Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_009121835.1 BUB52_RS13600 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_900129655.1:WP_009121835.1 Length = 398 Score = 464 bits (1195), Expect = e-135 Identities = 234/401 (58%), Positives = 301/401 (75%), Gaps = 4/401 (0%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGD-EKHVIERELPDH 59 M+VLV+N GSSSIKY+L +M+ ++V+ +G E+IG++GS L + D EK ++E+++P+H Sbjct: 1 MKVLVLNCGSSSIKYKLFDMDHKEVIAQGGIEKIGLKGSFLKLTLPDGEKKILEKDIPEH 60 Query: 60 EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119 ++ ILNTL+ + G IK L EI+AVGHR+VHGGE+F ESVL+ +EVL A + LA Sbjct: 61 TVGVEFILNTLISSEYGAIKSLDEINAVGHRMVHGGEKFSESVLLTQEVLDAFTACNDLA 120 Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179 PLHNPANL G+ A +LP VP + VFDTAFHQT+P AY+YA+PYE YEKY +RRYGFH Sbjct: 121 PLHNPANLKGVNAVSAILPDVPQIGVFDTAFHQTMPDYAYMYAVPYELYEKYGVRRYGFH 180 Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239 GTSHRYVSKR E LG + E KIITCHIGNG SV+A+K GKC+DTSMG TPLEGL+MGT Sbjct: 181 GTSHRYVSKRVCEFLGVQPEGKKIITCHIGNGGSVSAIKDGKCMDTSMGLTPLEGLMMGT 240 Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299 RSGD+D FIM+KE + + ++LNKKSGV G+ G SSDMRD+E A G+ Sbjct: 241 RSGDIDAGAVTFIMDKENLDANGVSNLLNKKSGVMGIF-GESSDMRDLENAVAAGNPRAI 299 Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359 L ++Y YRI KY+GAYAAA+ GVD IVFT GVGEN R +VC L F+GVK+D +KN Sbjct: 300 LAEKMYFYRIKKYVGAYAAALGGVDIIVFTGGVGENQCNCRSEVCEGLGFMGVKVDLEKN 359 Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400 + +RG+E +IST DS+VKV+V+PT+EELMIA DT I+ K Sbjct: 360 K--VRGEEAVISTDDSKVKVVVIPTDEELMIASDTMAILSK 398 Lambda K H 0.318 0.138 0.391 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: 535 Number of extensions: 23 Number of successful extensions: 4 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: 403 Length of database: 398 Length adjustment: 31 Effective length of query: 372 Effective length of database: 367 Effective search space: 136524 Effective search space used: 136524 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_009121835.1 BUB52_RS13600 (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.1270360.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-162 525.1 0.2 6e-162 524.9 0.2 1.0 1 NCBI__GCF_900129655.1:WP_009121835.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900129655.1:WP_009121835.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 524.9 0.2 6e-162 6e-162 4 403 .. 1 395 [. 1 397 [. 0.98 Alignments for each domain: == domain 1 score: 524.9 bits; conditional E-value: 6e-162 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 +k+lvln+Gsss+k++l+d+ ++v+++g +e+i l+++++k +++k+ +++i++h+ +v+++lntl NCBI__GCF_900129655.1:WP_009121835.1 1 MKVLVLNCGSSSIKYKLFDMD-HKEVIAQGGIEKIGLKGSFLKLTLPDGEKKILEKDIPEHTVGVEFILNTLI 72 69******************9.58899****************99999999999******************9 PP TIGR00016 77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148 + + +k+l+ei+++GHR+vhGgekf+esv++t+evl++ +lAPlHnpa+l+g++av+ +l+++++ NCBI__GCF_900129655.1:WP_009121835.1 73 SsEYGAIKSLDEINAVGHRMVHGGEKFSESVLLTQEVLDAFTACNDLAPLHNPANLKGVNAVS--AILPDVPQ 143 98999**********************************************************..999***** PP TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221 + vFDtafHqt+p+ ay+Ya+Py+ly+++gvRrYGfHGtsh+yv++r+ + l+ + + ++i+cH+GnG+svs NCBI__GCF_900129655.1:WP_009121835.1 144 IGVFDTAFHQTMPDYAYMYAVPYELYEKYGVRRYGFHGTSHRYVSKRVCEFLGVQPEGKKIITCHIGNGGSVS 216 ************************************************************************* PP TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294 a+k+Gk++dtsmGltPLeGl+mGtRsGdiD +++++++++++l ++ + ++lnkksG++gi g ssD+Rd+++ NCBI__GCF_900129655.1:WP_009121835.1 217 AIKDGKCMDTSMGLTPLEGLMMGTRSGDIDAGAVTFIMDKENLDANGVSNLLNKKSGVMGIFGESSDMRDLEN 289 ************************************************************************* PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 ++++gn +a lA k+y +Ri+ky+g+y+a+l g +D ivFtgG+Gen+ ++r +v+e+l ++G+k+dle+n+ NCBI__GCF_900129655.1:WP_009121835.1 290 AVAAGNPRAILAEKMYFYRIKKYVGAYAAALGG-VDIIVFTGGVGENQCNCRSEVCEGLGFMGVKVDLEKNK- 360 *******************************76.**************************************. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403 +g+e+vist++skvkv+vipt+eel+ia D++ + NCBI__GCF_900129655.1:WP_009121835.1 361 -VRGEEAVISTDDSKVKVVVIPTDEELMIASDTMAI 395 .9******************************9865 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: 27.22 // [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