Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_011426667.1 RHE_RS17585 acetate/propionate family kinase
Query= curated2:Q1QPW6 (404 letters) >NCBI__GCF_000092045.1:WP_011426667.1 Length = 392 Score = 300 bits (767), Expect = 6e-86 Identities = 173/393 (44%), Positives = 232/393 (59%), Gaps = 6/393 (1%) Query: 2 DSILVVNAGSSSVKFQVFSAEGEGKLLRQIKGQVDGIGSRPRLRASGADNEPLADRAYPI 61 D +L NAGSS+VK VFS +G + R + V + + P L D Sbjct: 5 DLLLTFNAGSSTVKVGVFSIDGA--VARHLGRGVIDLRAEP-LSLGLTRGSQTFDMPLKA 61 Query: 62 ESVSDVPAAMGVAGGWLRDELRISP-MAVGHRVVHGGPDYDRPVLIDHGVVARLERFVAL 120 E D+ + L DE ++ +AVGHRVVHGG + V +D +E + L Sbjct: 62 EVTDDLHGVIDETFALLADEFDMAAAVAVGHRVVHGGERFTSAVALDDAATDGIEALIPL 121 Query: 121 APLHQPNNLDPIRSLLANFPALPQVACFDTAFHRTHDAVADYYAIPYQFYVEGVRRYGFH 180 APLHQP L IR+L P L Q A FDTAFH T D + AIP + EG++RYGFH Sbjct: 122 APLHQPQALRFIRALRHLKPHLVQTASFDTAFHATQDDLVRRLAIPRSLHEEGIKRYGFH 181 Query: 181 GLSYEYVAKTLPHVAPEIAKGRVIVAHLGSGASMCALKGGRSIESTMGFTALDGLPMGTR 240 GLSY+++A L AP AK +VAHLGSGAS+CA++ G S + +MGF+ LDG+PM TR Sbjct: 182 GLSYKFIASELARKAPHAAKA--VVAHLGSGASLCAMEDGISRDCSMGFSTLDGIPMATR 239 Query: 241 PGQIDPGVVLYLVSEKGMSPAKAQDFLYRDCGLKGLSGVSNDMRELEASEDPKAKLAVDY 300 PG +DPGV+L+L E+ S + +D LY GL G+SG+S D R+L P+A+ A+D Sbjct: 240 PGCLDPGVILHLAGERKRSLGEIEDLLYHRSGLLGVSGISADTRDLLTDGRPEARQAIDL 299 Query: 301 FVYRVGLNAGMLAAALQGLDAFVFTAGIGENSMRIRARIADQLAWLGVTLDPTQNSRHAR 360 F R+ G +AA L GLDA VFTAGIGE+ IRA +A +L WLG+++D T N+ + Sbjct: 300 FTLRIAGEIGRMAATLGGLDAVVFTAGIGEHQPEIRAGVAKRLFWLGLSIDETANAADSF 359 Query: 361 LISGSDSRIPVYVIPTDEELMIAQHTLSLLLDR 393 IS +SRI +V+ TDEE +IA LS+L R Sbjct: 360 TISTGESRIAAHVVATDEEQVIADEALSVLRAR 392 Lambda K H 0.320 0.137 0.403 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: 423 Number of extensions: 15 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: 404 Length of database: 392 Length adjustment: 31 Effective length of query: 373 Effective length of database: 361 Effective search space: 134653 Effective search space used: 134653 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_011426667.1 RHE_RS17585 (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.71106.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-94 302.8 0.0 2e-94 302.5 0.0 1.0 1 NCBI__GCF_000092045.1:WP_011426667.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000092045.1:WP_011426667.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 302.5 0.0 2e-94 2e-94 4 402 .. 5 387 .. 2 390 .. 0.88 Alignments for each domain: == domain 1 score: 302.5 bits; conditional E-value: 2e-94 TIGR00016 4 kkilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeee..klaie.dheeavkkll 72 ++l naGss +k ++ + + l +g+++ + + ++ g+++ k +++ d + +++ + NCBI__GCF_000092045.1:WP_011426667.1 5 DLLLTFNAGSSTVKVGVFSIDGaVARHLGRGVIDLRAEPLS--LGLTRGSQTFDMplKAEVTdDLHGVIDETF 75 57899**************9973456699****98877766..445666665544114444414444555555 PP TIGR00016 73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllk 145 l + +++ ++GHRvvhGge+ft++v ++d + ++i+ +++lAPlH p++l i+a+ +lk++l NCBI__GCF_000092045.1:WP_011426667.1 76 ALLAD----EFDMAAAVAVGHRVVHGGERFTSAVALDDAATDGIEALIPLAPLHQPQALRFIRALRHLKPHLV 144 55554....345666778************************************************7766665 PP TIGR00016 146 aknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGa 218 + a FDtafH t + a+P+sl+ e g++rYGfHG+s+k+++ ++a++ + + +v+HlG Ga NCBI__GCF_000092045.1:WP_011426667.1 145 --QTASFDTAFHATQDDLVRRLAIPRSLH-EEGIKRYGFHGLSYKFIASELARKA---PHAAKAVVAHLGSGA 211 ..9**********************8776.679**************99888755...558899********* PP TIGR00016 219 svsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRd 291 s++a+++G s d smG+ L+G+ m tR G +Dp++i +la ++++sl eie++l +sGllg+sg+s+D Rd NCBI__GCF_000092045.1:WP_011426667.1 212 SLCAMEDGISRDCSMGFSTLDGIPMATRPGCLDPGVILHLAGERKRSLGEIEDLLYHRSGLLGVSGISADTRD 284 ************************************************************************* PP TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364 +l + g+ ea+ A+++++ Ria ig+++a+l g lDa+vFt+GiGe + e+r+ v ++l lGl +d+ NCBI__GCF_000092045.1:WP_011426667.1 285 LLTD---GRPEARQAIDLFTLRIAGEIGRMAATLGG-LDAVVFTAGIGEHQPEIRAGVAKRLFWLGLSIDETA 353 9975...5889***********************76.*********************************999 PP TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalr 402 n ++ ist es++ + v+ t+ee via +al NCBI__GCF_000092045.1:WP_011426667.1 354 NA----ADSFTISTGESRIAAHVVATDEEQVIADEALS 387 98....89999**********************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (392 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: 16.95 // [ok]
This GapMind analysis is from Apr 09 2024. 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