Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_028485656.1 B076_RS0100890 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000483485.1:WP_028485656.1 Length = 361 Score = 430 bits (1105), Expect = e-125 Identities = 217/356 (60%), Positives = 268/356 (75%), Gaps = 7/356 (1%) Query: 83 VDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPNVT 142 VDLG RSYPI+IG +L Q DL++ ++ G +VL+VTNTTVAPLYL++ A D Sbjct: 6 VDLGDRSYPIFIGEDILGQADLVKPYVKGTQVLIVTNTTVAPLYLEQCKQAFAD----FE 61 Query: 143 VESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRGVN 202 VE+VILPDGEQ+KN+E L +VFD I R DR CT VALGGGVIGDM G+AAA++ RGVN Sbjct: 62 VEAVILPDGEQYKNLEVLNQVFDALIGKRFDRSCTLVALGGGVIGDMTGFAAAAFQRGVN 121 Query: 203 FIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASGLA 262 FIQIPTT+++QVDSSVGGKTG+NHPLGKNMIGAF+QPQCV+IDT TLNTL DREL++GLA Sbjct: 122 FIQIPTTLLSQVDSSVGGKTGVNHPLGKNMIGAFHQPQCVIIDTKTLNTLEDRELSAGLA 181 Query: 263 EVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRATL 322 EVIKYGLI D FFEW E N+ ++ R P A AI+RSC NKA +V+ DEKESG+RA Sbjct: 182 EVIKYGLIGDTPFFEWLESNLEAVMQRQPQALAEAIERSCANKARIVALDEKESGMRALF 241 Query: 323 NLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAKLP 382 NLGHTFGHA+E G+GYG+WLHGE V+AGT+ AV MS+ +G +D + R++ I ++AKLP Sbjct: 242 NLGHTFGHAIEAGMGYGKWLHGEGVSAGTMQAVYMSQLMGQLDQADFDRIKAIFERAKLP 301 Query: 383 TSPPET--MTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETL 436 PP M E + +MA DKKV G +RL+LLK +G TGDY + L TL Sbjct: 302 VCPPSVNDMPNEKYLDLMAGDKKVQAGTIRLVLLK-RIGEAYVTGDYPAELLQRTL 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: 431 Number of extensions: 15 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: 361 Length adjustment: 31 Effective length of query: 411 Effective length of database: 330 Effective search space: 135630 Effective search space used: 135630 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_028485656.1 B076_RS0100890 (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.947.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-117 376.9 0.0 5.4e-117 376.8 0.0 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028485656.1 B076_RS0100890 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028485656.1 B076_RS0100890 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 376.8 0.0 5.4e-117 5.4e-117 1 341 [. 13 354 .. 13 357 .. 0.95 Alignments for each domain: == domain 1 score: 376.8 bits; conditional E-value: 5.4e-117 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++ +ge++l ++ + ++ k ++++++t+ +v+ l+ e+ ++a ++ +ev+ +++pdge++K+le+ lcl|NCBI__GCF_000483485.1:WP_028485656.1 13 YPIFIGEDILGQA-DLVKPyvKGTQVLIVTNTTVAPLYLEQCKQAFAD--FEVEAVILPDGEQYKNLEV 78 6788999999854.34444445699*****************999977..******************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 ++++ d+l+ + ++r+ +lva+GGGv+gD++GF+Aa+++RG++++q+PTtll++vDssvGGKtg+n+pl lcl|NCBI__GCF_000483485.1:WP_028485656.1 79 LNQVFDALIGKRFDRSCTLVALGGGVIGDMTGFAAAAFQRGVNFIQIPTTLLSQVDSSVGGKTGVNHPL 147 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGaf+qP+ V+id+k+l+tl +rel++G+aEviK+gli d +fe+le+n +++ +++ +al+e lcl|NCBI__GCF_000483485.1:WP_028485656.1 148 GKNMIGAFHQPQCVIIDTKTLNTLEDRELSAGLAEVIKYGLIGDTPFFEWLESNLEAVMQRQP-QALAE 215 ********************************************************9998655.***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 +i+rs+ Ka++V+ Dekesg+Ral N+GHt+gHaiEa ++y+ + HGe V+ G ++++++s+ +g+l+ lcl|NCBI__GCF_000483485.1:WP_028485656.1 216 AIERSCANKARIVALDEKESGMRALFNLGHTFGHAIEAGMGYGkWLHGEGVSAGTMQAVYMSQLMGQLD 284 ******************************************99************************* PP TIGR01357 274 aellerlvallkklglptklkk..klsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340 + + +r++a++++++lp+ ++ ++ e++l+ + DKK ++++i+lvll++iG+a+++ ++++e l+ lcl|NCBI__GCF_000483485.1:WP_028485656.1 285 QADFDRIKAIFERAKLPVCPPSvnDMPNEKYLDLMAGDKKVQAGTIRLVLLKRIGEAYVTGDYPAELLQ 353 ******************9998888999******************************99888777665 PP TIGR01357 341 e 341 + lcl|NCBI__GCF_000483485.1:WP_028485656.1 354 R 354 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (361 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: 11.44 // [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