Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 353219 BT3693 acetate kinase (NCBI ptt file)
Query= BRENDA::Q9WYB1 (403 letters) >FitnessBrowser__Btheta:353219 Length = 399 Score = 466 bits (1199), Expect = e-136 Identities = 235/401 (58%), Positives = 304/401 (75%), Gaps = 3/401 (0%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGD-EKHVIERELPDH 59 M++LV+N GSSSIKY+L +M ++V+ +G E+IG++GS L + + EK V+E+++P+H Sbjct: 1 MKILVLNCGSSSIKYKLFDMTTKEVIAQGGIEKIGLKGSFLKLTLPNGEKKVLEKDIPEH 60 Query: 60 EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119 ++ ILNTL+ + G IK L EI+AVGHR+VHGGERF ESVL+++EVL+A + LA Sbjct: 61 TIGVEFILNTLISPEYGAIKSLDEINAVGHRMVHGGERFSESVLLNKEVLEAFAACNDLA 120 Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179 PLHNPANL G+ A +LP +P V VFDTAFHQT+P AY+YAIPYE YEKY +RRYGFH Sbjct: 121 PLHNPANLKGVNAVSAILPNIPQVGVFDTAFHQTMPDYAYMYAIPYEMYEKYGVRRYGFH 180 Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239 GTSHRYVSKR E LG KIITCHIGNG S+AA+K GKC+DT+MG TPLEGL+MGT Sbjct: 181 GTSHRYVSKRVCEFLGVNPVGQKIITCHIGNGGSIAAIKDGKCIDTTMGLTPLEGLMMGT 240 Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299 RSGD+D FIMEKEG++ + ++LNKKSGV G+S G SSDMR++ A G+E Sbjct: 241 RSGDIDAGAVTFIMEKEGLNTTGISNLLNKKSGVLGIS-GVSSDMRELLAACANGNERAI 299 Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359 L ++Y YRI KYIGAYAAA+ GVD I+FT GVGEN RE VC +EF+G+KLD N Sbjct: 300 LAEKMYYYRIKKYIGAYAAALGGVDIILFTGGVGENQFECRESVCKDMEFMGIKLDNNVN 359 Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400 + +RG+E IIST DS+VKV+V+PT+EEL+IA DT +I++K Sbjct: 360 AK-VRGEEAIISTADSKVKVVVIPTDEELLIASDTMDILKK 399 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: 536 Number of extensions: 18 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: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 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 353219 BT3693 (acetate kinase (NCBI ptt file))
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.11284.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-162 526.7 0.7 2e-162 526.5 0.7 1.0 1 lcl|FitnessBrowser__Btheta:353219 BT3693 acetate kinase (NCBI ptt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353219 BT3693 acetate kinase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 526.5 0.7 2e-162 2e-162 4 403 .. 1 396 [. 1 398 [. 0.98 Alignments for each domain: == domain 1 score: 526.5 bits; conditional E-value: 2e-162 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk.d 78 +kilvln+Gsss+k++l+d++ +++v+++g +e+i l+++++k +++k+ +++i++h+ +v+++lntl + + lcl|FitnessBrowser__Btheta:353219 1 MKILVLNCGSSSIKYKLFDMT-TKEVIAQGGIEKIGLKGSFLKLTLPNGEKKVLEKDIPEHTIGVEFILNTLISpE 75 69*******************.59999**********************************************999 PP TIGR00016 79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDt 154 +k+l+ei+++GHR+vhGge+f+esv++++evl++ + +lAPlHnpa+l+g++av+ +l++ ++v vFDt lcl|FitnessBrowser__Btheta:353219 76 YGAIKSLDEINAVGHRMVHGGERFSESVLLNKEVLEAFAACNDLAPLHNPANLKGVNAVS--AILPNIPQVGVFDT 149 9***********************************************************..999*********** PP TIGR00016 155 afHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksid 230 afHqt+p+ ay+Ya+Py++y+++gvRrYGfHGtsh+yv++r+ + l+ + ++i+cH+GnG+s++a+k+Gk+id lcl|FitnessBrowser__Btheta:353219 150 AFHQTMPDYAYMYAIPYEMYEKYGVRRYGFHGTSHRYVSKRVCEFLGVNPVGQKIITCHIGNGGSIAAIKDGKCID 225 ************************************************9999************************ PP TIGR00016 231 tsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklA 306 t+mGltPLeGl+mGtRsGdiD +++++++e++gl + i ++lnkksG+lgisg+ssD+R++l++ ++gne+a lA lcl|FitnessBrowser__Btheta:353219 226 TTMGLTPLEGLMMGTRSGDIDAGAVTFIMEKEGLNTTGISNLLNKKSGVLGISGVSSDMRELLAACANGNERAILA 301 **************************************************************************** PP TIGR00016 307 lkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteesk 382 k+y +Ri+kyig+y+a+l g +D i+FtgG+Gen+ e+re v++++e++G+kld++ n +g+e++ist +sk lcl|FitnessBrowser__Btheta:353219 302 EKMYYYRIKKYIGAYAAALGG-VDIILFTGGVGENQFECRESVCKDMEFMGIKLDNNVNA-KVRGEEAIISTADSK 375 *******************76.************************************99.7899*********** PP TIGR00016 383 vkvlviptneelviaeDalrl 403 vkv+vipt+eel+ia D++ + lcl|FitnessBrowser__Btheta:353219 376 VKVVVIPTDEELLIASDTMDI 396 *****************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (399 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: 11.00 // [ok]
This GapMind analysis is from Sep 17 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