Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_034525942.1 LOSG293_RS00980 acetate kinase
Query= BRENDA::Q9F1X7 (397 letters) >NCBI__GCF_000740055.1:WP_034525942.1 Length = 398 Score = 439 bits (1129), Expect = e-128 Identities = 209/396 (52%), Positives = 300/396 (75%) Query: 1 MSKIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKN 60 MSK++A+NAGSSTLK+KL+ +PEE+V+AEG+++R+ LPAS ++K +G+K+ +T D Sbjct: 1 MSKVLAINAGSSTLKWKLFNLPEESVIAEGMVDRLNLPASVFKLKLANGEKHNETRDNIT 60 Query: 61 HEQAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAP 120 + +A ++L +L L I++ EI GVGHRVVAGGE F S V+TP+VL KI++L+ AP Sbjct: 61 NREAAAMVLTRLKSLHILEHLHEIVGVGHRVVAGGEEFKDSTVVTPEVLDKIKALSAYAP 120 Query: 121 LHEPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHG 180 LH P I+ F+ +LPD VAVFDT+ +P N++YS+PYEYYEK+ ARKYG HG Sbjct: 121 LHNPVQAYYIQTFQTLLPDATQVAVFDTSLFTEMPPVNYMYSIPYEYYEKFGARKYGAHG 180 Query: 181 IGNRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATR 240 +RYV+ RAAE+LGKP + LK++ HLG+G+SI +GK+ DTSMGFTP+ G+TM TR Sbjct: 181 TSHRYVAHRAAEILGKPFDSLKIVTLHLGSGSSITAFDHGKAIDTSMGFTPLAGVTMGTR 240 Query: 241 SGDVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREVEAAQATNPRAKVA 300 SGD+D SL+AY+M+K +T++ +MI +LN KSGLLGIS +S D R++E Q +NP+AK+A Sbjct: 241 SGDIDASLVAYLMQKLNLTNVEDMIDILNQKSGLLGISELSPDQRDLEEVQDSNPKAKLA 300 Query: 301 REIYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKNDV 360 +I+VNR+I YVG+Y+ ++ G DA+VFTAG GEN I +R+ +A+ L+YFGI VD +KN+V Sbjct: 301 LDIFVNRVISYVGSYIGKLNGIDALVFTAGSGENGIELRQNIADQLSYFGITVDPDKNNV 360 Query: 361 RGVVRDISAKDSKIKTLLVPTDEELMIVRDVQTLAN 396 RG ++ +++ + L+VPT+EELMIVRDV+ L + Sbjct: 361 RGKETILNKENAPVDVLIVPTNEELMIVRDVERLGH 396 Lambda K H 0.316 0.135 0.372 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: 444 Number of extensions: 12 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: 397 Length of database: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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_034525942.1 LOSG293_RS00980 (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.2209038.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-141 458.2 0.1 1.2e-141 458.0 0.1 1.0 1 NCBI__GCF_000740055.1:WP_034525942.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000740055.1:WP_034525942.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.0 0.1 1.2e-141 1.2e-141 4 404 .. 2 395 .. 1 396 [. 0.97 Alignments for each domain: == domain 1 score: 458.0 bits; conditional E-value: 1.2e-141 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 +k+l +naGss lk++l++ + e+v+++g+v+r++l+ ++ k + +++k++e+ + +ea +++l++lk NCBI__GCF_000740055.1:WP_034525942.1 2 SKVLAINAGSSTLKWKLFNLPE-ESVIAEGMVDRLNLPASVFKLKLANGEKHNETRDNITNREAAAMVLTRLK 73 79*******************6.9999*************998888888888888888888889999****** PP TIGR00016 77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149 +il++l+ei +GHRvv Gge+f++s++vt evl+kik +s +APlHnp ++ i++++ + l++a +v NCBI__GCF_000740055.1:WP_034525942.1 74 -SLHILEHLHEIVGVGHRVVAGGEEFKDSTVVTPEVLDKIKALSAYAPLHNPVQAYYIQTFQ--TLLPDATQV 143 .699**********************************************************..8889999** PP TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222 avFDt+ + +p +y+Y++Py++y+++g R+YG+HGtsh+yv++raa++l+kp d+l+++++HlG G+s++a NCBI__GCF_000740055.1:WP_034525942.1 144 AVFDTSLFTEMPPVNYMYSIPYEYYEKFGARKYGAHGTSHRYVAHRAAEILGKPFDSLKIVTLHLGSGSSITA 216 ************************************************************************* PP TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls.ldeieetlnkksGllgisglssDlRdild 294 Gk+idtsmG+tPL+G+ mGtRsGdiD +++ yl+++l+l+ ++++ ++ln+ksGllgis+ls D Rd+++ NCBI__GCF_000740055.1:WP_034525942.1 217 FDHGKAIDTSMGFTPLAGVTMGTRSGDIDASLVAYLMQKLNLTnVEDMIDILNQKSGLLGISELSPDQRDLEE 289 *****************************************984799************************99 PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 + ++n +aklAl+++v+R+ +y+g+yi +l+g +Da+vFt+G Gen e+r+++ ++l +G+ +d+++nn NCBI__GCF_000740055.1:WP_034525942.1 290 VQ-DSNPKAKLALDIFVNRVISYVGSYIGKLNG-IDALVFTAGSGENGIELRQNIADQLSYFGITVDPDKNN- 359 87.999*************************88.**************************************. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404 +gke+++++e++ v vl++ptneel+i++D+ rl NCBI__GCF_000740055.1:WP_034525942.1 360 -VRGKETILNKENAPVDVLIVPTNEELMIVRDVERLG 395 .9*******************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (398 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: 23.16 // [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