Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_009491778.1 C683_RS05475 acetate kinase
Query= BRENDA::Q9F1X7 (397 letters) >NCBI__GCF_000313915.1:WP_009491778.1 Length = 397 Score = 453 bits (1166), Expect = e-132 Identities = 224/395 (56%), Positives = 300/395 (75%), Gaps = 1/395 (0%) Query: 1 MSKIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKN 60 MS +IAVNAGSS+LK+KL+E+PEE +A G+ ERI L +++K DG+ EK + N Sbjct: 1 MSYVIAVNAGSSSLKWKLFEVPEEKEVASGIAERIGLDMGKIKLKKADGETVEKELPIPN 60 Query: 61 HEQAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAP 120 H +A+ +L+ L++ II I VGHRVVAGGE + SVV+ +VL +IE L+ELAP Sbjct: 61 HNEALTEILNSLIEEKIIPSLDAITAVGHRVVAGGESYKDSVVVDEEVLAEIERLSELAP 120 Query: 121 LHEPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHG 180 LH PA I+ F++VLP++ +VAVFDT+FH T+P +N+LYSLP YYE+Y AR+YG HG Sbjct: 121 LHNPAEAKVIRVFREVLPNVQNVAVFDTSFHQTMPVENYLYSLPMRYYEEYKARRYGAHG 180 Query: 181 IGNRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATR 240 ++YVSQRAAELLGKP E+LK+I HLG GASI V +GKS DTSMGFTP+ G+TM TR Sbjct: 181 TSHKYVSQRAAELLGKPIEELKIITCHLGNGASITAVDHGKSVDTSMGFTPLAGLTMGTR 240 Query: 241 SGDVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREV-EAAQATNPRAKV 299 SGD+D SL+ ++M+KEG+TD+ E I +LN +SGLLG+SG+S+DMR++ +AA+ N +A+V Sbjct: 241 SGDIDASLIPFIMKKEGITDVQEFIDILNNESGLLGLSGLSSDMRDLRDAARNGNEQAEV 300 Query: 300 AREIYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKND 359 A +I+ NRII+Y+G+Y+AEM G DAIVFT G+GEN +RK+V L +FG+ +D EKND Sbjct: 301 AIKIFKNRIIKYIGSYMAEMNGCDAIVFTGGIGENDRAVRKDVCASLTFFGVDLDEEKND 360 Query: 360 VRGVVRDISAKDSKIKTLLVPTDEELMIVRDVQTL 394 VRG IS ++SKI LLVPT+EELMIVRDV+ L Sbjct: 361 VRGKEGIISKENSKISVLLVPTEEELMIVRDVERL 395 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: 485 Number of extensions: 22 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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_009491778.1 C683_RS05475 (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.1881071.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-165 536.6 0.3 1.9e-165 536.4 0.3 1.0 1 NCBI__GCF_000313915.1:WP_009491778.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000313915.1:WP_009491778.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 536.4 0.3 1.9e-165 1.9e-165 5 404 .. 3 396 .. 1 397 [] 0.98 Alignments for each domain: == domain 1 score: 536.4 bits; conditional E-value: 1.9e-165 TIGR00016 5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 ++ +naGssslk++l++ + ek ++sg++eri l+ +ik ++ ++++ e++l i++h+ea++++ln+l NCBI__GCF_000313915.1:WP_009491778.1 3 YVIAVNAGSSSLKWKLFEVPE-EKEVASGIAERIGLDMGKIKLKKADGETVEKELPIPNHNEALTEILNSLI- 73 6999****************7.5556******************9999************************. PP TIGR00016 78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150 ++ki+ +l+ i+++GHRvv Gge++++sv+v++evl++i+++selAPlHnpae+++i+ + +vl++++nva NCBI__GCF_000313915.1:WP_009491778.1 74 EEKIIPSLDAITAVGHRVVAGGESYKDSVVVDEEVLAEIERLSELAPLHNPAEAKVIRVFR--EVLPNVQNVA 144 799**********************************************************..999******* PP TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223 vFDt+fHqt+p e+ylY+lP+++y+e++ RrYG+HGtshkyv+qraa+ll+kp+++l++i+cHlGnGas++av NCBI__GCF_000313915.1:WP_009491778.1 145 VFDTSFHQTMPVENYLYSLPMRYYEEYKARRYGAHGTSHKYVSQRAAELLGKPIEELKIITCHLGNGASITAV 217 ************************************************************************* PP TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls.ldeieetlnkksGllgisglssDlRdildk 295 Gks+dtsmG+tPL+Gl mGtRsGdiD ++i ++++++g + ++e ++ln +sGllg+sglssD+Rd+ d+ NCBI__GCF_000313915.1:WP_009491778.1 218 DHGKSVDTSMGFTPLAGLTMGTRSGDIDASLIPFIMKKEGITdVQEFIDILNNESGLLGLSGLSSDMRDLRDA 290 ****************************************985799*************************** PP TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368 ++gne+a++A+k++ +Ri kyig+y+a+++g DaivFtgGiGen+ vr++v+ +l ++G++ld+e+n NCBI__GCF_000313915.1:WP_009491778.1 291 ARNGNEQAEVAIKIFKNRIIKYIGSYMAEMNG-CDAIVFTGGIGENDRAVRKDVCASLTFFGVDLDEEKND-- 360 ******************************88.**************************************.. PP TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrla 404 +gke++is+e+sk+ vl +pt+eel+i++D+ rl+ NCBI__GCF_000313915.1:WP_009491778.1 361 VRGKEGIISKENSKISVLLVPTEEELMIVRDVERLT 396 9*******************************9997 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 17.14 // [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