Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_010959692.1 MCA_RS01630 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000008325.1:WP_010959692.1 Length = 359 Score = 426 bits (1096), Expect = e-124 Identities = 216/361 (59%), Positives = 262/361 (72%), Gaps = 5/361 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 + V+LG R YPIYIG GLL PDL+Q H+ G +VLVVTN VAPLYLD+ +++L + Sbjct: 4 LHVELGERGYPIYIGRGLLGHPDLIQAHLPGGQVLVVTNEVVAPLYLDRMLASLAGKDTG 63 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 SV+LPDGE K +++ M VFD + R R VALGGGVIGD+ G+AAA Y RG Sbjct: 64 ----SVVLPDGEAHKTLDSAMAVFDALLARRFGRNAAIVALGGGVIGDLAGFAAACYQRG 119 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 V FIQ+PTT+++QVDSSVGGKT +NHP GKNMIGAFYQP+CVL DTDTL+TLPDREL++G Sbjct: 120 VPFIQVPTTLLSQVDSSVGGKTAVNHPRGKNMIGAFYQPRCVLADTDTLDTLPDRELSAG 179 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 LAEVIKYG IRD EF W E N+ LL RDP A YAI+RSC NKA++V++DE E+GVRA Sbjct: 180 LAEVIKYGFIRDPEFLAWLEANVERLLQRDPEALAYAIERSCINKAEIVAEDETETGVRA 239 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 TLNLGHTFGHA+ETG+GYG LHGEAVA G A D+SRRLGWI D V RV ++L++A+ Sbjct: 240 TLNLGHTFGHAIETGMGYGVCLHGEAVAIGMCQAADLSRRLGWIGDDEVARVIRLLERAR 299 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRAFS 440 LP PP + + F MAVDKK DG LRL+LLK SLG D L TL + Sbjct: 300 LPVVPPRELDADAFLEHMAVDKKNVDGGLRLVLLK-SLGEATLPVAVDAGLLRATLECYG 358 Query: 441 K 441 + Sbjct: 359 R 359 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: 424 Number of extensions: 12 Number of successful extensions: 2 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: 359 Length adjustment: 31 Effective length of query: 411 Effective length of database: 328 Effective search space: 134808 Effective search space used: 134808 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_010959692.1 MCA_RS01630 (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.24728.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-118 379.4 0.0 1e-117 379.2 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010959692.1 MCA_RS01630 3-dehydroquinate syn Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010959692.1 MCA_RS01630 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.2 0.0 1e-117 1e-117 1 332 [. 13 343 .. 13 354 .. 0.94 Alignments for each domain: == domain 1 score: 379.2 bits; conditional E-value: 1e-117 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g+gll + ++ +++v+t+e v+ l+ +++++ l+ g + +v+pdge +K+l++ lcl|NCBI__GCF_000008325.1:WP_010959692.1 13 YPIYIGRGLLGHPD-LIQAhlPGGQVLVVTNEVVAPLYLDRMLASLA--GKDTGSVVLPDGEAHKTLDS 78 56888888888553.3332233489***************9999994..89****************** PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 + ++ d+ll++ + r+ ++va+GGGv+gDlaGF+Aa y+RG++++qvPTtll++vDssvGGKt++n+p+ lcl|NCBI__GCF_000008325.1:WP_010959692.1 79 AMAVFDALLARRFGRNAAIVALGGGVIGDLAGFAAACYQRGVPFIQVPTTLLSQVDSSVGGKTAVNHPR 147 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGafyqP+ Vl d+++l tlp+rel++G+aEviK+g+i d e++++le n + ll++ + eal+ lcl|NCBI__GCF_000008325.1:WP_010959692.1 148 GKNMIGAFYQPRCVLADTDTLDTLPDRELSAGLAEVIKYGFIRDPEFLAWLEANVERLLQR-DPEALAY 215 ********************************************************99986.55***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 +i+rs+ Kae+V+eDe+e+g+Ra+LN+GHt+gHaiE+ ++y+ + HGeaVaiGm ++a ls++lg + lcl|NCBI__GCF_000008325.1:WP_010959692.1 216 AIERSCINKAEIVAEDETETGVRATLNLGHTFGHAIETGMGYGvCLHGEAVAIGMCQAADLSRRLGWIG 284 *******************************************99************************ PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalas 332 +++ r+++ll+++ lp+ +++l+++++l+++ DKKn ++ ++lvll+++G+a+l lcl|NCBI__GCF_000008325.1:WP_010959692.1 285 DDEVARVIRLLERARLPVVPPRELDADAFLEHMAVDKKNVDGGLRLVLLKSLGEATLPV 343 ******************************************************99874 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: 7.28 // [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