GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Oscillibacter ruminantium GH1

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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