Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_011445549.1 SARO_RS09510 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_000013325.1:WP_011445549.1 Length = 369 Score = 261 bits (667), Expect = 2e-74 Identities = 157/348 (45%), Positives = 210/348 (60%), Gaps = 8/348 (2%) Query: 1 MERIVVTLGERSYPITIASGLFNEPASFL-PLKSGEQVMLVTNETLAPLYLDKVRGVLEQ 59 M I V + Y + I +G+ P ++V +VT+E +A + + V + Sbjct: 1 MAVIPVAIAGAPYEVRIEAGVLARAGEHCRPFLRKDRVAIVTDEHVAAEWRETVTASFDS 60 Query: 60 AGVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQ 119 GV + ++LP GE KS L + LL++ R +VALGGGV+GDLTGFAA+ + Sbjct: 61 VGVRSEWLVLPAGESTKSWEHLARLVDWLLEQEVERKDRIVALGGGVIGDLTGFAASIVK 120 Query: 120 RGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELA 179 RG FIQ+PTTLL+QVDSSVGGKTA+N P GKN++GAF+QPA V+ D L TLP R++ Sbjct: 121 RGCGFIQIPTTLLAQVDSSVGGKTAINTPAGKNLVGAFHQPALVLADPLALDTLPLRDVR 180 Query: 180 SGLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERE-TG 238 +G AEV+KYG+I D FF W E N LL D A I KA +VAADE+E G Sbjct: 181 AGYAEVVKYGLIDDAPFFEWCEANGAKLLAGDLAARETAIAHSVAAKARIVAADEKEIAG 240 Query: 239 LRALLNLGHTFGHAIEAEMGYGNWL-HGEAVAAGMVMAARTSERLGQFSSAETQRIITLL 297 +RALLNLGHTFGHA+EAE G+ + L HGE VA GMV+AAR S R G S + +R+ + Sbjct: 241 IRALLNLGHTFGHALEAETGFTDRLHHGEGVALGMVLAARFSARQGLMSRQDAERVARHV 300 Query: 298 KRAGLPVNGPREM----SAQAYLPHMLRDKKVLAGEMRLILPLAIGKS 341 + GLP RE+ + HML DKK+ AG + +L IG++ Sbjct: 301 EAVGLPAT-LRELGLSCDGRRLADHMLHDKKMDAGTLPFLLMRGIGQT 347 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: 332 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: 369 Length adjustment: 30 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 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_011445549.1 SARO_RS09510 (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.1936.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-113 364.5 0.0 3.2e-113 364.4 0.0 1.0 1 lcl|NCBI__GCF_000013325.1:WP_011445549.1 SARO_RS09510 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013325.1:WP_011445549.1 SARO_RS09510 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 364.4 0.0 3.2e-113 3.2e-113 1 339 [. 13 358 .. 13 363 .. 0.97 Alignments for each domain: == domain 1 score: 364.4 bits; conditional E-value: 3.2e-113 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y+v ++ g+l+++ e+++ +++++ ++tde+v+++ e++ + s gv+ ++lv+p+ge++Ks+e+ lcl|NCBI__GCF_000013325.1:WP_011445549.1 13 YEVRIEAGVLARAGEHCRPflRKDRVAIVTDEHVAAEWRETVTASFDSVGVRSEWLVLPAGESTKSWEH 81 6899************99987779********************************************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 +a+l+d+lle+++erk+ +va+GGGv+gDl+GF+A++ +RG ++q+PTtlla+vDssvGGKt+in+p lcl|NCBI__GCF_000013325.1:WP_011445549.1 82 LARLVDWLLEQEVERKDRIVALGGGVIGDLTGFAASIVKRGCGFIQIPTTLLAQVDSSVGGKTAINTPA 150 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNl+Gaf+qP +Vl d+ l tlp r +r+G+aEv+K+gli da +fe++e n ++ll +l+a e+ lcl|NCBI__GCF_000013325.1:WP_011445549.1 151 GKNLVGAFHQPALVLADPLALDTLPLRDVRAGYAEVVKYGLIDDAPFFEWCEANGAKLLA-GDLAARET 218 ******************************************************999886.5789**** PP TIGR01357 206 likrsievKaevVeeDekes.glRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgl 271 +i++s+ Ka++V++Deke g+RalLN+GHt+gHa+Ea+++++ l+HGe Va+Gmv++a++s + gl lcl|NCBI__GCF_000013325.1:WP_011445549.1 219 AIAHSVAAKARIVAADEKEIaGIRALLNLGHTFGHALEAETGFTdrLHHGEGVALGMVLAARFSARQGL 287 *******************88**********************999*********************** PP TIGR01357 272 lkaellerlvallkklglptklkk...klsveellkallkDKKnegskiklvlleeiGkaalasevtee 337 ++++++er+++ ++++glp +l++ + + l++++l+DKK++++++ + l++ iG+++la++v+ + lcl|NCBI__GCF_000013325.1:WP_011445549.1 288 MSRQDAERVARHVEAVGLPATLRElglSCDGRRLADHMLHDKKMDAGTLPFLLMRGIGQTFLAKDVDLT 356 ************************99889999******************************9988766 PP TIGR01357 338 el 339 e+ lcl|NCBI__GCF_000013325.1:WP_011445549.1 357 EV 358 65 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (369 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: 7.53 // [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