Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate H281DRAFT_03816 H281DRAFT_03816 5-dehydro-4-deoxyglucarate dehydratase
Query= reanno::BFirm:BPHYT_RS24155 (305 letters) >FitnessBrowser__Burk376:H281DRAFT_03816 Length = 305 Score = 535 bits (1377), Expect = e-157 Identities = 266/305 (87%), Positives = 284/305 (93%) Query: 1 MTTPQELKQIVSEGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS 60 MT+PQELK IVSEGLLSFPVTDFD QGDFRADTYA+RLEWLAPYGA+ALF AGGTGEFFS Sbjct: 1 MTSPQELKAIVSEGLLSFPVTDFDAQGDFRADTYAQRLEWLAPYGATALFAAGGTGEFFS 60 Query: 61 LTHNDYSNVVKTATEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEAC 120 LT +DY+NV++TATE CKGKVPILAGAGGPTRVAI YA+EAER GANG+LLMPHYLTEA Sbjct: 61 LTKSDYTNVIRTATETCKGKVPILAGAGGPTRVAIEYAREAERLGANGVLLMPHYLTEAS 120 Query: 121 QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVS 180 QEGIAAH E+VC +V N+GVI+YNRANSKLNADMLE LA+RCPNLIGFKDGVGEIE MV+ Sbjct: 121 QEGIAAHVEQVCHAVKNIGVIVYNRANSKLNADMLERLADRCPNLIGFKDGVGEIEAMVT 180 Query: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV 240 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAM+FYRAIAADDHAT Sbjct: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMEFYRAIAADDHATT 240 Query: 241 GKLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIK 300 +LIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVG AGPVRAPLTDLTEEE G+L ALI Sbjct: 241 SRLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGRDAGPVRAPLTDLTEEECGQLAALIA 300 Query: 301 TLGPQ 305 LGPQ Sbjct: 301 KLGPQ 305 Lambda K H 0.319 0.136 0.398 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: 428 Number of extensions: 12 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: 305 Length of database: 305 Length adjustment: 27 Effective length of query: 278 Effective length of database: 278 Effective search space: 77284 Effective search space used: 77284 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate H281DRAFT_03816 H281DRAFT_03816 (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.4818.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-141 455.4 0.0 4.3e-141 455.2 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_03816 H281DRAFT_03816 5-dehydro-4-deox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_03816 H281DRAFT_03816 5-dehydro-4-deoxyglucarate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.2 0.0 4.3e-141 4.3e-141 1 297 [. 4 301 .. 4 303 .. 0.99 Alignments for each domain: == domain 1 score: 455.2 bits; conditional E-value: 4.3e-141 TIGR03249 1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqv 66 pqelk+ +++GllsfPvt+fda+g+++ +++++++e+l+++++ alf+agGtGeffsltk+++ +v lcl|FitnessBrowser__Burk376:H281DRAFT_03816 4 PQELKAIVSEGLLSFPVTDFDAQGDFRADTYAQRLEWLAPYGATALFAAGGTGEFFSLTKSDYTNV 69 89**************************************************************** PP TIGR03249 67 vevaveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesv 132 ++ a+e++kgkvP+lag+Gg ++vaie+ar+ae+ Ga+G+ll+P+yl+ea+qeG+aa+v++v+++v lcl|FitnessBrowser__Burk376:H281DRAFT_03816 70 IRTATETCKGKVPILAGAGGPTRVAIEYAREAERLGANGVLLMPHYLTEASQEGIAAHVEQVCHAV 135 *****************************************************************9 PP TIGR03249 133 d.lgvivyqrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevt 197 + +gvivy+r+n++l+ad+lerla+r+pnl+GfkdG+G+ie +++i+++lGdr+ ylgGlPtaev+ lcl|FitnessBrowser__Burk376:H281DRAFT_03816 136 KnIGVIVYNRANSKLNADMLERLADRCPNLIGFKDGVGEIEAMVTIRRRLGDRFSYLGGLPTAEVY 201 55**************************************************************** PP TIGR03249 198 alaylalGvtsyssaifnfiPkiarkfyealrkgdeatvkeilkevilPiveirnrkkGyavslik 263 a+ay+alGv +yssa+fnfiPk+a++fy+a++ +d+at +++++e++lP+++irnr++Gyavs++k lcl|FitnessBrowser__Burk376:H281DRAFT_03816 202 AAAYKALGVPVYSSAVFNFIPKTAMEFYRAIAADDHATTSRLIDEFFLPYLAIRNRRAGYAVSIVK 267 ****************************************************************** PP TIGR03249 264 aGlevvGrdvgpvraPlvdlekeelaeleellkk 297 aG+++vGrd+gpvraPl+dl++ee+ +l++l+ k lcl|FitnessBrowser__Burk376:H281DRAFT_03816 268 AGAKLVGRDAGPVRAPLTDLTEEECGQLAALIAK 301 *******************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (305 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: 00:00:00.01 # Mc/sec: 6.31 // [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