Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_084075967.1 BUB04_RS02635 3-dehydroquinate synthase
Query= BRENDA::Q3M4V2 (363 letters) >NCBI__GCF_900129305.1:WP_084075967.1 Length = 670 Score = 211 bits (537), Expect = 5e-59 Identities = 128/292 (43%), Positives = 174/292 (59%), Gaps = 5/292 (1%) Query: 73 AGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGINVVQVPTT 132 A E +K L+ ++KL ALE +R+S VA+GGGV GD+ GF A+ ++RG+ VVQVPTT Sbjct: 374 AREAHKRLSQVEKLARRALEAGADRTSVFVAVGGGVTGDVIGFLASIYMRGVPVVQVPTT 433 Query: 133 LLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGMAEVIKYGV 192 LLA VDS +GGKTGV+ GKNL+G+FH P VL+DP L TLP RE++ GMAEVIKY Sbjct: 434 LLAQVDSCLGGKTGVDLDEGKNLLGSFHHPEAVLVDPDFLTTLPEREWQNGMAEVIKYAF 493 Query: 193 IWDAELFNQLEQSKRLDQLRYIKPE-LMDAILTRSCQAKADVVGKDEKEGGLRAILNYGH 251 + L L R Y P + I+T S + K V DE++ GLR +LN GH Sbjct: 494 LEGGRLLEILTSLARRKGNPYPLPAGPAEEIVTESLRIKHRYVAADERDFGLRQLLNLGH 553 Query: 252 TVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIEKAGLPTKLP 311 T GHA+E+++ Y L HG AVG+G+ A +I V LG A L++ GLP + P Sbjct: 554 TTGHALEAVSGY-ALAHGHAVGLGIRVALRIGVLLGETDPALEKTAEDLLKAFGLPLRSP 612 Query: 312 AGLDIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTDEVTSDHIRQVLQQM 363 D E ++ A++ DKK + +V+P +IG V D S R VL+ + Sbjct: 613 LAADPERVLAAMRHDKKKGGEGLVWVIPRKIGRV---DRFRSVPDRAVLEAL 661 Lambda K H 0.319 0.136 0.388 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: 525 Number of extensions: 21 Number of successful extensions: 3 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: 363 Length of database: 670 Length adjustment: 34 Effective length of query: 329 Effective length of database: 636 Effective search space: 209244 Effective search space used: 209244 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: 52 (24.6 bits)
Align candidate WP_084075967.1 BUB04_RS02635 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))
# 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.aa/TIGR01357.hmm # target sequence database: /tmp/gapView.7392.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01357 [M=344] Accession: TIGR01357 Description: aroB: 3-dehydroquinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-99 317.6 0.0 8.5e-99 316.9 0.0 1.2 1 lcl|NCBI__GCF_900129305.1:WP_084075967.1 BUB04_RS02635 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_084075967.1 BUB04_RS02635 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 316.9 0.0 8.5e-99 8.5e-99 5 342 .. 323 660 .. 320 662 .. 0.93 Alignments for each domain: == domain 1 score: 316.9 bits; conditional E-value: 8.5e-99 TIGR01357 5 vgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakl 71 +g+ ++l ++l++ ++ v+++d++v++l ek++ +evl++ +++e +K l++v+kl lcl|NCBI__GCF_900129305.1:WP_084075967.1 323 IGRRSARSLGAWLRDkfPGRRPVIFVDRRVADLWREKILPPG----AEVLWVEWEAREAHKRLSQVEKL 387 555566666666666432377888999999999988887765....67********************* PP TIGR01357 72 ldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNl 140 ++ le++++r sv va+GGGv gD++GF+A++y+RG+++vqvPTtlla+vDs GGKtg++l++gkNl lcl|NCBI__GCF_900129305.1:WP_084075967.1 388 ARRALEAGADRTSVFVAVGGGVTGDVIGFLASIYMRGVPVVQVPTTLLAQVDSCLGGKTGVDLDEGKNL 456 ********************************************************************* PP TIGR01357 141 iGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllkl..aelealeeli 207 +G+f++P+aVl+d+++l+tlpere+++GmaEviK++++ + +l+e l++ ++ + +ee++ lcl|NCBI__GCF_900129305.1:WP_084075967.1 457 LGSFHHPEAVLVDPDFLTTLPEREWQNGMAEVIKYAFLEGGRLLEILTSLARRKGNPypLPAGPAEEIV 525 *************************************************9985444355555789**** PP TIGR01357 208 krsievKaevVeeDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkael 276 ++s+++K + V++De++ glR+lLN+GHt gHa+Ea+++y l HG+aV +G+ v++++ lg +++ l lcl|NCBI__GCF_900129305.1:WP_084075967.1 526 TESLRIKHRYVAADERDFGLRQLLNLGHTTGHALEAVSGYALAHGHAVGLGIRVALRIGVLLGETDPAL 594 ********************************************************************* PP TIGR01357 277 lerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeellea 342 + ++llk++glp + + + e +l+a+ +DKK+ g+ + v++++iG++ ++v+++++lea lcl|NCBI__GCF_900129305.1:WP_084075967.1 595 EKTAEDLLKAFGLPLRSPLAADPERVLAAMRHDKKKGGEGLVWVIPRKIGRVDRFRSVPDRAVLEA 660 ******************************************************999999999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (670 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: 20.21 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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