Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate BWI76_RS20235 BWI76_RS20235 acetate kinase
Query= BRENDA::P63411 (400 letters) >FitnessBrowser__Koxy:BWI76_RS20235 Length = 400 Score = 773 bits (1997), Expect = 0.0 Identities = 388/400 (97%), Positives = 393/400 (98%) Query: 1 MSSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAG 60 MSSKLVLVLNCGSSSLKFAI+DAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEA LGAG Sbjct: 1 MSSKLVLVLNCGSSSLKFAILDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAELGAG 60 Query: 61 AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFA 120 AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVID+SVIQGIKDSASFA Sbjct: 61 AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDDSVIQGIKDSASFA 120 Query: 121 PLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180 PLHNPAHLIGIAEALKSFP LKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG Sbjct: 121 PLHNPAHLIGIAEALKSFPNLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180 Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240 AHGTSHFYVTQEAAK+LNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM Sbjct: 181 AHGTSHFYVTQEAAKVLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240 Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300 GTRSGDIDPAIIFHLHD LGMSVD INKMLTKESGLLGLTEVTSDCRYVEDNY K DAK Sbjct: 241 GTRSGDIDPAIIFHLHDALGMSVDAINKMLTKESGLLGLTEVTSDCRYVEDNYQEKADAK 300 Query: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER Sbjct: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360 Query: 361 NLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400 NLAARFGKSGFINKEGTRPA+VIPTNEELVIAQDA+RLTA Sbjct: 361 NLAARFGKSGFINKEGTRPAIVIPTNEELVIAQDANRLTA 400 Lambda K H 0.318 0.134 0.384 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: 628 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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: 50 (23.9 bits)
Align candidate BWI76_RS20235 BWI76_RS20235 (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.11483.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-189 614.3 0.0 4.7e-189 614.2 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS20235 BWI76_RS20235 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS20235 BWI76_RS20235 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 614.2 0.0 4.7e-189 4.7e-189 1 404 [. 1 399 [. 1 400 [] 0.98 Alignments for each domain: == domain 1 score: 614.2 bits; conditional E-value: 4.7e-189 TIGR00016 1 mkskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkl 71 m+sk++lvln+Gssslkfa+lda n++++ lsgl+e+++l+earik+++dg+k+e+e a ++h+ea++++ lcl|FitnessBrowser__Koxy:BWI76_RS20235 1 MSSKLVLVLNCGSSSLKFAILDAVNGDEY-LSGLAECFHLPEARIKWKMDGSKQEAELGAGAAHSEALNFI 70 57899************************.9**************************************** PP TIGR00016 72 lntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkv 142 +nt+ ++k ++++++++iGHR+vhGgek+t+sv+++d+v+++ikd +++APlHnpa+l+gi ++lk+++ lcl|FitnessBrowser__Koxy:BWI76_RS20235 71 VNTILAQK--PELSAQLTAIGHRIVHGGEKYTSSVVIDDSVIQGIKDSASFAPLHNPAHLIGIAEALKSFP 139 *****866..99*********************************************************** PP TIGR00016 143 llkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcH 213 lk+knvavFDtafHqt+pee+ylYalPyslyke+gvRrYG+HGtsh yvtq+aak+lnkp+++ln+i+cH lcl|FitnessBrowser__Koxy:BWI76_RS20235 140 NLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYGAHGTSHFYVTQEAAKVLNKPVEELNIITCH 210 *********************************************************************** PP TIGR00016 214 lGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisg 284 lGnG+svsa++nGk++dtsmGltPLeGlvmGtRsGdiDpaii++l++ lg+s+d+i+++l+k+sGllg+++ lcl|FitnessBrowser__Koxy:BWI76_RS20235 211 LGNGGSVSAIRNGKCVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDALGMSVDAINKMLTKESGLLGLTE 281 *********************************************************************** PP TIGR00016 285 lssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklev 355 ++sD+R+++d++ +++ +ak+A++vy+hR+akyig+y+a ++g+lDa+vFtgGiGenaa+vrel+l kl v lcl|FitnessBrowser__Koxy:BWI76_RS20235 282 VTSDCRYVEDNY-QEKADAKRAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGV 351 ************.6667****************************************************** PP TIGR00016 356 lGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404 lG+++d+e+n aar+gk+++i+ +e++ ++viptneelvia+Da rl+ lcl|FitnessBrowser__Koxy:BWI76_RS20235 352 LGFEVDHERNLAARFGKSGFIN-KEGTRPAIVIPTNEELVIAQDANRLT 399 *********************9.89999*****************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (400 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: 00:00:00.01 # Mc/sec: 9.64 // [ok]
This GapMind analysis is from Sep 17 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