Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_011815043.1 HHAL_RS11405 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000015585.1:WP_011815043.1 Length = 354 Score = 381 bits (978), Expect = e-110 Identities = 195/354 (55%), Positives = 254/354 (71%), Gaps = 9/354 (2%) Query: 83 VDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPNVT 142 V+LG RSYPIYIG G+LDQ +L H+ R L+V+N TVAPLY ++ P Sbjct: 6 VELGERSYPIYIGDGVLDQ-GVLAEHLVADRALLVSNETVAPLYAERLAV------PGAE 58 Query: 143 VESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRGVN 202 V+SV L DGE++K ++T +V+D IE R DR T +ALGGGV+GDM G+ AA+Y RGV Sbjct: 59 VQSVTLHDGERYKTLQTCEQVYDALIEGRFDRSATVIALGGGVVGDMAGFCAATYQRGVG 118 Query: 203 FIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASGLA 262 +IQ+PTT++AQVDSSVGGKTG+NHP GKNMIGAF+QP+ V+ DT L TLP+RE +GLA Sbjct: 119 YIQVPTTLLAQVDSSVGGKTGVNHPRGKNMIGAFHQPRAVVADTGVLATLPEREYNAGLA 178 Query: 263 EVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRATL 322 EV+KYGLIRD FF+W E ++ L RDP A +A+ SC NKA+VV+ DE+E+G RA L Sbjct: 179 EVVKYGLIRDPAFFDWLEAHVDALRRRDPEALAHAVAESCRNKAEVVAADEREAGERALL 238 Query: 323 NLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAKLP 382 NLGHTFGHA+ET Y WLHGEAVAAG VMA MS RLGW+ + ++R +L+ LP Sbjct: 239 NLGHTFGHAIETYTDYCTWLHGEAVAAGMVMAARMSVRLGWLQRNGLERTIALLEAFGLP 298 Query: 383 TSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETL 436 T PP + F+ +M+VDKK G+LRL+LL+ S+G+ V TG++ +AL +TL Sbjct: 299 TRPP-AIPEARFRELMSVDKKNRGGQLRLVLLR-SVGDAVVTGEFAPEALTDTL 350 Lambda K H 0.318 0.133 0.385 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: 383 Number of extensions: 8 Number of successful extensions: 5 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: 442 Length of database: 354 Length adjustment: 31 Effective length of query: 411 Effective length of database: 323 Effective search space: 132753 Effective search space used: 132753 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_011815043.1 HHAL_RS11405 (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.16966.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-120 388.7 0.0 1.5e-120 388.5 0.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011815043.1 HHAL_RS11405 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011815043.1 HHAL_RS11405 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.5 0.0 1.5e-120 1.5e-120 1 339 [. 13 346 .. 13 351 .. 0.95 Alignments for each domain: == domain 1 score: 388.5 bits; conditional E-value: 1.5e-120 TIGR01357 1 ykvkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletva 69 y++++g+g+l++ v + + a++++++++e+v+ l+ae+l+ g+ev+ ++++dge++K+l+t++ lcl|NCBI__GCF_000015585.1:WP_011815043.1 13 YPIYIGDGVLDQGVLAEHLVADRALLVSNETVAPLYAERLAVP----GAEVQSVTLHDGERYKTLQTCE 77 6899******9655443335799*************9988654....678******************* PP TIGR01357 70 klldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgk 138 +++d+l+e ++r+ +++a+GGGvvgD+aGF Aaty+RG+ ++qvPTtlla+vDssvGGKtg+n+p+gk lcl|NCBI__GCF_000015585.1:WP_011815043.1 78 QVYDALIEGRFDRSATVIALGGGVVGDMAGFCAATYQRGVGYIQVPTTLLAQVDSSVGGKTGVNHPRGK 146 ********************************************************************* PP TIGR01357 139 NliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeeli 207 N+iGaf+qP+aV+ d+ vl+tlpere+ +G+aEv+K+gli d ++f++le + ++l+++ + eal++++ lcl|NCBI__GCF_000015585.1:WP_011815043.1 147 NMIGAFHQPRAVVADTGVLATLPEREYNAGLAEVVKYGLIRDPAFFDWLEAHVDALRRR-DPEALAHAV 214 ******************************************************99986.55******* PP TIGR01357 208 krsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkae 275 ++s++ KaevV++De+e+g RalLN+GHt+gHaiE+ ++y + HGeaVa Gmv++a++s +lg l+++ lcl|NCBI__GCF_000015585.1:WP_011815043.1 215 AESCRNKAEVVAADEREAGERALLNLGHTFGHAIETYTDYCtWLHGEAVAAGMVMAARMSVRLGWLQRN 283 ****************************************99*************************** PP TIGR01357 276 llerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339 ler++all+++glpt+ + + + + ++ DKKn+g++++lvll+++G+a+++ e+ e+l lcl|NCBI__GCF_000015585.1:WP_011815043.1 284 GLERTIALLEAFGLPTRPPA-IPEARFRELMSVDKKNRGGQLRLVLLRSVGDAVVTGEFAPEAL 346 *******************7.9999****************************99988877665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (354 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: 9.58 // [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