Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_034527995.1 LOSG293_RS05510 acetate kinase
Query= BRENDA::Q9F1X7 (397 letters) >NCBI__GCF_000740055.1:WP_034527995.1 Length = 395 Score = 526 bits (1354), Expect = e-154 Identities = 255/394 (64%), Positives = 325/394 (82%), Gaps = 1/394 (0%) Query: 1 MSKIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKN 60 M K +AVNAGSSTLKFKL++MPEE ++ GV+ERI L S V IKYGDG+K+E+T D+++ Sbjct: 1 MGKSMAVNAGSSTLKFKLFQMPEETEISSGVVERIGLKDSLVLIKYGDGQKFEETLDIES 60 Query: 61 HEQAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAP 120 HEQAIQI+LDQLLDL IIK+Y+EI GVGHRVVAGGE F S +I V+++IESL E AP Sbjct: 61 HEQAIQIMLDQLLDLKIIKDYNEITGVGHRVVAGGELFSDSALIDDKVIEQIESLAEYAP 120 Query: 121 LHEPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHG 180 LH PA +GI+AFKK+LPDI SVAVFDT+FH ++P N++Y LPYEYYEK+ ARKYG HG Sbjct: 121 LHNPAEAMGIRAFKKLLPDIPSVAVFDTSFHTSMPAVNYMYPLPYEYYEKFGARKYGAHG 180 Query: 181 IGNRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATR 240 +RYV+ +AAE+LG+P EDLK++ H+GAGASI ++NGKS+DTSMGFTP+TG+ MATR Sbjct: 181 TSHRYVAHKAAEMLGRPLEDLKLVTLHIGAGASITAIQNGKSYDTSMGFTPLTGVMMATR 240 Query: 241 SGDVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREVEAAQATNPRAKVA 300 +GD+D SL+ Y+MEK + ++EMI +LN KSGL+G+SGVSADMR+VE Q N RAK+A Sbjct: 241 TGDIDVSLVKYLMEKLNI-GMDEMIDILNHKSGLIGVSGVSADMRDVEGVQDKNDRAKLA 299 Query: 301 REIYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKNDV 360 R++Y+ RI+RYVG Y+AE+ G DAIVFTAGVGEN TIR+EVA+ L +FGI VD EKN + Sbjct: 300 RDMYIERIVRYVGQYIAELDGVDAIVFTAGVGENDFTIRQEVADKLGFFGIKVDPEKNHI 359 Query: 361 RGVVRDISAKDSKIKTLLVPTDEELMIVRDVQTL 394 RGV RD+SA D+ +KTLL+PT+EELMIVRD++ L Sbjct: 360 RGVQRDLSADDATVKTLLIPTNEELMIVRDIERL 393 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: 479 Number of extensions: 15 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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_034527995.1 LOSG293_RS05510 (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.2222140.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-155 503.8 0.4 1.7e-155 503.6 0.4 1.0 1 NCBI__GCF_000740055.1:WP_034527995.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000740055.1:WP_034527995.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 503.6 0.4 1.7e-155 1.7e-155 6 404 .. 4 394 .. 1 395 [] 0.98 Alignments for each domain: == domain 1 score: 503.6 bits; conditional E-value: 1.7e-155 TIGR00016 6 ilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkd 78 + +naGss lkf+l+++ + e+ + sg+veri l+++ + ++ +++k ee+l+ie+he+a++ +l++l d NCBI__GCF_000740055.1:WP_034527995.1 4 SMAVNAGSSTLKFKLFQMPE-ETEISSGVVERIGLKDSLVLIKYGDGQKFEETLDIESHEQAIQIMLDQLL-D 74 589****************6.8888****************999999************************.8 PP TIGR00016 79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvav 151 ki+k+ +ei+ +GHRvv Gge f++s++++d+v+++i+ ++e+APlHnpae+ gi+a++ k l++ + vav NCBI__GCF_000740055.1:WP_034527995.1 75 LKIIKDYNEITGVGHRVVAGGELFSDSALIDDKVIEQIESLAEYAPLHNPAEAMGIRAFK--KLLPDIPSVAV 145 ************************************************************..889999***** PP TIGR00016 152 FDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavk 224 FDt+fH+ +p +y+Y+lPy++y+++g R+YG+HGtsh+yv+++aa++l++pl+dl+l+++H+G Gas++a++ NCBI__GCF_000740055.1:WP_034527995.1 146 FDTSFHTSMPAVNYMYPLPYEYYEKFGARKYGAHGTSHRYVAHKAAEMLGRPLEDLKLVTLHIGAGASITAIQ 218 ************************************************************************* PP TIGR00016 225 nGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkke 297 nGks+dtsmG+tPL G++m tR+GdiD ++++yl+e+l+ +de+ ++ln ksGl+g+sg+s+D+Rd++ + NCBI__GCF_000740055.1:WP_034527995.1 219 NGKSYDTSMGFTPLTGVMMATRTGDIDVSLVKYLMEKLNIGMDEMIDILNHKSGLIGVSGVSADMRDVEGVQ- 290 ********************************************************************9887. PP TIGR00016 298 egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaars 370 ++n++aklA ++y++Ri +y+g+yia+l+g +DaivFt+G+Gen+ ++r++v +kl ++G+k+d+e+n+ + NCBI__GCF_000740055.1:WP_034527995.1 291 DKNDRAKLARDMYIERIVRYVGQYIAELDG-VDAIVFTAGVGENDFTIRQEVADKLGFFGIKVDPEKNH--IR 360 8899************************88.**************************************..77 PP TIGR00016 371 gkesvisteeskvkvlviptneelviaeDalrla 404 g ++ +s ++++vk l iptneel+i++D+ rl NCBI__GCF_000740055.1:WP_034527995.1 361 GVQRDLSADDATVKTLLIPTNEELMIVRDIERLK 394 888889************************9986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.98 // [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