Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_019895269.1 A377_RS0105765 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000384235.1:WP_019895269.1 Length = 365 Score = 438 bits (1127), Expect = e-127 Identities = 216/367 (58%), Positives = 279/367 (76%), Gaps = 5/367 (1%) Query: 73 ASSQAPTVVEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTIS 132 A + P + V+L RSYPI IG GL+ Q + ++ ++HG +VL+VTNTTVAPLYL + Sbjct: 3 ADTAEPVTLGVELAERSYPIVIGQGLMGQSEWVRPYVHGTQVLIVTNTTVAPLYLQQACE 62 Query: 133 ALTDGNPNVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGY 192 A + V++V+LPDGE++KN+E L ++FD AI DR CTFVALGGGVIGDM G+ Sbjct: 63 AFAE----YEVQTVVLPDGERYKNLEILNRIFDVAIAHHFDRHCTFVALGGGVIGDMTGF 118 Query: 193 AAASYLRGVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTL 252 AAASY RGV FIQ+PTT++AQVDSSVGGKTG+NHP GKNMIGAF+QP+ VLID TLNTL Sbjct: 119 AAASYQRGVRFIQMPTTLLAQVDSSVGGKTGVNHPQGKNMIGAFHQPESVLIDVATLNTL 178 Query: 253 PDRELASGLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQD 312 PDREL++GLAEVIKYGLI DA FF+W E +M LLAR+P T AI+RSC NKA +V++D Sbjct: 179 PDRELSAGLAEVIKYGLIGDAPFFDWLEAHMGQLLAREPAILTEAIRRSCANKAAIVAKD 238 Query: 313 EKESGVRATLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRV 372 EKE+G+RA NLGHTFGHA+E G+GYG WLHGEAVAAG + AV MSR LG + + QR+ Sbjct: 239 EKEAGLRALFNLGHTFGHAIEAGMGYGVWLHGEAVAAGMMQAVYMSRLLGDLTHADQQRI 298 Query: 373 QKILQQAKLPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKAL 432 +++++ A+LP +PPE ++ E F ++MA DKKV G++RL+LLK +G TGDY L Sbjct: 299 ERVMRAARLPVTPPEALSTERFLALMAGDKKVQAGRIRLVLLK-QIGEAYVTGDYPDALL 357 Query: 433 DETLRAF 439 +TL ++ Sbjct: 358 TQTLESY 364 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: 409 Number of extensions: 11 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: 442 Length of database: 365 Length adjustment: 31 Effective length of query: 411 Effective length of database: 334 Effective search space: 137274 Effective search space used: 137274 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_019895269.1 A377_RS0105765 (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.7613.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-120 388.4 0.0 1.8e-120 388.2 0.0 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019895269.1 A377_RS0105765 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019895269.1 A377_RS0105765 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.2 0.0 1.8e-120 1.8e-120 1 340 [. 20 358 .. 20 362 .. 0.95 Alignments for each domain: == domain 1 score: 388.2 bits; conditional E-value: 1.8e-120 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g+gl+ + e+++ + ++++++t+ +v+ l+ ++ ea ++ +ev+++v+pdge++K+le lcl|NCBI__GCF_000384235.1:WP_019895269.1 20 YPIVIGQGLMGQS-EWVRPyvHGTQVLIVTNTTVAPLYLQQACEAFAE--YEVQTVVLPDGERYKNLEI 85 6799999999954.6777765569**************8777777755..9****************** PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 ++++ d ++++++r+ + va+GGGv+gD++GF+Aa+y+RG+r++q+PTtlla+vDssvGGKtg+n+p+ lcl|NCBI__GCF_000384235.1:WP_019895269.1 86 LNRIFDVAIAHHFDRHCTFVALGGGVIGDMTGFAAASYQRGVRFIQMPTTLLAQVDSSVGGKTGVNHPQ 154 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGaf+qP+ Vlid+++l+tlp+rel++G+aEviK+gli da +f++le + +ll + e ++l+e lcl|NCBI__GCF_000384235.1:WP_019895269.1 155 GKNMIGAFHQPESVLIDVATLNTLPDRELSAGLAEVIKYGLIGDAPFFDWLEAHMGQLLAR-EPAILTE 222 ********************************************************99975.66***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 +i+rs+ Ka +V++Deke+glRal N+GHt+gHaiEa ++y+ + HGeaVa Gm++++++s+ lg l lcl|NCBI__GCF_000384235.1:WP_019895269.1 223 AIRRSCANKAAIVAKDEKEAGLRALFNLGHTFGHAIEAGMGYGvWLHGEAVAAGMMQAVYMSRLLGDLT 291 ********************************************************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340 + + +r++++++++ lp++ ++ ls+e +l+ + DKK ++++i+lvll++iG+a+++ ++++ l+ lcl|NCBI__GCF_000384235.1:WP_019895269.1 292 HADQQRIERVMRAARLPVTPPEALSTERFLALMAGDKKVQAGRIRLVLLKQIGEAYVTGDYPDALLT 358 ********************************************************99888776555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (365 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: 8.00 // [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