Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate H281DRAFT_05315 H281DRAFT_05315 5-dehydro-4-deoxy-D-glucarate aldolase (EC 4.1.2.20)
Query= SwissProt::P23522 (256 letters) >FitnessBrowser__Burk376:H281DRAFT_05315 Length = 268 Score = 323 bits (827), Expect = 3e-93 Identities = 153/248 (61%), Positives = 192/248 (77%) Query: 7 PNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALK 66 PN F+ A+ + IGCW++L++PI TE+LG+ GFDW++LD EHAPND+ T IPQLMALK Sbjct: 13 PNSFRQAVRGGETLIGCWASLASPIVTELLGVIGFDWMLLDAEHAPNDVLTLIPQLMALK 72 Query: 67 GSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS 126 S SAPVVR P N+ V+IKRLLD GF NFL+PFV++ ++A AVA+TRYPP+GIRGVSV Sbjct: 73 DSRSAPVVRPPGNDSVVIKRLLDSGFSNFLVPFVDSADDAARAVAATRYPPQGIRGVSVG 132 Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186 HR N + TV DYF +N N+ ++VQIES+Q VD +D I A +GVDG+FVGPSDLAA GH Sbjct: 133 HRGNRYATVPDYFDIANDNVCVIVQIESRQAVDAIDEILAVDGVDGVFVGPSDLAAGYGH 192 Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246 LGNA HPDVQ+AI H+F RA A GKPSGILAPV+ADA RY + G +AV +DLG+ R+A Sbjct: 193 LGNAGHPDVQQAIAHVFERAQAAGKPSGILAPVQADAERYRDMGCRIIAVCADLGLLRNA 252 Query: 247 TQKLADTF 254 Q + F Sbjct: 253 AQTVHQHF 260 Lambda K H 0.318 0.134 0.392 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: 234 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: 256 Length of database: 268 Length adjustment: 25 Effective length of query: 231 Effective length of database: 243 Effective search space: 56133 Effective search space used: 56133 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate H281DRAFT_05315 H281DRAFT_05315 (5-dehydro-4-deoxy-D-glucarate aldolase (EC 4.1.2.20))
to HMM TIGR03239 (garL: 2-dehydro-3-deoxyglucarate aldolase (EC 4.1.2.20))
# 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/TIGR03239.hmm # target sequence database: /tmp/gapView.3280.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03239 [M=249] Accession: TIGR03239 Description: GarL: 2-dehydro-3-deoxyglucarate aldolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-128 412.2 0.4 4.5e-128 412.0 0.4 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_05315 H281DRAFT_05315 5-dehydro-4-deox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_05315 H281DRAFT_05315 5-dehydro-4-deoxy-D-glucarate aldolase (EC 4.1.2.20) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.0 0.4 4.5e-128 4.5e-128 1 248 [. 14 261 .. 14 262 .. 0.99 Alignments for each domain: == domain 1 score: 412.0 bits; conditional E-value: 4.5e-128 TIGR03239 1 nrfrqkllarktliglwsalgnpitaevlglagfdwllldgehapndvltlipqlmalkdsasapv 66 n frq++ ++tlig+w++l++pi +e+lg+ gfdw+lld+ehapndvltlipqlmalkds sapv lcl|FitnessBrowser__Burk376:H281DRAFT_05315 14 NSFRQAVRGGETLIGCWASLASPIVTELLGVIGFDWMLLDAEHAPNDVLTLIPQLMALKDSRSAPV 79 88**************************************************************** PP TIGR03239 67 vrvplnepviikrlldigfynllipfvesaeeaeravaatryppegirgvsvaqrsnrygtvadyf 132 vr+p n+ v+ikrlld gf n+l+pfv+sa++a+ravaatrypp+girgvsv +r nry+tv+dyf lcl|FitnessBrowser__Burk376:H281DRAFT_05315 80 VRPPGNDSVVIKRLLDSGFSNFLVPFVDSADDAARAVAATRYPPQGIRGVSVGHRGNRYATVPDYF 145 ****************************************************************** PP TIGR03239 133 kkindnitvlvqiesrkgvdavdeiaavdgvdgvfvgpsdlaaalgylgnpnhpdvqkairhifdr 198 ndn++v+vqiesr+ vda+dei avdgvdgvfvgpsdlaa +g+lgn++hpdvq+ai h+f+r lcl|FitnessBrowser__Burk376:H281DRAFT_05315 146 DIANDNVCVIVQIESRQAVDAIDEILAVDGVDGVFVGPSDLAAGYGHLGNAGHPDVQQAIAHVFER 211 ****************************************************************** PP TIGR03239 199 aaahgkavgilapveadarrylelgatfvavgsdlgvfrsatkalsekfk 248 a+a+gk++gilapv+ada ry ++g +++av +dlg++r+a+++++++f lcl|FitnessBrowser__Burk376:H281DRAFT_05315 212 AQAAGKPSGILAPVQADAERYRDMGCRIIAVCADLGLLRNAAQTVHQHFM 261 ********************************************999985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (249 nodes) Target sequences: 1 (268 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.22 // [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