Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_012502008.1 CPAR_RS03885 3-dehydroquinate synthase
Query= BRENDA::Q3M4V2 (363 letters) >NCBI__GCF_000020505.1:WP_012502008.1 Length = 367 Score = 255 bits (651), Expect = 1e-72 Identities = 146/334 (43%), Positives = 207/334 (61%), Gaps = 9/334 (2%) Query: 16 IAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGFQVASYCLPAGE 75 I + +D IG+ LGKK +++ + K +G + S++ GF+ +PA E Sbjct: 8 IIVRTPVIDSIGELYETRGLGKKSVVLFDENTRKLYGDKIIASMQRQGFRTVELVVPARE 67 Query: 76 RYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGINVVQVPTTLLA 135 K++++ KLY +E ++RS ++ +GGGV+GD+ G+ AA++ RGI VVQ+PTTLLA Sbjct: 68 TSKSVSTAWKLYGQMIETDVDRSWNLLCVGGGVVGDLGGYIAASYYRGIPVVQLPTTLLA 127 Query: 136 MVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGMAEVIKYGVIWD 195 M DS+IGGK +NHP GKNLIG FH P VLIDP L+TLP RE GMAEV+KYG I D Sbjct: 128 MTDSSIGGKVAINHPLGKNLIGYFHMPALVLIDPAFLRTLPAREIFGGMAEVVKYGFIAD 187 Query: 196 AELFNQLEQSKRLDQL-RYIKPELMDAILTRSCQAKADVVGKDEKE-GGLRAILNYGHTV 253 + F+ L ++ D++ R +P + DA+ +RS KADVV KD +E GLRA LN+GHT Sbjct: 188 RKFFDML--AEHWDEVTRLEEPWISDAV-SRSAFTKADVVEKDFRETSGLRATLNFGHTF 244 Query: 254 GHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIEKAGLPTKLP-- 311 H +E + YR L+HGEAV IGM A ++ LG +A+ + ALI + P L Sbjct: 245 AHGLEKMAEYRNLRHGEAVTIGMACALYLSYRLGFLAEAELNEGLALIARFRFPRNLVNK 304 Query: 312 --AGLDIEGIIEALQLDKKVKDGKVRFVLPTQIG 343 LD+E + +A+ DKK D ++RFVL +IG Sbjct: 305 RFISLDLEELFDAMHSDKKKIDKQLRFVLLDRIG 338 Lambda K H 0.319 0.136 0.388 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: 334 Number of extensions: 23 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: 363 Length of database: 367 Length adjustment: 30 Effective length of query: 333 Effective length of database: 337 Effective search space: 112221 Effective search space used: 112221 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_012502008.1 CPAR_RS03885 (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.5058.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-121 389.6 0.0 7.4e-121 389.5 0.0 1.0 1 lcl|NCBI__GCF_000020505.1:WP_012502008.1 CPAR_RS03885 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020505.1:WP_012502008.1 CPAR_RS03885 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.5 0.0 7.4e-121 7.4e-121 2 342 .. 7 355 .. 6 357 .. 0.97 Alignments for each domain: == domain 1 score: 389.5 bits; conditional E-value: 7.4e-121 TIGR01357 2 kvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 +++v++ +++++ e +++ +k vv++de+++kl+++k+ + +++g+++ +lvvp++e+sKs++t+ lcl|NCBI__GCF_000020505.1:WP_012502008.1 7 HIIVRTPVIDSIGELYETrgLGKKSVVLFDENTRKLYGDKIIASMQRQGFRTVELVVPARETSKSVSTA 75 689999*******9999954459**************99999999999********************* PP TIGR01357 69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137 +kl+ q++e +++r++ l+++GGGvvgDl+G++Aa+y+RGi++vq+PTtllam Dss+GGK++in+plg lcl|NCBI__GCF_000020505.1:WP_012502008.1 76 WKLYGQMIETDVDRSWNLLCVGGGVVGDLGGYIAASYYRGIPVVQLPTTLLAMTDSSIGGKVAINHPLG 144 ********************************************************************* PP TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206 kNliG f++P +Vlid+++l+tlp re+ GmaEv+K+g+iad+++f+ l ++++++++l e+ +++++ lcl|NCBI__GCF_000020505.1:WP_012502008.1 145 KNLIGYFHMPALVLIDPAFLRTLPAREIFGGMAEVVKYGFIADRKFFDMLAEHWDEVTRL-EEPWISDA 212 *******************************************************99986.66****** PP TIGR01357 207 ikrsievKaevVeeDekes.glRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 ++rs +Ka+vVe+D +e+ glRa+LNfGHt++H++E++++y+ l+HGeaV+iGm+++++ls +lg+l lcl|NCBI__GCF_000020505.1:WP_012502008.1 213 VSRSAFTKADVVEKDFRETsGLRATLNFGHTFAHGLEKMAEYRnLRHGEAVTIGMACALYLSYRLGFLA 281 ******************99************************************************* PP TIGR01357 274 aellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalas.evtee 337 + +l++ +al+ ++ p++l + +l++eel++a+ +DKK+ ++++++vll++iG+a+l++ ev++ lcl|NCBI__GCF_000020505.1:WP_012502008.1 282 EAELNEGLALIARFRFPRNLVNkrfiSLDLEELFDAMHSDKKKIDKQLRFVLLDRIGHAFLHDrEVPKA 350 *******************99889999***********************************9899998 PP TIGR01357 338 ellea 342 ++l+a lcl|NCBI__GCF_000020505.1:WP_012502008.1 351 DVLHA 355 88876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (367 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