Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate SM_b21184 SM_b21184 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >FitnessBrowser__Smeli:SM_b21184 Length = 392 Score = 257 bits (656), Expect = 5e-73 Identities = 161/402 (40%), Positives = 235/402 (58%), Gaps = 22/402 (5%) Query: 3 VLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGS-RLVHRVGDEKHVIEREL----- 56 +LVIN+GSSS+K+Q+ + + + A+ GI RL D +I R L Sbjct: 4 LLVINAGSSSLKFQIFGIATAGLERQVRAKLDGIATQPRLKATAADGTELINRRLDATAV 63 Query: 57 PDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116 PD EAL ++ + L ++ ++ A+GHRVVHGG + VL++ VL + Sbjct: 64 PDLPEAL-----SVARDWLATLRGF-DLRAIGHRVVHGGPDYVRPVLIETTVLDRLASYQ 117 Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176 LAPLH P NL I+ AM + P VP VA FDTAFH+ + YA+P +YE+ +RRY Sbjct: 118 DLAPLHQPNNLAPIRLAMDIKPDVPQVACFDTAFHRGRTEHTDCYALPRTFYEQ-GVRRY 176 Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236 GFHG S+ Y++ R E+ ++ ++I H+G+GAS+ A+K G+ V+T+MGFT L+GL Sbjct: 177 GFHGISYEYIAGRLREV-APEVARGRVIVAHLGSGASMCALKDGRSVETTMGFTALDGLP 235 Query: 237 MGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDE 296 MGTR G LDP + ++ +G+S Q + D+L +SG+ GLS G S+DMR++ + D Sbjct: 236 MGTRPGQLDPGVVLHLLTDQGMSAQAVSDLLYHRSGLKGLS-GISNDMRELLGS---DDP 291 Query: 297 WCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDK 356 ++ + +R A G AAA+ G+DA VFTAG+GENS R V L +LG +LD Sbjct: 292 RASFAIDHFVHRCALDAGMLAAALGGLDAFVFTAGIGENSAPIRARVSEGLAWLGAELDP 351 Query: 357 QKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398 N+ +IS SRV + V+PT+EELMIAR T I+ Sbjct: 352 AAND----AGASVISKAGSRVALHVMPTDEELMIARHTLAII 389 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: 360 Number of extensions: 17 Number of successful extensions: 6 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: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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 SM_b21184 SM_b21184 (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.9065.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-107 345.3 0.0 2.4e-107 345.1 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SM_b21184 SM_b21184 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b21184 SM_b21184 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 345.1 0.0 2.4e-107 2.4e-107 5 402 .. 3 387 .. 1 390 [. 0.89 Alignments for each domain: == domain 1 score: 345.1 bits; conditional E-value: 2.4e-107 TIGR00016 5 kilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 +lv+naGssslkf+++ ++ + + +++ + i + t dg e + + ++av l ++l lcl|FitnessBrowser__Smeli:SM_b21184 3 ALLVINAGSSSLKFQIFGIATaGLERQVRAKLDGIATQPRLKATAADGT----ELINRRLDATAVPDLPEALSV 72 68***************99874334448888999998888555555553....334444445566666666665 PP TIGR00016 78 dkkilk..elseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149 ++ l ++++iGHRvvhGg ++ v++++ vl++++ +lAPlH p++l i+ ++ +++++++v lcl|FitnessBrowser__Smeli:SM_b21184 73 ARDWLAtlRGFDLRAIGHRVVHGGPDYVRPVLIETTVLDRLASYQDLAPLHQPNNLAPIRLAM--DIKPDVPQV 144 33333300345899***********************************************99..88999**** PP TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223 a+FDtafH+ e++ YalP+ +y e+gvRrYGfHG+s++y++ r+ ++ ++ ++iv+HlG Gas++a+ lcl|FitnessBrowser__Smeli:SM_b21184 145 ACFDTAFHRGRTEHTDCYALPRTFY-EQGVRRYGFHGISYEYIAGRLREVAPE-VARGRVIVAHLGSGASMCAL 216 *********************8877.57*******************998776.999***************** PP TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkke 297 k+G+s++t+mG+t L+Gl mGtR G++Dp+++ +l + +g+s++++ ++l +sGl g+sg+s+D+R++l lcl|FitnessBrowser__Smeli:SM_b21184 217 KDGRSVETTMGFTALDGLPMGTRPGQLDPGVVLHLLTDQGMSAQAVSDLLYHRSGLKGLSGISNDMRELLGSD- 289 *********************************************************************9987. PP TIGR00016 298 egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsg 371 + +a+ A++ +vhR a g +a+l g lDa vFt+GiGen+a +r++v e+l+ lG +ld++ n lcl|FitnessBrowser__Smeli:SM_b21184 290 --DPRASFAIDHFVHRCALDAGMLAAALGG-LDAFVFTAGIGENSAPIRARVSEGLAWLGAELDPAAND----A 356 ..7899**********************76.***********************************999....7 PP TIGR00016 372 kesvisteeskvkvlviptneelviaeDalr 402 svis+ s+v + v+pt+eel+ia+ +l lcl|FitnessBrowser__Smeli:SM_b21184 357 GASVISKAGSRVALHVMPTDEELMIARHTLA 387 889***********************98775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (392 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: 8.36 // [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