Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_024890056.1 Z164_RS0107325 acetate/propionate family kinase
Query= curated2:Q6N143 (398 letters) >NCBI__GCF_000559025.1:WP_024890056.1 Length = 405 Score = 347 bits (889), Expect = e-100 Identities = 195/401 (48%), Positives = 251/401 (62%), Gaps = 13/401 (3%) Query: 4 VLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGH-RPHFKVVNSDGSTRYDTYLP 62 ++LVLN GSSSIKFAL+ A P A + G + +G P F G + L Sbjct: 8 LILVLNCGSSSIKFALFAADVHPLARTPLWNGKVQGIGGPAPDF---GETGVAPHRVELD 64 Query: 63 EGTSHDDAMAVLIGWIETTFPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAFDRLA 122 G H A+ V+ I T R+ AV HRVVHGG + P V + +A LR++ LA Sbjct: 65 AGHPHSAALQVIRERIRTRLNGRRVVAVAHRVVHGGTKYSAPTRVDAQTLADLRSYVPLA 124 Query: 123 PLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRYGFHG 182 PLHQP + A++ L + HP + Q+ACFDTAFH LP+V LP +G+RRYGFHG Sbjct: 125 PLHQPFALEAMDILLREHPDIVQVACFDTAFHRTLPKVEQLLPLPHAAWARGLRRYGFHG 184 Query: 183 LSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDGLMMGSR 242 LSYEY+A LP+ G +A GRV+VAHLG+GAS+CAM S+ATTMGF+ALDGLMMG+R Sbjct: 185 LSYEYMAAALPERHGD-LASGRVIVAHLGSGASLCAMRGLHSVATTMGFSALDGLMMGTR 243 Query: 243 CGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLA------SDDPHA 296 G LDPG V+YL+E + ++ ++ +LY ESGLLGVSGIS + R LL D A Sbjct: 244 TGALDPGAVIYLMEIEKLSLEQVAHILYHESGLLGVSGISAEPRVLLQKETGNDEDAARA 303 Query: 297 CEAIELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDA 356 +A+ L+V RI RE+G+L A LGGLD LVFT G+GEH+ EIRRRVCE +L + LDP A Sbjct: 304 RDALSLYVRRIVREIGALVAVLGGLDLLVFTAGVGEHSPEIRRRVCESLGFLPLRLDPPA 363 Query: 357 NASLSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRLADGG 397 N L+ A ISA DS+V PT+E+ + AR L G Sbjct: 364 N--LANAPVISAADSEVIVGVEPTNEEWVAARAALTLCRTG 402 Lambda K H 0.321 0.137 0.413 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: 520 Number of extensions: 21 Number of successful extensions: 5 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: 398 Length of database: 405 Length adjustment: 31 Effective length of query: 367 Effective length of database: 374 Effective search space: 137258 Effective search space used: 137258 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate WP_024890056.1 Z164_RS0107325 (acetate/propionate family 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.2468544.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-102 328.2 0.0 3.6e-102 328.0 0.0 1.0 1 NCBI__GCF_000559025.1:WP_024890056.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000559025.1:WP_024890056.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 328.0 0.0 3.6e-102 3.6e-102 4 404 .. 7 399 .. 4 400 .. 0.92 Alignments for each domain: == domain 1 score: 328.0 bits; conditional E-value: 3.6e-102 TIGR00016 4 kkilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 ++ilvln+Gsss+kfal+ a +++ l++g v+ i + ++ e a + h++a++ + + NCBI__GCF_000559025.1:WP_024890056.1 7 SLILVLNCGSSSIKFALFAADVhplARTPLWNGKVQGIGGPAPDFGETG-VAPHRVELDAGHPHSAALQVIRE 78 78****************98765566777*********99888544333.3456778889999********** PP TIGR00016 74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146 ++ + + + + ++ HRvvhGg+k++ + v++++l++++ ++lAPlH p +le+++++l ++++ NCBI__GCF_000559025.1:WP_024890056.1 79 RIRT----RLNGRRVVAVAHRVVHGGTKYSAPTRVDAQTLADLRSYVPLAPLHQPFALEAMDILL--REHPDI 145 **97....5677899************************************************99..999999 PP TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219 +va+FDtafH+t+p+ l +lP+ ++ g+RrYGfHG+s++y++ + + + l++ ++iv+HlG Gas NCBI__GCF_000559025.1:WP_024890056.1 146 VQVACFDTAFHRTLPKVEQLLPLPHAAWA-RGLRRYGFHGLSYEYMAAALPERHGD-LASGRVIVAHLGSGAS 216 ************************88886.69*********************998.99************** PP TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292 ++a++ +s+ t+mG+ L+Gl+mGtR+G +Dp+++ yl+e ++lsl+++ ++l +sGllg+sg+s++ R++ NCBI__GCF_000559025.1:WP_024890056.1 217 LCAMRGLHSVATTMGFSALDGLMMGTRTGALDPGAVIYLMEIEKLSLEQVAHILYHESGLLGVSGISAEPRVL 289 ************************************************************************* PP TIGR00016 293 ldkke...egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362 l+k + e +a+ Al++yv Ri + ig+ +a l g lD +vFt+G+Ge + e+r++v+e+l +l l+ld+ NCBI__GCF_000559025.1:WP_024890056.1 290 LQKETgndEDAARARDALSLYVRRIVREIGALVAVLGG-LDLLVFTAGVGEHSPEIRRRVCESLGFLPLRLDP 361 *99863225555677899******************76.********************************** PP TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404 n + vis +s+v v v ptnee+v a+ al l+ NCBI__GCF_000559025.1:WP_024890056.1 362 PANL----ANAPVISAADSEVIVGVEPTNEEWVAARAALTLC 399 *999....7789**********************99988876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (405 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 16.83 // [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