Align acetate kinase (EC 2.7.2.15) (characterized)
to candidate WP_033101565.1 JG50_RS0113070 acetate kinase
Query= metacyc::MONOMER-20612 (399 letters) >NCBI__GCF_000763315.1:WP_033101565.1 Length = 397 Score = 476 bits (1225), Expect = e-139 Identities = 229/397 (57%), Positives = 302/397 (76%), Gaps = 1/397 (0%) Query: 1 MNVLVINCGSSSLKYQFIDMTSEEVLAKGLVERIGIEGSILKHQTTGKDKVSIEQPMHDH 60 M +LVINCGSSS+KYQ DMT E VLA GLVE+IG E +I+KH+ G++K I + DH Sbjct: 1 MKILVINCGSSSIKYQLFDMTDESVLASGLVEKIGTESAIIKHEPAGREKKVIISEILDH 60 Query: 61 KIALQLVLEALMNSEYGAIKDLKEIAAVGHRVVHGGEAFSHSALIDEHVKKAIEDCIELA 120 ++ L+ VL+ LM+ + G IK E++AVGHRVVHGGE F+ S ++D V++AI + +LA Sbjct: 61 RVGLKKVLDLLMDEKEGVIKSADEVSAVGHRVVHGGETFARSVVVDSEVRRAIRETFDLA 120 Query: 121 PLHNPPNLIGINACQEILPNVPMVAVFDTAFHQTMPKSSYLYGLPYEYYEKYKVRRYGFH 180 PLHNPPNLIGI+A Q LP+ VAVFDTAFHQTMP +Y+Y LP Y KYKVRRYGFH Sbjct: 121 PLHNPPNLIGIDAAQANLPHAVHVAVFDTAFHQTMPDYAYMYPLPRILYHKYKVRRYGFH 180 Query: 181 GTSHKYVAQKTAEILNKNLEDINIITCHLGNGASVTAVEKGHSVDTSMGFTPLEGLIMGT 240 GTSHKYV+Q+ AE L K LE++ II+CH+GNGAS+TAV+ G SVDTSMG TPLEGL+MGT Sbjct: 181 GTSHKYVSQRAAEFLGKPLEELKIISCHIGNGASITAVQGGKSVDTSMGMTPLEGLMMGT 240 Query: 241 RCGDIDPAMVTFLMEKENLSTAQINDVMNKKSGVLGISKVSSDFRDIETEAEKGNENAKI 300 RCGDIDPA+V F++ KE L+ +++N +MNK SG+LG+S +SSD R++ GN NA++ Sbjct: 241 RCGDIDPAIVPFVIAKEELTLSEVNSMMNKHSGLLGVSGISSDMREVMEAMFDGNANARL 300 Query: 301 ALETYYKKVKKYIGAYMAEMGSVDAIVFTAGLGENSSSARLAICGGMEGIGIEIDAKEND 360 A++ Y K+KK IGAY+A M VDAI+FTAG+GEN++ R +C G+ G+++D +N Sbjct: 301 AIDMYVYKIKKTIGAYVAAMDGVDAIIFTAGVGENAAQIREKVCEGLTFFGVDLDRDKNG 360 Query: 361 MRGEE-KVVSKPSSKISVLVVPTNEELMIARDTLEIV 396 MR +E + +S SK+ VLV+PTNEELMIAR+TL +V Sbjct: 361 MRSKEIQRISTEKSKVEVLVIPTNEELMIARETLALV 397 Lambda K H 0.315 0.133 0.371 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: 412 Number of extensions: 11 Number of successful extensions: 2 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: 399 Length of database: 397 Length adjustment: 31 Effective length of query: 368 Effective length of database: 366 Effective search space: 134688 Effective search space used: 134688 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_033101565.1 JG50_RS0113070 (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.1810031.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-168 546.4 1.6 2e-168 546.3 1.6 1.0 1 NCBI__GCF_000763315.1:WP_033101565.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000763315.1:WP_033101565.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 546.3 1.6 2e-168 2e-168 4 403 .. 1 396 [. 1 397 [] 0.98 Alignments for each domain: == domain 1 score: 546.3 bits; conditional E-value: 2e-168 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 +kilv+n+Gsss+k++l+d+++ e+vl+sglve+i e a+ik g +k+ ++ +i dh+ ++kk+l+ l+ NCBI__GCF_000763315.1:WP_033101565.1 1 MKILVINCGSSSIKYQLFDMTD-ESVLASGLVEKIGTESAIIKHEPAGREKKVIISEILDHRVGLKKVLDLLM 72 69*******************7.999**********************************************9 PP TIGR00016 77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148 + ++ ++k+ +e++++GHRvvhGge+f+ sv+v++ev ++i++ +lAPlHnp++l+gi+a++ l++a + NCBI__GCF_000763315.1:WP_033101565.1 73 DeKEGVIKSADEVSAVGHRVVHGGETFARSVVVDSEVRRAIRETFDLAPLHNPPNLIGIDAAQ--ANLPHAVH 143 97899**********************************************************..8999999* PP TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221 vavFDtafHqt+p+ ay+Y+lP+ ly++++vRrYGfHGtshkyv+qraa+ l+kpl++l++i+cH+GnGas++ NCBI__GCF_000763315.1:WP_033101565.1 144 VAVFDTAFHQTMPDYAYMYPLPRILYHKYKVRRYGFHGTSHKYVSQRAAEFLGKPLEELKIISCHIGNGASIT 216 ************************************************************************* PP TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294 av+ Gks+dtsmG+tPLeGl+mGtR+GdiDpai+ ++ +++l+l+e+++++nk+sGllg+sg+ssD+R++++ NCBI__GCF_000763315.1:WP_033101565.1 217 AVQGGKSVDTSMGMTPLEGLMMGTRCGDIDPAIVPFVIAKEELTLSEVNSMMNKHSGLLGVSGISSDMREVME 289 ************************************************************************* PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 ++ +gn +a+lA+++yv++i+k ig+y+a+++g +Dai+Ft+G+Genaa++re+v+e+l ++G++ld ++n NCBI__GCF_000763315.1:WP_033101565.1 290 AMFDGNANARLAIDMYVYKIKKTIGAYVAAMDG-VDAIIFTAGVGENAAQIREKVCEGLTFFGVDLDRDKNG- 360 *******************************88.**************************************. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403 rs++ + iste+skv+vlviptneel+ia+++l l NCBI__GCF_000763315.1:WP_033101565.1 361 MRSKEIQRISTEKSKVEVLVIPTNEELMIARETLAL 396 68888899***********************98866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (397 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 19.67 // [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