Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_008990778.1 I215_RS04525 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_000300875.1:WP_008990778.1 Length = 395 Score = 387 bits (994), Expect = e-112 Identities = 203/399 (50%), Positives = 282/399 (70%), Gaps = 9/399 (2%) Query: 2 RVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIER-ELPDHE 60 ++LVIN+GSSSIK+QL+ M GE V+ G+ E IG+ + +H + ++ E E+ +H+ Sbjct: 3 KILVINAGSSSIKFQLMRMPGEIVIASGLVESIGLSNAA-IHYKSKKMNISETVEIENHQ 61 Query: 61 EALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAP 120 L+ I L+D + G IK + EID VGHRVVHGG+ F +V +D++V I+ + LAP Sbjct: 62 VGLERIAALLMDSERGAIKSVDEIDVVGHRVVHGGKDFSSTVFIDDKVKATIKRLFSLAP 121 Query: 121 LHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHG 180 LHNP N GI+ A K+ P VAVFDTAFHQTIP++AY YAIP + ++ IR YGFHG Sbjct: 122 LHNPHNYTGIEVAEKVFPNAKKVAVFDTAFHQTIPERAYKYAIPDSFLKENYIRLYGFHG 181 Query: 181 TSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTR 240 TSH+YVS +A + + KK + K+I+ H+GNG S+ AV+ GK VD SMGF P+ GL+MGTR Sbjct: 182 TSHKYVSTKAKDFISKK--KSKLISIHLGNGCSITAVQNGKSVDHSMGFGPVNGLIMGTR 239 Query: 241 SGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKL 300 SGD+D ++ F+++ G + E+ +IL+KKSG+ G++ GF SD+R+IE+ A KGD C+L Sbjct: 240 SGDIDQSVIFYMVNTLGYTLDEVSEILHKKSGMIGMT-GF-SDLREIEDRAEKGDRRCQL 297 Query: 301 VLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNE 360 LE+ YRI KYIG+YAAAMNGVD IVFTAG+GENS + R +C +++LG++L+ KN Sbjct: 298 ALEMNAYRIKKYIGSYAAAMNGVDVIVFTAGIGENSSVLRRMICDDMDYLGIELEDYKN- 356 Query: 361 ETIRGKEG-IISTPDSRVKVLVVPTNEELMIARDTKEIV 398 +R E IIS S+V VLVVPTNEEL IA+D E++ Sbjct: 357 -NVRSTENRIISKESSKVLVLVVPTNEELEIAKDCYEMI 394 Lambda K H 0.318 0.138 0.391 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: 424 Number of extensions: 19 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: 403 Length of database: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_008990778.1 I215_RS04525 (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.72243.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-150 487.3 7.1 1.7e-150 487.2 7.1 1.0 1 NCBI__GCF_000300875.1:WP_008990778.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000300875.1:WP_008990778.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.2 7.1 1.7e-150 1.7e-150 4 404 .. 2 394 .. 1 395 [] 0.97 Alignments for each domain: == domain 1 score: 487.2 bits; conditional E-value: 1.7e-150 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 kkilv+naGsss+kf+l+ + +e v++sglve i l++a i +++ + + +e+++ie+h+ ++++++ l+ NCBI__GCF_000300875.1:WP_008990778.1 2 KKILVINAGSSSIKFQLMRMP-GEIVIASGLVESIGLSNAAIHYKSK-KMNISETVEIENHQVGLERIAALLM 72 89*******************.7*****************8886554.5788999*****************9 PP TIGR00016 77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148 + ++ +k+ +ei+++GHRvvhGg++f+++v ++d+v + ik++ +lAPlHnp + +gie + kv ++ak+ NCBI__GCF_000300875.1:WP_008990778.1 73 DsERGAIKSVDEIDVVGHRVVHGGKDFSSTVFIDDKVKATIKRLFSLAPLHNPHNYTGIEVAE--KVFPNAKK 143 98999**********************************************************..899999** PP TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221 vavFDtafHqtipe+ay Ya+P s+ ke+ +R YGfHGtshkyv+ +a++ + k ++++li++HlGnG s++ NCBI__GCF_000300875.1:WP_008990778.1 144 VAVFDTAFHQTIPERAYKYAIPDSFLKENYIRLYGFHGTSHKYVSTKAKDFISK--KKSKLISIHLGNGCSIT 214 ******************************************************..999************** PP TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294 av+nGks+d smG+ P++Gl+mGtRsGdiD ++i+y+ +tlg +lde+ e+l kksG++g++g sDlR+i+d NCBI__GCF_000300875.1:WP_008990778.1 215 AVQNGKSVDHSMGFGPVNGLIMGTRSGDIDQSVIFYMVNTLGYTLDEVSEILHKKSGMIGMTG-FSDLREIED 286 ***************************************************************.68******* PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 + e+g+ +++lAl++ ++Ri+kyig+y+a+++g +D ivFt+GiGen++ +r++++++++ lG++l+ +nn NCBI__GCF_000300875.1:WP_008990778.1 287 RAEKGDRRCQLALEMNAYRIKKYIGSYAAAMNG-VDVIVFTAGIGENSSVLRRMICDDMDYLGIELEDYKNN- 357 *******************************88.**********************************9999. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404 rs+++++is+e skv vlv+ptneel ia+D+++++ NCBI__GCF_000300875.1:WP_008990778.1 358 VRSTENRIISKESSKVLVLVVPTNEELEIAKDCYEMI 394 89*******************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (395 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.24 // [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