Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_011798166.1 PNAP_RS22490 acetate/propionate family kinase
Query= SwissProt::P37877 (395 letters) >NCBI__GCF_000015505.1:WP_011798166.1 Length = 593 Score = 318 bits (814), Expect = 3e-91 Identities = 178/394 (45%), Positives = 244/394 (61%), Gaps = 30/394 (7%) Query: 3 KIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDHAV 62 +I+ INAGSSS+KF +F+M ++T K +E I G K T + IP V Sbjct: 2 RILVINAGSSSVKFSVFDMDTQTTRFKHEIE----------IGTIGFKAT-LAQIP---V 47 Query: 63 AVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPLHN 122 A L E G + ID IGHRV HGGE F D+ L+ D+ I IE ++ LAPLHN Sbjct: 48 A-------LVEAGETR----IDAIGHRVAHGGEHFRDATLVDDDVIAAIEVLAPLAPLHN 96 Query: 123 PANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGTSH 182 P + GI+ + PN P +AVFDTAFH ++P ++ Y++P + + K G+R+YGFHGTSH Sbjct: 97 PPALYGIETGRIYWPNAPQIAVFDTAFHASIPACAHTYAVP-QAWRKAGLRRYGFHGTSH 155 Query: 183 KYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRSGN 242 KYV ER A+ L +DLR+ISCHLGNGAS+ A++ G S+DTSMG T L G+ MG+RSG+ Sbjct: 156 KYVMERVAQELKASTRDLRIISCHLGNGASVCAIDRGVSVDTSMGVTALEGLVMGSRSGD 215 Query: 243 IDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETALEV 302 +DP + Y+ + DE+ N L +SGL +SG +D+R I A E + +A+ AL V Sbjct: 216 VDPGIFGYLQRSLALSIDEIENALYHESGLTALSGLGNDMRRIETAAAEADPQAQLALNV 275 Query: 303 FASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNVRGE 362 FA R KYIG+YAA M G D + FT GIGENS +R R+ LEF+G+Y D N+ Sbjct: 276 FAYRARKYIGAYAAAMGGCDVLAFTGGIGENSASMRRRICDRLEFLGLYLDEDRNSSVKL 335 Query: 363 EAF----ISYPHSPVKVMIIPTDEEVMIARDVVR 392 + F I PHS ++V++ T E+ MIA++V R Sbjct: 336 DGFAAPQIQQPHSRIRVIVTQTREQWMIAKEVHR 369 Lambda K H 0.317 0.136 0.381 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: 516 Number of extensions: 30 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: 395 Length of database: 593 Length adjustment: 34 Effective length of query: 361 Effective length of database: 559 Effective search space: 201799 Effective search space used: 201799 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: 52 (24.6 bits)
Align candidate WP_011798166.1 PNAP_RS22490 (acetate/propionate family 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.26279.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-129 418.4 0.0 1.9e-125 404.7 0.0 2.1 1 lcl|NCBI__GCF_000015505.1:WP_011798166.1 PNAP_RS22490 acetate/propionate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011798166.1 PNAP_RS22490 acetate/propionate family kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.7 0.0 1.9e-125 1.9e-125 4 403 .. 1 370 [. 1 372 [. 0.92 Alignments for each domain: == domain 1 score: 404.7 bits; conditional E-value: 1.9e-125 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkll 72 ++ilv+naGsss+kf+++d+ + +++ + k+e++ + +++++++ lcl|NCBI__GCF_000015505.1:WP_011798166.1 1 MRILVINAGSSSVKFSVFDMDT-QTT---RF-------------------KHEIEIGTIGFKATLAQIP 46 579****************994.222...11...................2223333444556677777 PP TIGR00016 73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklk 141 +l+ + i++iGHRv+hGge+f ++++v+d+v+++i+ +++lAPlHnp++l gie+ lcl|NCBI__GCF_000015505.1:WP_011798166.1 47 VALV-----EAGETRIDAIGHRVAHGGEHFRDATLVDDDVIAAIEVLAPLAPLHNPPALYGIETGR--I 108 7777.....467889*************************************************99..9 PP TIGR00016 142 vllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnli 210 ++a+++avFDtafH ip a+ Ya+P +++++ g+RrYGfHGtshkyv +r+a+ l ++ dl++i lcl|NCBI__GCF_000015505.1:WP_011798166.1 109 YWPNAPQIAVFDTAFHASIPACAHTYAVP-QAWRKAGLRRYGFHGTSHKYVMERVAQELKASTRDLRII 176 99***************************.89999********************************** PP TIGR00016 211 vcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGl 279 +cHlGnGasv+a+ G s+dtsmG+t LeGlvmG+RsGd+Dp+i yl+ l ls+deie++l +sGl lcl|NCBI__GCF_000015505.1:WP_011798166.1 177 SCHLGNGASVCAIDRGVSVDTSMGVTALEGLVMGSRSGDVDPGIFGYLQRSLALSIDEIENALYHESGL 245 ********************************************************************* PP TIGR00016 280 lgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrel 348 ++sgl +D+R i+ + +e + +a+lAl+v+++R +kyig+y+a++ g D + FtgGiGen+a++r++ lcl|NCBI__GCF_000015505.1:WP_011798166.1 246 TALSGLGNDMRRIETAAAEADPQAQLALNVFAYRARKYIGAYAAAMGG-CDVLAFTGGIGENSASMRRR 313 **********************************************76.******************** PP TIGR00016 349 vleklevlGlkldlelnnaarsg..kesvisteeskvkvlviptneelviaeDalrl 403 ++++le+lGl+ld+++n + i +++s+++v+v +t e+++ia+++ r+ lcl|NCBI__GCF_000015505.1:WP_011798166.1 314 ICDRLEFLGLYLDEDRNSSVKLDgfAAPQIQQPHSRIRVIVTQTREQWMIAKEVHRF 370 *****************9654431145679**********************99886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (593 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 6.04 // [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