Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_012469650.1 GLOV_RS07870 3-dehydroquinate synthase
Query= BRENDA::Q3M4V2 (363 letters) >NCBI__GCF_000020385.1:WP_012469650.1 Length = 359 Score = 308 bits (788), Expect = 2e-88 Identities = 166/339 (48%), Positives = 221/339 (65%), Gaps = 3/339 (0%) Query: 5 INVNLPTQSYEIAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGF 64 I + L + SY+I I L IG + + L +V+NPT+ + V SL+ AGF Sbjct: 4 ITIQLDSHSYDIGIGEGLLSGIGAACKAVGLAGAAAVVTNPTVAPLYAGVVTGSLQQAGF 63 Query: 65 QVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGI 124 +P GE +KT ++ +YD LE L+R S +VALGGGV+GD+ GFAAAT+LRGI Sbjct: 64 TPVVIEIPDGEEFKTGETLNSVYDRLLEAGLDRRSFIVALGGGVVGDLAGFAAATFLRGI 123 Query: 125 NVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGM 184 VQVPTTLLA VDS++GGKTG++HP GKNLIGAF+QP VL D LKTL R +RAG+ Sbjct: 124 PFVQVPTTLLAQVDSSVGGKTGIDHPLGKNLIGAFYQPHLVLSDVSTLKTLSERHYRAGL 183 Query: 185 AEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKEGGLR 244 AEVIKYG + DAELF LE ++D L P+L+ ++ R C+ KA VV +DE+EGGLR Sbjct: 184 AEVIKYGAVLDAELFALLE--AKVDGLLKRDPQLLGRVIARCCEIKAWVVEQDEREGGLR 241 Query: 245 AILNYGHTVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIEKA 304 A+LNYGHT+GHA E+L+ YR L HGEAV IGMV A Q++ G D +R L+++ Sbjct: 242 AVLNYGHTLGHAFETLSGYRDLVHGEAVAIGMVQAAQLSQREGYCSVGDVERITTLVQQV 301 Query: 305 GLPTKLPAGLDIEGIIEALQLDKKVKDGKVRFVLPTQIG 343 GLP+ P + E +I +L DKK + G +++V IG Sbjct: 302 GLPSDAPV-VATEDLITSLAKDKKNRSGTLQYVCNRGIG 339 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: 352 Number of extensions: 13 Number of successful extensions: 2 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: 359 Length adjustment: 29 Effective length of query: 334 Effective length of database: 330 Effective search space: 110220 Effective search space used: 110220 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: 49 (23.5 bits)
Align candidate WP_012469650.1 GLOV_RS07870 (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.6423.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-118 381.3 0.0 2.5e-118 381.1 0.0 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012469650.1 GLOV_RS07870 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012469650.1 GLOV_RS07870 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.1 0.0 2.5e-118 2.5e-118 1 340 [. 13 352 .. 13 356 .. 0.96 Alignments for each domain: == domain 1 score: 381.1 bits; conditional E-value: 2.5e-118 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++ +gegll+ + ++++ a + v+t+ +v+ l+a + l+++g++ v+ +pdgee K+ et lcl|NCBI__GCF_000020385.1:WP_012469650.1 13 YDIGIGEGLLSGIGAACKAvgLAGAAAVVTNPTVAPLYAGVVTGSLQQAGFTPVVIEIPDGEEFKTGET 81 67889999999888888776666999******************************************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 +++++d+lle++l+r+s +va+GGGvvgDlaGF+Aat+lRGi++vqvPTtlla+vDssvGGKtgi++pl lcl|NCBI__GCF_000020385.1:WP_012469650.1 82 LNSVYDRLLEAGLDRRSFIVALGGGVVGDLAGFAAATFLRGIPFVQVPTTLLAQVDSSVGGKTGIDHPL 150 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNliGafyqP++Vl d+++l+tl+er++r+G+aEviK+g++ daelf+ le + + llk+ + + l + lcl|NCBI__GCF_000020385.1:WP_012469650.1 151 GKNLIGAFYQPHLVLSDVSTLKTLSERHYRAGLAEVIKYGAVLDAELFALLEAKVDGLLKR-DPQLLGR 218 ******************************************************9999986.55***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 +i+r++e+Ka vVe+De+e glRa+LN+GHtlgHa E+l++y+ l HGeaVaiGmv++a+ls++ g+++ lcl|NCBI__GCF_000020385.1:WP_012469650.1 219 VIARCCEIKAWVVEQDEREGGLRAVLNYGHTLGHAFETLSGYRdLVHGEAVAIGMVQAAQLSQREGYCS 287 ********************************************************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340 ++er+++l++++glp++ + +++e l+ +l kDKKn++++++ v+ + iG+ + + ++t +l lcl|NCBI__GCF_000020385.1:WP_012469650.1 288 VGDVERITTLVQQVGLPSDAPV-VATEDLITSLAKDKKNRSGTLQYVCNRGIGSYVFH-QFTPAQLA 352 *********************6.********************************999.77766655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (359 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: 8.34 // [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