Align Shikimate kinase; SK; EC 2.7.1.71 (characterized)
to candidate WP_011869103.1 MMARC5_RS06880 shikimate kinase
Query= SwissProt::Q58835 (282 letters) >NCBI__GCF_000016125.1:WP_011869103.1 Length = 283 Score = 372 bits (955), Expect = e-108 Identities = 179/281 (63%), Positives = 233/281 (82%) Query: 1 MEGKAYALASGTIINAIATGKGSAFGLDLKVYAKVKLIDDGKNKIEGKVLDNPNIKPNLI 60 M A +L SGTIINAIATG GSAFG+DLK+ A V+L+D+ K I G +DNP +KP+L+ Sbjct: 1 MRCSAVSLGSGTIINAIATGFGSAFGVDLKIKADVELVDNCKKIINGISIDNPTLKPSLV 60 Query: 61 VRCVKNTLDYFGLNYSAYVETKTEIPIKSGLSSSSATSNAVVLATFDALGEKIDDELILN 120 RCVKN LD+F ++YSA + T +IPIKSGLSSSSA SNA VLAT ALGEK+D +L+L+ Sbjct: 61 ERCVKNVLDHFEVDYSAKISTSGDIPIKSGLSSSSAASNAAVLATIGALGEKVDSDLVLD 120 Query: 121 LGIKSSFDEKLTVTGAYDDATASYYGGITITDNIERKILKRDKMRDDLNVLILIPNLEKN 180 L IKSSF+EKLT+TGAYDDATASY+GGIT+ +N+ERKILK+D+ ++D+ V++L+P +KN Sbjct: 121 LAIKSSFEEKLTITGAYDDATASYFGGITVCNNMERKILKKDEFKEDIKVIVLMPEFQKN 180 Query: 181 VDVNRMKLIKDYVEIAFNEAINGNYFKALFLNGILYASALNFPTNIAIDALDAGAITAGL 240 VDVNRMKLIKDYVEIAF + + G+Y+KALFLNG+LY+SALNFP+NI++DAL+AGAITAGL Sbjct: 181 VDVNRMKLIKDYVEIAFEKCMEGDYYKALFLNGLLYSSALNFPSNISVDALEAGAITAGL 240 Query: 241 SGTGPSYIAMVEDENVEKVKEKLNRYGKVILTKPNNDGASI 281 SGTGPSY+A+ E+ + V+ L +YG ++TKP+ +GA I Sbjct: 241 SGTGPSYVALCYSEDKKNVENALKKYGNTVITKPSTNGARI 281 Lambda K H 0.314 0.135 0.369 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: 293 Number of extensions: 9 Number of successful extensions: 1 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: 282 Length of database: 283 Length adjustment: 26 Effective length of query: 256 Effective length of database: 257 Effective search space: 65792 Effective search space used: 65792 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: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_011869103.1 MMARC5_RS06880 (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.6222.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-89 285.1 1.6 3.3e-89 284.8 1.6 1.0 1 lcl|NCBI__GCF_000016125.1:WP_011869103.1 MMARC5_RS06880 shikimate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016125.1:WP_011869103.1 MMARC5_RS06880 shikimate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 284.8 1.6 3.3e-89 3.3e-89 2 265 .. 8 271 .. 7 272 .. 0.97 Alignments for each domain: == domain 1 score: 284.8 bits; conditional E-value: 3.3e-89 TIGR01920 2 sggitivnAlatGlGsAfgidLkveakvrlsd.geakvslkvreeeeldpelierilealieklgikeg 69 g++ti+nA+atG GsAfg+dLk++a v+l d ++ +++ + ++++l+p+l+er+++++++++ + ++ lcl|NCBI__GCF_000016125.1:WP_011869103.1 8 LGSGTIINAIATGFGSAFGVDLKIKADVELVDnCKKIINGISIDNPTLKPSLVERCVKNVLDHFEVDYS 76 599*****************************888889999**************************** PP TIGR01920 70 leveveseiPagsGLksSsAlvnAlvlavlkakgeeiddieilrlgaelskeagvsvTGAfDDaaasll 138 +++ + ++iP++sGL+sSsA++nA vla++ a+ge++d+ +l l++++s+e+++++TGA+DDa+as++ lcl|NCBI__GCF_000016125.1:WP_011869103.1 77 AKISTSGDIPIKSGLSSSSAASNAAVLATIGALGEKVDSDLVLDLAIKSSFEEKLTITGAYDDATASYF 145 ********************************************************************* PP TIGR01920 139 ggivltdNrkmkilkrdkleee.tavvlvpkeeekeeevdlnelrkiskvveeavklAlkGeylkAmvl 206 ggi++ +N ++kilk+d+++e+ +++vl+p++ +++vd+n+++ i+++ve a++ ++G+y kA++l lcl|NCBI__GCF_000016125.1:WP_011869103.1 146 GGITVCNNMERKILKKDEFKEDiKVIVLMPEF---QKNVDVNRMKLIKDYVEIAFEKCMEGDYYKALFL 211 *********************98999999997...889******************************* PP TIGR01920 207 ngvlyataLgyplepaekalekGAavaglsGkGPsyvalteepe.eevaealeeageViv 265 ng+ly++aL++p ++ ++ale+GA++aglsG+GPsyval ++ ++v++al+++g+ ++ lcl|NCBI__GCF_000016125.1:WP_011869103.1 212 NGLLYSSALNFPSNISVDALEAGAITAGLSGTGPSYVALCYSEDkKNVENALKKYGNTVI 271 ***************************************98888799********87554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (266 nodes) Target sequences: 1 (283 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.63 // [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