Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_072909552.1 BUB13_RS14845 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_900142125.1:WP_072909552.1 Length = 360 Score = 324 bits (831), Expect = 2e-93 Identities = 169/357 (47%), Positives = 237/357 (66%), Gaps = 2/357 (0%) Query: 1 MERIVVTLGERSYPITIASGLFNEPAS-FLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQ 59 +E+I V LG RSYPI I + + L ++ +V +V+ +A LY + L++ Sbjct: 2 VEKITVPLGSRSYPIIIGADVLPSIGERLLEIEFPRRVAVVSTAVVAKLYGGIIGKSLQR 61 Query: 60 AGVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQ 119 AG + LPDGE++K+L L++++ L++ R T L+ALGGGV+GD+ GFAAA++ Sbjct: 62 AGFEFIEINLPDGEEHKNLQTLESIYDELIKNNFDRGTGLIALGGGVIGDMVGFAAATFL 121 Query: 120 RGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELA 179 RG+ F QVPTTLL+QVDSSVGGKTAVNHPLGKN+IGAFYQP V++D+ L +L PRE++ Sbjct: 122 RGIPFAQVPTTLLAQVDSSVGGKTAVNHPLGKNLIGAFYQPEIVLIDVATLSSLEPREVS 181 Query: 180 SGLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGL 239 +G+AEV+KYG+I D FF+WLE+ AL D A+ +++ C++KA++V DE+E + Sbjct: 182 AGMAEVVKYGVIKDKTFFSWLEKEYKALQNRDTLALIEVVKKSCQIKADIVEVDEKEGSI 241 Query: 240 RALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKR 299 RA LN GHTFGHA+EA GYG W HGEAV+ GMV+AA+ + G S + QRII LL + Sbjct: 242 RAFLNYGHTFGHAVEALSGYGQWKHGEAVSVGMVVAAKIAAERGLCSVEDVQRIIDLLLK 301 Query: 300 AGLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAI 356 LPV P+ S Q Y+ M RDKKV G + ++L IGK ++ E V + I Sbjct: 302 LDLPVEPPKH-SLQDYVTAMQRDKKVKQGTLTMVLNEGIGKVQLTKIPDIESVFSTI 357 Lambda K H 0.320 0.136 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: 295 Number of extensions: 14 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: 362 Length of database: 360 Length adjustment: 29 Effective length of query: 333 Effective length of database: 331 Effective search space: 110223 Effective search space used: 110223 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_072909552.1 BUB13_RS14845 (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.28203.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-121 392.0 0.1 1.5e-121 391.8 0.1 1.0 1 lcl|NCBI__GCF_900142125.1:WP_072909552.1 BUB13_RS14845 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900142125.1:WP_072909552.1 BUB13_RS14845 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 391.8 0.1 1.5e-121 1.5e-121 1 334 [. 14 347 .. 14 355 .. 0.97 Alignments for each domain: == domain 1 score: 391.8 bits; conditional E-value: 1.5e-121 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g ++l ++ e l e + +++ v+++ v+kl++ + + l+++g+e +++ +pdgee+K+l+t lcl|NCBI__GCF_900142125.1:WP_072909552.1 14 YPIIIGADVLPSIGERLLEieFPRRVAVVSTAVVAKLYGGIIGKSLQRAGFEFIEINLPDGEEHKNLQT 82 689999*****9999999965569********************************************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 +++++d+l++++++r + l+a+GGGv+gD++GF+Aat+lRGi++ qvPTtlla+vDssvGGKt++n+pl lcl|NCBI__GCF_900142125.1:WP_072909552.1 83 LESIYDELIKNNFDRGTGLIALGGGVIGDMVGFAAATFLRGIPFAQVPTTLLAQVDSSVGGKTAVNHPL 151 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNliGafyqP+ Vlid+++l++l re+++GmaEv+K+g+i+d+ +f++lek k+l+++ ++ al e lcl|NCBI__GCF_900142125.1:WP_072909552.1 152 GKNLIGAFYQPEIVLIDVATLSSLEPREVSAGMAEVVKYGVIKDKTFFSWLEKEYKALQNR-DTLALIE 219 *******************************************************999986.559999* PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 ++k+s+++Ka++Ve Deke ++Ra+LN+GHt+gHa+Eal++y+ ++HGeaV++Gmvv+ak++ + gl++ lcl|NCBI__GCF_900142125.1:WP_072909552.1 220 VVKKSCQIKADIVEVDEKEGSIRAFLNYGHTFGHAVEALSGYGqWKHGEAVSVGMVVAAKIAAERGLCS 288 ******************************************99************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasev 334 e+++r+++ll kl lp++ +k +s++ ++ a+++DKK +++++++vl e iGk++l+ ++ lcl|NCBI__GCF_900142125.1:WP_072909552.1 289 VEDVQRIIDLLLKLDLPVEPPK-HSLQDYVTAMQRDKKVKQGTLTMVLNEGIGKVQLT-KI 347 *********************7.*******************************9987.54 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (360 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.48 // [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