Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_040660986.1 ON16_RS06275 phosphate acetyltransferase
Query= metacyc::MONOMER-13062 (328 letters) >NCBI__GCF_000307265.1:WP_040660986.1 Length = 330 Score = 313 bits (803), Expect = 3e-90 Identities = 162/326 (49%), Positives = 219/326 (67%), Gaps = 7/326 (2%) Query: 3 LFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALNVS 62 +FE L SK+K K+VF EG D RI+ A++RL + PVL+GN + A+ + + Sbjct: 1 MFEFLISKLKAHPRKIVFTEGTDARILEASARLLSGTFLTPVLVGNPDAVAAAAEDVGFN 60 Query: 63 LDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVDGM 122 + G E++D EN ++MV ++VE RKGK QA L+ NYFGT +V M D + Sbjct: 61 IRGAEVIDPENF--SEMEKMVASLVELRKGKVDEAQARTLLRQGNYFGTMLVKMGYADAL 118 Query: 123 VSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQK----GDQRYL-FADCAININPNET 177 + GA + T DTVRPALQIIKTKPG ++S F++ + GD+ L DCAINI PNE Sbjct: 119 LGGATYSTADTVRPALQIIKTKPGSKIVSSCFILVRPSATGDREVLAMGDCAINIKPNED 178 Query: 178 QLAEIAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGE 237 +L EI +E+ TARLF +DP++A LS+ST GS K +V+K+ NA + P + +DGE Sbjct: 179 ELVEIGLETAATARLFGVDPKMAFLSYSTLGSGKGEDVDKMRNACAKVKAAAPELSVDGE 238 Query: 238 MQFDAAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLN 297 MQFDAA P VA K +S+VAGHA F+FP++ +GNIGYKIAQR+G F+A GPILQGLN Sbjct: 239 MQFDAAVSPRVAHTKCPESQVAGHANTFIFPDINAGNIGYKIAQRLGSFDAYGPILQGLN 298 Query: 298 KPVSDLSRGCNAEDVYKVSIITATQA 323 P++DLSRGCNA++VY ++IITA A Sbjct: 299 APINDLSRGCNAQEVYSMAIITAALA 324 Lambda K H 0.315 0.133 0.369 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: 320 Number of extensions: 13 Number of successful extensions: 3 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: 328 Length of database: 330 Length adjustment: 28 Effective length of query: 300 Effective length of database: 302 Effective search space: 90600 Effective search space used: 90600 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: 49 (23.5 bits)
Align candidate WP_040660986.1 ON16_RS06275 (phosphate acetyltransferase)
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))
# 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/TIGR00651.hmm # target sequence database: /tmp/gapView.2107214.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00651 [M=304] Accession: TIGR00651 Description: pta: phosphate acetyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-112 359.7 0.0 8.5e-112 359.5 0.0 1.0 1 NCBI__GCF_000307265.1:WP_040660986.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000307265.1:WP_040660986.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 359.5 0.0 8.5e-112 8.5e-112 1 304 [] 16 321 .. 16 321 .. 0.99 Alignments for each domain: == domain 1 score: 359.5 bits; conditional E-value: 8.5e-112 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 iv+ Eg+++r+l+A a l++ +++vl++n +++ + +a++v ++ +v+dp+ + ++ek v l+e+rk NCBI__GCF_000307265.1:WP_040660986.1 16 IVFTEGTDARILEASARLLSGTFLTPVLVGNPDAVAA-AAEDVGFNIRGAEVIDPENFSEMEKMVASLVELRK 87 8*************************99999988887.99********************************* PP TIGR00651 74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee... 143 k v+e++ar+ lr ++++++lv++g+ad+l Ga ++ta+t+rpalqiikt++g+k+vss+fi+ +++ NCBI__GCF_000307265.1:WP_040660986.1 88 GK-VDEAQARTLLRQGNYFGTMLVKMGYADALLGGATYSTADTVRPALQIIKTKPGSKIVSSCFILVRPSatg 159 **.****************************************************************999999 PP TIGR00651 144 ..evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekep 214 evl +DCa++++Pn +eL ei l++a++a+ +g +pk+a+lsyst gsgkge+v+k+++A + +k +p NCBI__GCF_000307265.1:WP_040660986.1 160 drEVLAMGDCAINIKPNEDELVEIGLETAATARLFG-VDPKMAFLSYSTLGSGKGEDVDKMRNACAKVKAAAP 231 99**********************************.************************************ PP TIGR00651 215 dllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDL 287 +l++dGe+qfDaA+ + va+ k+pes+vag+an+f+FPd++aGnigYki+qRl++++a+GPilqGl+ P+nDL NCBI__GCF_000307265.1:WP_040660986.1 232 ELSVDGEMQFDAAVSPRVAHTKCPESQVAGHANTFIFPDINAGNIGYKIAQRLGSFDAYGPILQGLNAPINDL 304 ************************************************************************* PP TIGR00651 288 sRGasvedivnvviita 304 sRG+++++++ ++iita NCBI__GCF_000307265.1:WP_040660986.1 305 SRGCNAQEVYSMAIITA 321 ***************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (330 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: 00:00:00.00 # Mc/sec: 18.05 // [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