Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_101446022.1 BD749_RS15575 3-dehydroquinate synthase
Query= curated2:A6LEZ7 (353 letters) >NCBI__GCF_002846395.1:WP_101446022.1 Length = 345 Score = 243 bits (620), Expect = 5e-69 Identities = 136/346 (39%), Positives = 204/346 (58%), Gaps = 6/346 (1%) Query: 4 QKVVICKDLKSELQDFLSSLKYDKLFILMDTNTKEKCFPLVEDIPAFQKAPILVMEAGDM 63 + + I +D+ +L+ L +L + K+ +L+D NT C+P V+ P I+ +++G+ Sbjct: 3 ENIYIGRDVLPQLKAALQNLAFSKVAVLVDENTLHHCYPQVK--PYLPAHDIIQIQSGEA 60 Query: 64 NKGFVSLAQIWTALSNEGASRNSLLVNLGGGMITDMGGFAGATFKRGIRTINIPTTLMAS 123 +K + IW +++ R S+LVNLGGG+I DMGGF ATFKRG+ + +PTTL+A Sbjct: 61 HKTLQTCEYIWQRMTDLNLDRWSVLVNLGGGVIGDMGGFCAATFKRGLYFVQVPTTLLAQ 120 Query: 124 VDAAVGGKTGINFNGLKNEVGSFYPPLCVFIDCDFLRTLDRDNILSGYAEMIKHGLISSM 183 VDA+VGGKTGI+F+GLKN +G + P V ID FL TL + + SGYAE+IKH LI+ Sbjct: 121 VDASVGGKTGIDFHGLKNHIGVYKEPHAVLIDPTFLGTLPQRQVKSGYAEIIKHWLIADA 180 Query: 184 ENYASVMLFDIDTMNYSYLNSLVGQSVAVKERIVEEDPKEQGIRKALNFGHTIGHAFES- 242 + + T ++ ++L+ SV +K +VE DP E G RK LNFGHT+GHA ES Sbjct: 181 AAFEEQRHIGLLTEDW---DTLIRHSVGIKAAVVEADPLEGGYRKVLNFGHTVGHAVESY 237 Query: 243 LSFLKMRPILHGHAVAAGIVSELYLSHKLCGFPMEKLSQVVYYIKEYYPALFFDCTDYDT 302 L R +LHG A+A G++ E YLS K +L Q+ ++ Y + D Sbjct: 238 LMDQPGRALLHGEAIAVGMLCEAYLSMKKDLLSKRELEQIETFLVSVYEKVKLTEDDIQA 297 Query: 303 LYELMTHDKKNEGGIINFTLLKNVGDVRINQSVTKEKILESLDFYR 348 + L+ DKKN IN TLL+ +G +Q +T +I ++L +Y+ Sbjct: 298 ITRLVLQDKKNTHSTINCTLLQGIGKAVWDQPITLTEIQDALRYYQ 343 Lambda K H 0.321 0.139 0.402 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: 295 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: 353 Length of database: 345 Length adjustment: 29 Effective length of query: 324 Effective length of database: 316 Effective search space: 102384 Effective search space used: 102384 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_101446022.1 BD749_RS15575 (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.33919.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-103 330.8 0.0 6e-103 330.6 0.0 1.0 1 NCBI__GCF_002846395.1:WP_101446022.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101446022.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 330.6 0.0 6e-103 6e-103 2 338 .. 4 334 .. 3 340 .. 0.95 Alignments for each domain: == domain 1 score: 330.6 bits; conditional E-value: 6e-103 TIGR01357 2 kvkvgegllkklveelaeka.sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklld 73 ++++g+++l +l ++l++ a sk+ v++de++ +++ +++ l + ++++ +++ge +K+l+t++ +++ NCBI__GCF_002846395.1:WP_101446022.1 4 NIYIGRDVLPQLKAALQNLAfSKVAVLVDENTLHHCYPQVKPYLPA----HDIIQIQSGEAHKTLQTCEYIWQ 72 699**************9666***************9999999865....99********************* PP TIGR01357 74 qlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyq 146 ++ + +l+r svlv++GGGv+gD++GF Aat++RG+ +vqvPTtlla+vD+svGGKtgi++++ kN iG + + NCBI__GCF_002846395.1:WP_101446022.1 73 RMTDLNLDRWSVLVNLGGGVIGDMGGFCAATFKRGLYFVQVPTTLLAQVDASVGGKTGIDFHGLKNHIGVYKE 145 ************************************************************************* PP TIGR01357 147 PkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVe 219 P+aVlid+++l tlp+r++++G+aE+iKh liada+ fee +++ l+ e +++li++s+ +Ka vVe NCBI__GCF_002846395.1:WP_101446022.1 146 PHAVLIDPTFLGTLPQRQVKSGYAEIIKHWLIADAAAFEEQRHIGL-LT-----EDWDTLIRHSVGIKAAVVE 212 **************************************99887553.33.....679**************** PP TIGR01357 220 eDekesglRalLNfGHtlgHaiEallkyk....lsHGeaVaiGmvveaklseklgllkaellerlvallkklg 288 +D+ e g R++LNfGHt+gHa+E+ l + l HGea+a+Gm +ea+ls k+ ll++++le+++++l +++ NCBI__GCF_002846395.1:WP_101446022.1 213 ADPLEGGYRKVLNFGHTVGHAVESYLMDQpgraLLHGEAIAVGMLCEAYLSMKKDLLSKRELEQIETFLVSVY 285 ************************988777899**************************************** PP TIGR01357 289 lptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteee 338 ++kl++ +++++++ +l+DKKn +s+i+ ll+ iGka+ ++ +t +e NCBI__GCF_002846395.1:WP_101446022.1 286 EKVKLTE-DDIQAITRLVLQDKKNTHSTINCTLLQGIGKAVWDQPITLTE 334 ******7.9*******************************9887665555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (345 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 16.27 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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