Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_013684580.1 ARCVE_RS09615 shikimate kinase
Query= curated2:O29730 (280 letters) >NCBI__GCF_000194625.1:WP_013684580.1 Length = 285 Score = 268 bits (685), Expect = 1e-76 Identities = 140/280 (50%), Positives = 194/280 (69%), Gaps = 4/280 (1%) Query: 4 AKAYAAGTVLNALPTGIGSAFGIEMHTIVKLRPSDELK---VFVNGVERRSIVAERILNS 60 A+AYAAGTV+NAL TGIGSAFGIE+ T V + ++LK +++NGVE + V E+ L Sbjct: 5 ARAYAAGTVINALATGIGSAFGIELETRVSVSFEEDLKHSVLYLNGVEIDASVVEKALRH 64 Query: 61 MDVTAEVIVESEIPGGSGLGSSSAFVNALICAVKKMKGEELNAFEILRSNARFSLEAGIS 120 A V VESEIP SGLGSSSAF+NALI A K +EL+A++IL +NAR SLE GIS Sbjct: 65 FG-KAVVEVESEIPRRSGLGSSSAFMNALITAAFKAFNQELDAYKILTANARTSLECGIS 123 Query: 121 YTGAFDDASASMLGGFVVSDNRKMRLIRTDEFEGYSAVLIPKFSRGKVDWRRLRERASEV 180 YTGAFDDASAS+LGG V+S+N +M+LIR ++ G +LIP ++RG++ R+R + + Sbjct: 124 YTGAFDDASASLLGGLVISNNTRMKLIRWEKISGDVLILIPPWNRGEISLERIRSDVTLI 183 Query: 181 EGAVEAAMRGEYCKAMKLNTEYICKMLGYPLEIAEKGWEKGICCGISGNGPSYVAFGSKN 240 A+ A+ G+YC+AM N+ + C +GYP E E+ + G+C G+SGNGP+YVAFGS Sbjct: 184 GQAIREAIDGKYCRAMLSNSTHYCSAIGYPTEPVEEAIKLGVCAGLSGNGPTYVAFGSSE 243 Query: 241 EMEALAETWGEYGRVYVRRVADEPAEDVVIPTPFFRKLDG 280 +++ L W +YGRV R+++ PAE+V +P F + G Sbjct: 244 DIDELENVWDKYGRVIRTRLSERPAENVKVPDHMFLEFSG 283 Lambda K H 0.318 0.135 0.391 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: 248 Number of extensions: 7 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: 280 Length of database: 285 Length adjustment: 26 Effective length of query: 254 Effective length of database: 259 Effective search space: 65786 Effective search space used: 65786 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: 47 (22.7 bits)
Align candidate WP_013684580.1 ARCVE_RS09615 (shikimate kinase)
to HMM TIGR01920 (shikimate kinase (EC 2.7.1.71))
# 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/TIGR01920.hmm # target sequence database: /tmp/gapView.10655.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01920 [M=266] Accession: TIGR01920 Description: Shik_kin_archae: shikimate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-82 262.4 0.4 2.5e-82 262.2 0.4 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013684580.1 ARCVE_RS09615 shikimate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013684580.1 ARCVE_RS09615 shikimate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.2 0.4 2.5e-82 2.5e-82 1 265 [. 7 260 .. 7 261 .. 0.92 Alignments for each domain: == domain 1 score: 262.2 bits; conditional E-value: 2.5e-82 TIGR01920 1 asggitivnAlatGlGsAfgidLkveakvrlsdgeakvslkvreeeeldpelierilealieklgikeg 69 a++++t++nAlatG+GsAfgi+L++ ++v+ + k s+ + e+d++ ++e++++++g lcl|NCBI__GCF_000194625.1:WP_013684580.1 7 AYAAGTVINALATGIGSAFGIELETRVSVSFEE-DLKHSVLYLNGVEIDAS----VVEKALRHFGKA-- 68 89****************************998.43444444444555555....555566666655.. PP TIGR01920 70 leveveseiPagsGLksSsAlvnAlvlavlkakgeeiddieilrlgaelskeagvsvTGAfDDaaasll 138 veveseiP sGL sSsA++nAl+ a +ka ++e+d+ +il ++a+ s+e g+s+TGAfDDa+asll lcl|NCBI__GCF_000194625.1:WP_013684580.1 69 -VVEVESEIPRRSGLGSSSAFMNALITAAFKAFNQELDAYKILTANARTSLECGISYTGAFDDASASLL 136 .89****************************************************************** PP TIGR01920 139 ggivltdNrkmkilkrdkleeetavvlvpkeeekeeevdlnelrkiskvveeavklAlkGeylkAmvln 207 gg+v+++N +mk+++ +k+++ +++l+p+ ++ e +l+++r ++ +a++ A+ G+y++Am+ n lcl|NCBI__GCF_000194625.1:WP_013684580.1 137 GGLVISNNTRMKLIRWEKISG-DVLILIPPW-NRG-EISLERIRSDVTLIGQAIREAIDGKYCRAMLSN 202 *********************.6*******8.555.9******************************** PP TIGR01920 208 gvlyataLgyplepaekalekGAavaglsGkGPsyvalteepe.eevaealeeageViv 265 + y++a+gyp+ep+e+a++ G ++aglsG+GP yva+++ ++ e+++++ ++g+Vi lcl|NCBI__GCF_000194625.1:WP_013684580.1 203 STHYCSAIGYPTEPVEEAIKLG-VCAGLSGNGPTYVAFGSSEDiDELENVWDKYGRVIR 260 **********************.**********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (266 nodes) Target sequences: 1 (285 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: 00:00:00.01 # Mc/sec: 7.38 // [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