Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate BPHYT_RS20415 BPHYT_RS20415 5-dehydro-4-deoxyglucarate dehydratase
Query= reanno::BFirm:BPHYT_RS24155 (305 letters) >FitnessBrowser__BFirm:BPHYT_RS20415 Length = 305 Score = 531 bits (1368), Expect = e-156 Identities = 261/305 (85%), Positives = 285/305 (93%) Query: 1 MTTPQELKQIVSEGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS 60 MT+PQELK IVSEGLLSFPVTDFD G+FRADTYA RLEWLAPYGA+ALF AGGTGEFFS Sbjct: 1 MTSPQELKAIVSEGLLSFPVTDFDAHGEFRADTYAARLEWLAPYGATALFAAGGTGEFFS 60 Query: 61 LTHNDYSNVVKTATEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEAC 120 LT DY+NV++TAT+ C+GKVPILAGAGGPTRVAI YAQEAER GA+G+LLMPHYLTEA Sbjct: 61 LTKTDYTNVIRTATDTCRGKVPILAGAGGPTRVAIEYAQEAERLGASGVLLMPHYLTEAS 120 Query: 121 QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVS 180 QEGIAAH E+VCKSVPN+GVI+YNRANSKLNADMLE LA+RCPNLIGFKDGVGEIE MV+ Sbjct: 121 QEGIAAHVEQVCKSVPNIGVIVYNRANSKLNADMLERLADRCPNLIGFKDGVGEIEAMVT 180 Query: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV 240 IRRRLG+RFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAM+FYRA+AA+DHAT Sbjct: 181 IRRRLGERFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMEFYRAVAANDHATQ 240 Query: 241 GKLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIK 300 G+L+DEFFLPYLAIRNRRAGYAVSIVKAGAKLVGH AGPVRAPLTDLT+EE +LDALI+ Sbjct: 241 GRLLDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHDAGPVRAPLTDLTDEESAQLDALIR 300 Query: 301 TLGPQ 305 LG Q Sbjct: 301 KLGAQ 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: 442 Number of extensions: 15 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 BPHYT_RS20415 BPHYT_RS20415 (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.16414.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-140 451.4 0.0 7.2e-140 451.2 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS20415 BPHYT_RS20415 5-dehydro-4-deoxyg Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS20415 BPHYT_RS20415 5-dehydro-4-deoxyglucarate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.2 0.0 7.2e-140 7.2e-140 1 298 [. 4 302 .. 4 303 .. 0.99 Alignments for each domain: == domain 1 score: 451.2 bits; conditional E-value: 7.2e-140 TIGR03249 1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqvveva 70 pqelk+ +++GllsfPvt+fda+g+++ +++++++e+l+++++ alf+agGtGeffsltk+++ +v++ a lcl|FitnessBrowser__BFirm:BPHYT_RS20415 4 PQELKAIVSEGLLSFPVTDFDAHGEFRADTYAARLEWLAPYGATALFAAGGTGEFFSLTKTDYTNVIRTA 73 89******************************************************************** PP TIGR03249 71 veaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesv.dlgvivy 139 +++++gkvP+lag+Gg ++vaie+a++ae+ Ga+G+ll+P+yl+ea+qeG+aa+v++v++sv ++gvivy lcl|FitnessBrowser__BFirm:BPHYT_RS20415 74 TDTCRGKVPILAGAGGPTRVAIEYAQEAERLGASGVLLMPHYLTEASQEGIAAHVEQVCKSVpNIGVIVY 143 *************************************************************978****** PP TIGR03249 140 qrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevtalaylalGvtsy 209 +r+n++l+ad+lerla+r+pnl+GfkdG+G+ie +++i+++lG+r+ ylgGlPtaev+a+ay+alGv +y lcl|FitnessBrowser__BFirm:BPHYT_RS20415 144 NRANSKLNADMLERLADRCPNLIGFKDGVGEIEAMVTIRRRLGERFSYLGGLPTAEVYAAAYKALGVPVY 213 ********************************************************************** PP TIGR03249 210 ssaifnfiPkiarkfyealrkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrdvgpvraP 279 ssa+fnfiPk+a++fy+a++ +d+at ++l+e++lP+++irnr++Gyavs++kaG+++vG+d+gpvraP lcl|FitnessBrowser__BFirm:BPHYT_RS20415 214 SSAVFNFIPKTAMEFYRAVAANDHATQGRLLDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHDAGPVRAP 283 ********************************************************************** PP TIGR03249 280 lvdlekeelaeleellkka 298 l+dl++ee a+l++l++k+ lcl|FitnessBrowser__BFirm:BPHYT_RS20415 284 LTDLTDEESAQLDALIRKL 302 ****************985 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.50 // [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