RAGDRAVMEGILHTFFFPFAALRDRKAGYPVSIIKAGVELAGFAPGPVRPPLVDLTGEEREILQGLIEA 298 ***************************************************************999975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (301 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: 9.28 // [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