Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_022530349.1 L248_RS11225 acetate kinase
Query= SwissProt::P37877 (395 letters) >NCBI__GCF_000469325.1:WP_022530349.1 Length = 396 Score = 392 bits (1007), Expect = e-114 Identities = 202/394 (51%), Positives = 272/394 (69%), Gaps = 2/394 (0%) Query: 1 MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTIS-VNGEKNTEVTDIPD 59 M K++AINAGSS+LKFQ+ MP ET+L G ++R +V TI G+K+ ++ D Sbjct: 1 MPKVLAINAGSSTLKFQVIAMPEETLLASGGIDRASSPAAVLTIKDAQGQKHESRANLED 60 Query: 60 HAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAP 119 AV LL L G++ E+ GIGHRVV GGEKF+ +T + I++I ++E AP Sbjct: 61 IDQAVDTLLTTLVAQGVLSAPEELAGIGHRVVAGGEKFAAPTRVTPQVIQDIAALAEYAP 120 Query: 120 LHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHG 179 LHNP+ I AF + LP VP VAVFDTAFHQTMP +YLYS+P +YY +G R+YG HG Sbjct: 121 LHNPSEAAYIAAFTKRLPGVPEVAVFDTAFHQTMPRVNYLYSIPMQYYRDYGARRYGAHG 180 Query: 180 TSHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTR 239 TSH YV AA+LL R L DL+LI+ HLGNGAS AA+ G+S+DTSMGFTPLAG+ MGTR Sbjct: 181 TSHAYVAREAAKLLHRDLADLKLITLHLGNGASAAAITHGESLDTSMGFTPLAGLTMGTR 240 Query: 240 SGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETA 299 SG+IDP+L+ Y+ KT Q+ +++ LN +SG+LG++G SSD RDI A + GNERA Sbjct: 241 SGDIDPSLVAYLAGKTHQSFQDMVQVLNDQSGMLGLTGLSSDFRDIDAAAQAGNERAILG 300 Query: 300 LEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNV 359 +F +R+ KYIG+Y A M G+DAI+FT G+GE+ +R VLR L +MG+ DPA N Sbjct: 301 ERIFVNRVVKYIGAYTAEMGGLDAIVFTGGVGEHRGSLRHGVLRQLAYMGMTEDPAQVNA 360 Query: 360 RGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRL 393 + AF++ P + V+ ++I T+EEVMIAR V++L Sbjct: 361 QA-TAFLTTPEARVQALVITTNEEVMIARSVMKL 393 Lambda K H 0.317 0.136 0.381 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: 392 Number of extensions: 15 Number of successful extensions: 3 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: 395 Length of database: 396 Length adjustment: 31 Effective length of query: 364 Effective length of database: 365 Effective search space: 132860 Effective search space used: 132860 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_022530349.1 L248_RS11225 (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.479566.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-143 462.4 0.0 6.5e-143 462.2 0.0 1.0 1 NCBI__GCF_000469325.1:WP_022530349.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000469325.1:WP_022530349.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 462.2 0.0 6.5e-143 6.5e-143 4 404 .. 2 394 .. 1 395 [. 0.98 Alignments for each domain: == domain 1 score: 462.2 bits; conditional E-value: 6.5e-143 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 k+l +naGss lkf+++ + + e++l+sg ++r ++ a+++++ +++k+e + ed ++av++ll+tl+ NCBI__GCF_000469325.1:WP_022530349.1 2 PKVLAINAGSSTLKFQVIAMPE-ETLLASGGIDRASSPAAVLTIKDAQGQKHESRANLEDIDQAVDTLLTTLV 73 69*******************5.99***************9999999999*********************** PP TIGR00016 77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149 + + +l +e+a iGHRvv Ggekf+ + vt +v+++i+ ++e+APlHnp+e+ i a++ k l+ +++v NCBI__GCF_000469325.1:WP_022530349.1 74 A-QGVLSAPEELAGIGHRVVAGGEKFAAPTRVTPQVIQDIAALAEYAPLHNPSEAAYIAAFT--KRLPGVPEV 143 5.99**********************************************************..99999**** PP TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222 avFDtafHqt+p+ +ylY++P+++y+++g RrYG+HGtsh yv+++aakll + l+dl+li++HlGnGas +a NCBI__GCF_000469325.1:WP_022530349.1 144 AVFDTAFHQTMPRVNYLYSIPMQYYRDYGARRYGAHGTSHAYVAREAAKLLHRDLADLKLITLHLGNGASAAA 216 ************************************************************************* PP TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295 + G+s+dtsmG+tPL+Gl mGtRsGdiDp+++ yla ++ +s ++++++ln +sG+lg++glssD+Rdi ++ NCBI__GCF_000469325.1:WP_022530349.1 217 ITHGESLDTSMGFTPLAGLTMGTRSGDIDPSLVAYLAGKTHQSFQDMVQVLNDQSGMLGLTGLSSDFRDIDAA 289 ************************************************************************* PP TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368 ++gne+a l +++v+R+ kyig+y+a++ g lDaivFtgG+Ge ++r+ vl++l+ +G+ d+++ n NCBI__GCF_000469325.1:WP_022530349.1 290 AQAGNERAILGERIFVNRVVKYIGAYTAEMGG-LDAIVFTGGVGEHRGSLRHGVLRQLAYMGMTEDPAQVN-- 359 ******************************76.**********************************9998.. PP TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrla 404 + ++++t+e++v++lvi tnee++ia+ +++l+ NCBI__GCF_000469325.1:WP_022530349.1 360 -AQATAFLTTPEARVQALVITTNEEVMIARSVMKLT 394 .78899**************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (396 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: 00:00:00.01 # Mc/sec: 15.87 // [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