Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_045581906.1 AL072_RS00850 acetate/propionate family kinase
Query= SwissProt::P37877 (395 letters) >NCBI__GCF_001305595.1:WP_045581906.1 Length = 394 Score = 276 bits (707), Expect = 6e-79 Identities = 170/392 (43%), Positives = 231/392 (58%), Gaps = 20/392 (5%) Query: 4 IIAINAGSSSLKFQLFEMPS---ETVLTKGLVERIGIADSVFTISVNGE-----KNTEVT 55 I+ INAGSSSLKF +F V G + IG VF K+ E Sbjct: 5 ILVINAGSSSLKFSVFRDHGGGDPVVTLNGQISGIG-TQPVFEAKDAQRRPLAGKSWEAE 63 Query: 56 DIPDHAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDIS 115 + D + LL+ + E D + GHRVVHGG + + VLLT + E++ + Sbjct: 64 ERSDRKALLSYLLDWIEER---LDGATLIAAGHRVVHGGVRHAAPVLLTPAVMDELDGLV 120 Query: 116 ELAPLHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKY 175 LAPLH P N+ I+A E P +P VA FDTAFH+ P Q+ +++P E E+ G+R+Y Sbjct: 121 PLAPLHQPHNLAAIRALAEAHPELPQVACFDTAFHRNQPWQAQTFAIPRELTEE-GVRRY 179 Query: 176 GFHGTSHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVA 235 GFHG S++Y+ R E + L D R++ HLG+GAS+ A+ GG+S+D++MGFT L G+ Sbjct: 180 GFHGLSYEYIARRLPE-IAPELGDSRVVVAHLGSGASMCAIHGGRSVDSTMGFTALDGLP 238 Query: 236 MGTRSGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNER 295 MGTR G IDP ++ Y+M K G AD + L KSGLLG+SG S+D+R ++E+T + Sbjct: 239 MGTRCGTIDPGVLIYLMRK-GMDADGIEKMLYNKSGLLGVSGISNDMRALLEST---DPH 294 Query: 296 AETALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPA 355 A+ A+E+F RI K G+ AA M GVDA++FTAGIGE S VR RV L +MG+ D A Sbjct: 295 AQEAVELFCFRIAKETGALAASMGGVDALVFTAGIGERSAPVRARVGDKLAWMGMELDDA 354 Query: 356 LNNVRGEEAFISYPHSPVKVMIIPTDEEVMIA 387 N A IS P S + V +IPTDEE MIA Sbjct: 355 ANEANA--AKISTPGSRLPVYVIPTDEERMIA 384 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: 360 Number of extensions: 28 Number of successful extensions: 7 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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_045581906.1 AL072_RS00850 (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.1251500.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-112 362.3 0.0 1.6e-112 362.2 0.0 1.0 1 NCBI__GCF_001305595.1:WP_045581906.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001305595.1:WP_045581906.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.2 0.0 1.6e-112 1.6e-112 3 403 .. 2 390 .. 1 392 [. 0.88 Alignments for each domain: == domain 1 score: 362.2 bits; conditional E-value: 1.6e-112 TIGR00016 3 skkilvlnaGssslkfalldaensekv..llsglverikleeariktvedgekkeeeklaiedhe.eavkkll 72 s+ ilv+naGssslkf+++ +++ l+g + i + + +d++++ + + e+ e + k+ll NCBI__GCF_001305595.1:WP_045581906.1 2 SNAILVINAGSSSLKFSVFRDHGGGDPvvTLNGQISGIGTQPV--FEAKDAQRRPLAGKSWEAEErSDRKALL 72 678****************999854431256777777777766..5556665555444444333303345566 PP TIGR00016 73 ntlkkdkkilkel..seialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvl 143 + l + i + l + + + GHRvvhGg +++ v++t v++++ +++lAPlH p +l +i+a+ + + NCBI__GCF_001305595.1:WP_045581906.1 73 SYLLD--WIEERLdgATLIAAGHRVVHGGVRHAAPVLLTPAVMDELDGLVPLAPLHQPHNLAAIRALA--EAH 141 66663..45555511566677**********************************************9..999 PP TIGR00016 144 lkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGn 216 ++ ++va+FDtafH+ p +a +a+P++l +e gvRrYGfHG+s++y+++r+ ++ l d++++v+HlG NCBI__GCF_001305595.1:WP_045581906.1 142 PELPQVACFDTAFHRNQPWQAQTFAIPREL-TEEGVRRYGFHGLSYEYIARRLPEIAPE-LGDSRVVVAHLGS 212 99*************************776.567********************99877.9************ PP TIGR00016 217 GasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDl 289 Gas++a++ G+s+d +mG+t L+Gl mGtR+G iDp+++ yl+ +g+ +d ie++l ksGllg+sg+s+D+ NCBI__GCF_001305595.1:WP_045581906.1 213 GASMCAIHGGRSVDSTMGFTALDGLPMGTRCGTIDPGVLIYLMR-KGMDADGIEKMLYNKSGLLGVSGISNDM 284 ******************************************96.69************************** PP TIGR00016 290 RdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362 R +l+ + + +a+ A+++++ Riak g+ +as+ g +Da+vFt+GiGe +a vr++v +kl+ +G++ld NCBI__GCF_001305595.1:WP_045581906.1 285 RALLEST---DPHAQEAVELFCFRIAKETGALAASMGG-VDALVFTAGIGERSAPVRARVGDKLAWMGMELDD 353 ****999...6679**********************76.********************************** PP TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403 + n+ + + ist+ s++ v+vipt+ee +ia + r+ NCBI__GCF_001305595.1:WP_045581906.1 354 AANE----ANAAKISTPGSRLPVYVIPTDEERMIALHTRRV 390 9999....67789*********************9887765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (394 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15.57 // [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