Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_029911752.1 P166_RS0109480 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000711315.1:WP_029911752.1 Length = 360 Score = 437 bits (1124), Expect = e-127 Identities = 215/358 (60%), Positives = 277/358 (77%), Gaps = 7/358 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 + VDLG RSYPI+IG L++ P+L++ ++ G +VL+VTNTTVAPLYL++ +D Sbjct: 4 LNVDLGERSYPIFIGQQLINDPELIRPYVQGTQVLIVTNTTVAPLYLEQVEKTFSDYEVR 63 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 V V LPDGE++K++E L K+FD A+ +R DR+CTFVALGGGV+GDM G+AAA+Y RG Sbjct: 64 VAV----LPDGEEYKSLEVLNKIFDVALANRFDRKCTFVALGGGVVGDMTGFAAAAYQRG 119 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 VNFIQIPTT+++QVDSSVGGKTG+NHP GKNMIGAF+QP+CV+IDTD L+TL DREL++G Sbjct: 120 VNFIQIPTTLLSQVDSSVGGKTGVNHPFGKNMIGAFHQPECVVIDTDVLSTLEDRELSAG 179 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 LAEVIKYGLI D FFEW EQ M LLARDP A T AI+RSC+NKA +V+ DEKESG+RA Sbjct: 180 LAEVIKYGLISDYPFFEWLEQYMDELLARDPVALTEAIERSCQNKAKIVALDEKESGLRA 239 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 NLGHTFGHA+E G+GYG+WLHGE V+AG++ A+ +S+ +G I + R++KI + AK Sbjct: 240 LFNLGHTFGHAIEAGMGYGKWLHGEGVSAGSMQAIYLSKLMGNISQADFDRIEKIFKHAK 299 Query: 381 LPTSPPET--MTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETL 436 LPT PP M+ + F +MA DKKV G +RL+LLK +G TGDY Q L++TL Sbjct: 300 LPTLPPSVNEMSNQRFLDLMAGDKKVQAGHIRLVLLK-RIGEAYVTGDYSQSMLEQTL 356 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: 429 Number of extensions: 10 Number of successful extensions: 4 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: 360 Length adjustment: 31 Effective length of query: 411 Effective length of database: 329 Effective search space: 135219 Effective search space used: 135219 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_029911752.1 P166_RS0109480 (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.7471.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-116 375.9 0.0 1.1e-116 375.7 0.0 1.0 1 lcl|NCBI__GCF_000711315.1:WP_029911752.1 P166_RS0109480 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_029911752.1 P166_RS0109480 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.7 0.0 1.1e-116 1.1e-116 2 342 .. 14 355 .. 13 357 .. 0.95 Alignments for each domain: == domain 1 score: 375.7 bits; conditional E-value: 1.1e-116 TIGR01357 2 kvkvgegllk..klveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsle 66 ++ +g++l++ +l ++ + ++++++t+ +v+ l+ e++e++ ++ +ev v+v+pdgee+Ksle lcl|NCBI__GCF_000711315.1:WP_029911752.1 14 PIFIGQQLINdpEL---IRPyvQGTQVLIVTNTTVAPLYLEQVEKTFSD--YEVRVAVLPDGEEYKSLE 77 67788888873333...333434699********************987..9***************** PP TIGR01357 67 tvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlp 135 +++k+ d l++ ++rk + va+GGGvvgD++GF+Aa+y+RG++++q+PTtll++vDssvGGKtg+n+p lcl|NCBI__GCF_000711315.1:WP_029911752.1 78 VLNKIFDVALANRFDRKCTFVALGGGVVGDMTGFAAAAYQRGVNFIQIPTTLLSQVDSSVGGKTGVNHP 146 ********************************************************************* PP TIGR01357 136 lgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleale 204 gkN+iGaf+qP+ V+id++vl+tl +rel++G+aEviK+gli+d +fe+le+ ++ll ++ al+ lcl|NCBI__GCF_000711315.1:WP_029911752.1 147 FGKNMIGAFHQPECVVIDTDVLSTLEDRELSAGLAEVIKYGLISDYPFFEWLEQYMDELLARDP-VALT 214 *********************************************************9998655.99** PP TIGR01357 205 elikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgll 272 e+i+rs++ Ka++V+ DekesglRal N+GHt+gHaiEa ++y+ + HGe V+ G +++++ls+ +g++ lcl|NCBI__GCF_000711315.1:WP_029911752.1 215 EAIERSCQNKAKIVALDEKESGLRALFNLGHTFGHAIEAGMGYGkWLHGEGVSAGSMQAIYLSKLMGNI 283 *******************************************99************************ PP TIGR01357 273 kaellerlvallkklglptklkk..klsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339 ++ + +r+++++k+++lpt ++ ++s + +l+ + DKK ++++i+lvll++iG+a+++ ++++++l lcl|NCBI__GCF_000711315.1:WP_029911752.1 284 SQADFDRIEKIFKHAKLPTLPPSvnEMSNQRFLDLMAGDKKVQAGHIRLVLLKRIGEAYVTGDYSQSML 352 *******************9998889999*******************************999988887 PP TIGR01357 340 lea 342 ++ lcl|NCBI__GCF_000711315.1:WP_029911752.1 353 EQT 355 765 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.28 // [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