Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_053545723.1 CDES_RS11950 acetate kinase
Query= SwissProt::P77845 (397 letters) >NCBI__GCF_001277995.1:WP_053545723.1 Length = 397 Score = 744 bits (1922), Expect = 0.0 Identities = 370/397 (93%), Positives = 387/397 (97%) Query: 1 MALALVLNSGSSSIKFQLVNPENSAIDEPYVSGLVEQIGEPNGRIVLKIEGEKYTLETPI 60 M+LALVLNSGSSSIKFQLVNPENSA DEP+VSGLVEQIGEP GRIVLKIEGEK+TLE PI Sbjct: 1 MSLALVLNSGSSSIKFQLVNPENSATDEPFVSGLVEQIGEPMGRIVLKIEGEKHTLEAPI 60 Query: 61 ADHSEGLNLAFDLMDQHNCGPSQLEITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPL 120 ADHS GL LAFDLMD+HNCGP+Q++ITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPL Sbjct: 61 ADHSAGLGLAFDLMDEHNCGPTQVDITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPL 120 Query: 121 APLHNPANVDGIDVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVAAEHGIRRYGF 180 APLHNPANVDGI+VARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVA EHGIRRYGF Sbjct: 121 APLHNPANVDGIEVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVALEHGIRRYGF 180 Query: 181 HGTSHEFVSKRVVEILEKPTEDINTITFHLGNGASMAAVQGGRAVDTSMGMTPLAGLVMG 240 HGTSHEFVSKRVVE+LEKP EDINTITFHLGNGASMAA++GGRAVDTSMGMTPLAGLVMG Sbjct: 181 HGTSHEFVSKRVVELLEKPAEDINTITFHLGNGASMAAIEGGRAVDTSMGMTPLAGLVMG 240 Query: 241 TRSGDIDPGIVFHLSRTAGMSIDEIDNLLNKKSGVKGLSGVNDFRELREMIDNNDQDAWS 300 TRSGDIDPGIVFHLSRTAGMSIDEID LLNKKSGVKGLSGVNDFRELR+MID+NDQDAWS Sbjct: 241 TRSGDIDPGIVFHLSRTAGMSIDEIDTLLNKKSGVKGLSGVNDFRELRQMIDDNDQDAWS 300 Query: 301 AYNIYIHQLRRYLGSYMVALGRVDTIVFTAGVGENAQFVREDALAGLEMYGIEIDPERNA 360 AYN+YIHQLRRYLGSYM+ALGRVDTIVFTAGVGENAQFVREDAL GLEMYGIEIDPERNA Sbjct: 301 AYNVYIHQLRRYLGSYMIALGRVDTIVFTAGVGENAQFVREDALYGLEMYGIEIDPERNA 360 Query: 361 LPNDGPRLISTDASKVKVFVIPTNEELAIARYAVKFA 397 LPN+GPRLISTD SKVKVFVIPTNEELAIA+YAVKFA Sbjct: 361 LPNEGPRLISTDESKVKVFVIPTNEELAIAQYAVKFA 397 Lambda K H 0.318 0.137 0.395 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: 710 Number of extensions: 15 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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: 50 (23.9 bits)
Align candidate WP_053545723.1 CDES_RS11950 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))
# 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.carbon/TIGR00016.hmm # target sequence database: /tmp/gapView.1869578.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00016 [M=405] Accession: TIGR00016 Description: ackA: acetate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-140 452.0 0.0 9.1e-140 451.8 0.0 1.0 1 NCBI__GCF_001277995.1:WP_053545723.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001277995.1:WP_053545723.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.8 0.0 9.1e-140 9.1e-140 5 403 .. 3 396 .. 1 397 [] 0.95 Alignments for each domain: == domain 1 score: 451.8 bits; conditional E-value: 9.1e-140 TIGR00016 5 kilvlnaGssslkfalldaen..sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntl 75 + lvln+Gsss+kf+l++ en +++ ++sglve+i + ri + +g +k++ + i+dh++++ ++ + NCBI__GCF_001277995.1:WP_053545723.1 3 LALVLNSGSSSIKFQLVNPENsaTDEPFVSGLVEQIGEPMGRIVLKIEG-EKHTLEAPIADHSAGLGLAFDLM 74 679***************9994445559*********999988866666.77888999********8777666 PP TIGR00016 76 kkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148 +++ ++ +i+++GHRvvhGg f+ ++tde+++ i+d+++lAPlHnpa+++gie + k+l+++++ NCBI__GCF_001277995.1:WP_053545723.1 75 D-EHNCGPTQVDITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPLAPLHNPANVDGIEVAR--KILPDVPH 144 6.899*********************************************************9..99****** PP TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221 vavFDt f + +p a+lYa+ +++ e+g+RrYGfHGtsh++v++r+ +ll+kp++d+n i+ HlGnGas++ NCBI__GCF_001277995.1:WP_053545723.1 145 VAVFDTGFFHSLPPAAALYAINKDVALEHGIRRYGFHGTSHEFVSKRVVELLEKPAEDINTITFHLGNGASMA 217 ************************************************************************* PP TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294 a++ G+++dtsmG+tPL+GlvmGtRsGdiDp+i+++l+ t g+s+dei ++lnkksG+ g+sg +D+R++ + NCBI__GCF_001277995.1:WP_053545723.1 218 AIEGGRAVDTSMGMTPLAGLVMGTRSGDIDPGIVFHLSRTAGMSIDEIDTLLNKKSGVKGLSG-VNDFRELRQ 289 ***************************************************************.89******* PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 +++++++a A++vy+h +++y+g+y+ +l g++D+ivFt+G+Gena+ vre++l +le+ G+++d+e+n NCBI__GCF_001277995.1:WP_053545723.1 290 MIDDNDQDAWSAYNVYIHQLRRYLGSYMIAL-GRVDTIVFTAGVGENAQFVREDALYGLEMYGIEIDPERNAL 361 *******************************.67*************************************95 PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403 ++ ++ist+eskvkv+viptneel+ia+ a+++ NCBI__GCF_001277995.1:WP_053545723.1 362 -PNEGPRLISTDESKVKVFVIPTNEELAIAQYAVKF 396 .556679************************98875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (397 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: 16.65 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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