Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_040659222.1 ON16_RS02895 acetate kinase
Query= BRENDA::P0CW05 (408 letters) >NCBI__GCF_000307265.1:WP_040659222.1 Length = 399 Score = 474 bits (1221), Expect = e-138 Identities = 234/399 (58%), Positives = 301/399 (75%), Gaps = 2/399 (0%) Query: 1 MKVLVINAGSSSLKYQLIDMTNESALAIGLCERIGIDNSIITQKRFDGKKLEKQTD--LP 58 MKVLVINAGSSSLKYQL+D LA GLCERIGID + + +GK+ K D +P Sbjct: 1 MKVLVINAGSSSLKYQLMDPDTGVVLAKGLCERIGIDGKFTYKPQIEGKETLKAVDVAMP 60 Query: 59 NHKIALEEVVKALTDSEFGVIKSMDEINAVGHRVVHGGEKFNSSALINEGVEQAIKDCFE 118 H A++ V+ AL D + GVI SM EI+AVGHRVVHGGE FN S I++ V AI++C Sbjct: 61 THSEAIQAVLNALVDPKNGVIGSMKEIDAVGHRVVHGGEAFNKSVRIDDKVMAAIEECVP 120 Query: 119 LAPLHNPPNMMGISSCQEIMPGVPMVAVFDTAFHHTIPPYAYMYALPYELYEKYGIRKYG 178 LAPLHNP N+ GI +C+++MP VPMVAVFDTAFH T+P A+ YALPYE Y+ +R+YG Sbjct: 121 LAPLHNPANITGIRACEKVMPNVPMVAVFDTAFHQTMPAKAFTYALPYEYYKNDKVRRYG 180 Query: 179 FHGTSHFYVAKRAAAMLGKPEQDVKVITCHLGNGSSITAVKGGKSIETTMGFTPLEGVAM 238 FHGTSH YV +RAAAMLGKP ++K+ITCHLGNGSS+TAV GGKS++T+MGFTPL G+ M Sbjct: 181 FHGTSHKYVTERAAAMLGKPAAELKIITCHLGNGSSVTAVDGGKSVDTSMGFTPLAGLPM 240 Query: 239 GTRCGSIDPAVVPFIMEKEGLSTREIDTLMNKKSGVLGVSSLSNDFRDLDEAASKGNQKA 298 GTR G +D ++ F+M K LS E+ ++NKKSGV G+S +S+DFRDL+EAA GNQ+A Sbjct: 241 GTRSGDLDAGILQFLMNKYKLSIDEMLNILNKKSGVQGISEVSSDFRDLEEAAKAGNQQA 300 Query: 299 ELALEIFAYKIKKVIGEYIAVLNGVDAIVFTAGIGENSASIRKRILADLDGIGIKIDEEK 358 +LAL+ F Y +KK+IG Y A + GVDAIVFTAG+GEN A+ R + +DLD +G+K+D Sbjct: 301 QLALDTFQYGVKKLIGSYAAAMGGVDAIVFTAGVGENDAATRMAVASDLDFMGVKMDAAA 360 Query: 359 NKIRGQEIDISTPDATVRVLVIPTNEELTIARDTKEICE 397 N +RG+E IST D+ V+VL+IPT+EEL IA+DT +C+ Sbjct: 361 NNVRGKETVISTADSKVKVLLIPTDEELMIAKDTAALCK 399 Lambda K H 0.317 0.135 0.379 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: 491 Number of extensions: 13 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: 408 Length of database: 399 Length adjustment: 31 Effective length of query: 377 Effective length of database: 368 Effective search space: 138736 Effective search space used: 138736 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_040659222.1 ON16_RS02895 (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.4190952.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-163 527.8 0.3 9.1e-163 527.6 0.3 1.0 1 NCBI__GCF_000307265.1:WP_040659222.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000307265.1:WP_040659222.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 527.6 0.3 9.1e-163 9.1e-163 4 404 .. 1 398 [. 1 399 [] 0.97 Alignments for each domain: == domain 1 score: 527.6 bits; conditional E-value: 9.1e-163 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv..edgekkeeeklaiedheeavkkllnt 74 +k+lv+naGssslk++l+d + vl++gl+eri +++++ + e e+ ++ +a++ h+ea++++ln+ NCBI__GCF_000307265.1:WP_040659222.1 1 MKVLVINAGSSSLKYQLMDPD-TGVVLAKGLCERIGIDGKFTYKPqiEGKETLKAVDVAMPTHSEAIQAVLNA 72 69******************9.57889***********99887652133444566778999************ PP TIGR00016 75 lkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146 l++ ++ ++ +++ei+++GHRvvhGge f++sv ++d+v+++i++ ++lAPlHnpa+++gi+a kv++++ NCBI__GCF_000307265.1:WP_040659222.1 73 LVDpKNGVIGSMKEIDAVGHRVVHGGEAFNKSVRIDDKVMAAIEECVPLAPLHNPANITGIRACE--KVMPNV 143 **999************************************************************..99**** PP TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219 + vavFDtafHqt+p +a+ YalPy++yk+ +vRrYGfHGtshkyvt+raa +l+kp+++l++i+cHlGnG+s NCBI__GCF_000307265.1:WP_040659222.1 144 PMVAVFDTAFHQTMPAKAFTYALPYEYYKNDKVRRYGFHGTSHKYVTERAAAMLGKPAAELKIITCHLGNGSS 216 ************************************************************************* PP TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292 v+av Gks+dtsmG+tPL+Gl mGtRsGd+D +i+++l+++ +ls+de+ ++lnkksG+ gis++ssD+Rd+ NCBI__GCF_000307265.1:WP_040659222.1 217 VTAVDGGKSVDTSMGFTPLAGLPMGTRSGDLDAGILQFLMNKYKLSIDEMLNILNKKSGVQGISEVSSDFRDL 289 ************************************************************************* PP TIGR00016 293 ldkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldleln 365 +++ ++gn++a+lAl+++ + ++k ig+y+a++ g +DaivFt+G+Gen+a r v ++l+++G+k+d + n NCBI__GCF_000307265.1:WP_040659222.1 290 EEAAKAGNQQAQLALDTFQYGVKKLIGSYAAAMGG-VDAIVFTAGVGENDAATRMAVASDLDFMGVKMDAAAN 361 *********************************76.************************************* PP TIGR00016 366 naarsgkesvisteeskvkvlviptneelviaeDalrla 404 n +gke+vist +skvkvl ipt+eel+ia+D++ l+ NCBI__GCF_000307265.1:WP_040659222.1 362 N--VRGKETVISTADSKVKVLLIPTDEELMIAKDTAALC 398 *..9*******************************9987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 14.37 // [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