Align Propionate kinase; EC 2.7.2.15 (characterized)
to candidate 17189 b3115 propionate kinase/acetate kinase C, anaerobic (RefSeq)
Query= SwissProt::P11868 (402 letters) >FitnessBrowser__Keio:17189 Length = 402 Score = 794 bits (2051), Expect = 0.0 Identities = 402/402 (100%), Positives = 402/402 (100%) Query: 1 MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY 60 MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY Sbjct: 1 MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY 60 Query: 61 EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY 120 EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY Sbjct: 61 EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY 120 Query: 121 ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR 180 ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR Sbjct: 121 ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR 180 Query: 181 YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV 240 YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV Sbjct: 181 YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV 240 Query: 241 DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF 300 DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF Sbjct: 241 DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF 300 Query: 301 VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC 360 VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC Sbjct: 301 VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC 360 Query: 361 GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA 402 GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA Sbjct: 361 GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA 402 Lambda K H 0.318 0.134 0.386 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: 680 Number of extensions: 16 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: 402 Length of database: 402 Length adjustment: 31 Effective length of query: 371 Effective length of database: 371 Effective search space: 137641 Effective search space used: 137641 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 17189 b3115 (propionate kinase/acetate kinase C, anaerobic (RefSeq))
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.12213.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-176 573.3 0.1 1.4e-176 573.1 0.1 1.0 1 lcl|FitnessBrowser__Keio:17189 b3115 propionate kinase/acetate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17189 b3115 propionate kinase/acetate kinase C, anaerobic (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 573.1 0.1 1.4e-176 1.4e-176 3 404 .. 4 393 .. 2 394 .. 0.97 Alignments for each domain: == domain 1 score: 573.1 bits; conditional E-value: 1.4e-176 TIGR00016 3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkki 81 + ++lv+n+Gsss+kf++lda+++e + +sg+++ i++e+a+++ ++g +e + la++++e a+k+++ +l+k lcl|FitnessBrowser__Keio:17189 4 FPVVLVINCGSSSIKFSVLDASDCEVL-MSGIADGINSENAFLS--VNG--GEPAPLAHHSYEGALKAIAFELEK---- 73 678*******************98866.*************544..555..7999*******************8.... PP TIGR00016 82 lkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafHqti 160 +++++++aliGHR++hGg+ ftes+i+tdev+++i+++s+lAPlHn+a+l+gie++++l++ ++ +vavFDt+fHqt+ lcl|FitnessBrowser__Keio:17189 74 RNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNYANLSGIESAQQLFPGVT--QVAVFDTSFHQTM 150 799******************************************************8888777..************* PP TIGR00016 161 peeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGltPLe 239 + eaylY+lP+++y+elgvRrYGfHGtsh+yv+qra++lln ++dd+ l+v+HlGnGas++av+nG+s+dtsmG+tPLe lcl|FitnessBrowser__Keio:17189 151 APEAYLYGLPWKYYEELGVRRYGFHGTSHRYVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLE 229 ******************************************************************************* PP TIGR00016 240 GlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyi 318 Gl+mGtRsGd+D++++s++a+++++sl ++e+++nk+sGllgisglssDlR+++++++eg+e+a+lA+k++vhRia++i lcl|FitnessBrowser__Keio:17189 230 GLMMGTRSGDVDFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTFVHRIARHI 308 ******************************************************************************* PP TIGR00016 319 gkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelvia 397 + ++asl +lD+i+FtgGiGen++ +r+lv+e+l+vlGl++d+e+nn+++s+ e+++s+e+++v ++viptnee++ia lcl|FitnessBrowser__Keio:17189 309 AGHAASLR-RLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSCGERIVSSENARVICAVIPTNEEKMIA 386 *******5.5********************************************************************* PP TIGR00016 398 eDalrla 404 Da++l lcl|FitnessBrowser__Keio:17189 387 LDAIHLG 393 *****96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (402 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: 00:00:00.02 # Mc/sec: 7.58 // [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