Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_011779864.1 MVAN_RS13295 3-dehydroquinate synthase
Query= BRENDA::P9WPX9 (362 letters) >NCBI__GCF_000015305.1:WP_011779864.1 Length = 359 Score = 593 bits (1529), Expect = e-174 Identities = 294/353 (83%), Positives = 321/353 (90%) Query: 7 PVTVQVAVDPPYPVVIGTGLLDELEDLLADRHKVAVVHQPGLAETAEEIRKRLAGKGVDA 66 PVTV+V DPPYPV+IGTGLLD+L +L RHKVA++HQP L +TAE IR LA KG+DA Sbjct: 4 PVTVEVRTDPPYPVIIGTGLLDDLARVLDGRHKVAILHQPTLTQTAEVIRNHLADKGIDA 63 Query: 67 HRIEIPDAEAGKDLPVVGFIWEVLGRIGIGRKDALVSLGGGAATDVAGFAAATWLRGVSI 126 HRIEIPDAE GK+LPVVGFIWEVLGRIG+GRKDA+VSLGGGAATDVAGFAAATWLRGV I Sbjct: 64 HRIEIPDAEGGKELPVVGFIWEVLGRIGLGRKDAIVSLGGGAATDVAGFAAATWLRGVDI 123 Query: 127 VHLPTTLLGMVDAAVGGKTGINTDAGKNLVGAFHQPLAVLVDLATLQTLPRDEMICGMAE 186 VH+PTTLLGMVDAAVGGKTGINTDAGKNLVGAFHQP AVL+DLATL++LPR+E++ GMAE Sbjct: 124 VHVPTTLLGMVDAAVGGKTGINTDAGKNLVGAFHQPAAVLIDLATLESLPRNEIVAGMAE 183 Query: 187 VVKAGFIADPVILDLIEADPQAALDPAGDVLPELIRRAITVKAEVVAADEKESELREILN 246 +VKAGFIADPVILD+IEADPQAALDP G VLPELIRRA+ VKAEVVAADEKES+LREILN Sbjct: 184 IVKAGFIADPVILDMIEADPQAALDPTGQVLPELIRRAVVVKAEVVAADEKESQLREILN 243 Query: 247 YGHTLGHAIERRERYRWRHGAAVSVGLVFAAELARLAGRLDDATAQRHRTILSSLGLPVS 306 YGHTL HAIERRERY+WRHGAAVSVGLVFAAEL RLAGRLDDATA+RHR IL SLGLPV+ Sbjct: 244 YGHTLAHAIERRERYQWRHGAAVSVGLVFAAELGRLAGRLDDATAERHRAILISLGLPVT 303 Query: 307 YDPDALPQLLEIMAGDKKTRAGVLRFVVLDGLAKPGRMVGPDPGLLVTAYAGV 359 YD DALPQL+E M GDKKTRAGVLRFVVLDGL KPGR+ GPDP LL AYA V Sbjct: 304 YDADALPQLMEAMLGDKKTRAGVLRFVVLDGLGKPGRLEGPDPSLLAAAYAEV 356 Lambda K H 0.320 0.139 0.406 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: 625 Number of extensions: 25 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: 362 Length of database: 359 Length adjustment: 29 Effective length of query: 333 Effective length of database: 330 Effective search space: 109890 Effective search space used: 109890 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_011779864.1 MVAN_RS13295 (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.30052.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-107 343.6 0.0 7.6e-107 343.4 0.0 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011779864.1 MVAN_RS13295 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011779864.1 MVAN_RS13295 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 343.4 0.0 7.6e-107 7.6e-107 1 329 [. 15 339 .. 15 351 .. 0.95 Alignments for each domain: == domain 1 score: 343.4 bits; conditional E-value: 7.6e-107 TIGR01357 1 ykvkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletva 69 y+v++g+gll+ l++ l+ ++k+ ++++ ++ ++ ae ++++l+++g+ ++ + +pd+e K+l +v lcl|NCBI__GCF_000015305.1:WP_011779864.1 15 YPVIIGTGLLDDLARVLDG-RHKVAILHQPTL-TQTAEVIRNHLADKGIDAHRIEIPDAEGGKELPVVG 81 689*************997.445666655555.55779******************************* PP TIGR01357 70 klldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgk 138 +++ l + +l rk+++v++GGG+ +D+aGF+Aat+lRG+++v+vPTtll+mvD++vGGKtgin++ gk lcl|NCBI__GCF_000015305.1:WP_011779864.1 82 FIWEVLGRIGLGRKDAIVSLGGGAATDVAGFAAATWLRGVDIVHVPTTLLGMVDAAVGGKTGINTDAGK 150 ********************************************************************* PP TIGR01357 139 NliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeeli 207 Nl+Gaf+qP aVlidl++le+lp++e+ +GmaE++K g+iad +++ +e ++ l+ + ++l eli lcl|NCBI__GCF_000015305.1:WP_011779864.1 151 NLVGAFHQPAAVLIDLATLESLPRNEIVAGMAEIVKAGFIADPVILDMIEADPQAALDP-TGQVLPELI 218 ****************************************************9998875.67******* PP TIGR01357 208 krsievKaevVeeDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkael 276 +r++ vKaevV++Dekes lR++LN+GHtl+HaiE y+++HG aV++G+v++a+l + +g l+ lcl|NCBI__GCF_000015305.1:WP_011779864.1 219 RRAVVVKAEVVAADEKESQLREILNYGHTLAHAIERRERYQWRHGAAVSVGLVFAAELGRLAGRLDDAT 287 ********************************************************************* PP TIGR01357 277 lerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaa 329 +er++a+l +lglp+++ ++ +l++a+l DKK++++ +++v+l+ +Gk+ lcl|NCBI__GCF_000015305.1:WP_011779864.1 288 AERHRAILISLGLPVTYDA-DALPQLMEAMLGDKKTRAGVLRFVVLDGLGKPG 339 ******************7.99****************************975 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: 11.66 // [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