GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Mariniradius saccharolyticus AK6

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_008623525.1 C943_RS01285 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000330725.2:WP_008623525.1
          Length = 698

 Score =  344 bits (883), Expect = 3e-99
 Identities = 180/327 (55%), Positives = 234/327 (71%), Gaps = 2/327 (0%)

Query: 1   MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60
           ++  +F+  L+  AR +  HIVLPEG D+RIL AA +L+ Q I ++T+LG+   I     
Sbjct: 370 ITPRMFQYQLVSWARNKKKHIVLPEGIDERILKAADRLVRQGIVNVTLLGNLNDITGTIN 429

Query: 61  ELGLHL--NTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHN 118
            LGL L  +   +++P      E++A+   ELRK K++ ++ AR++M D+SYFGTMMVH 
Sbjct: 430 RLGLQLTQDNCQIIDPHDSIFFEDYAQTLFELRKGKNMPLEVARDLMTDVSYFGTMMVHK 489

Query: 119 GDADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTA 178
           G ADGMVSGA +TTAHTI+P+ Q IKT P  S+VSSIF M L  R+  FGDCA+N NPTA
Sbjct: 490 GHADGMVSGAMHTTAHTIRPALQFIKTKPGISLVSSIFFMCLPDRVTVFGDCAININPTA 549

Query: 179 EQLGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDG 238
           E+L EIA+ SA TA +FGI+PRVA+LSYS+G SG G DV++   A    R+   ++ V+G
Sbjct: 550 EELAEIAISSADTATKFGIEPRVAMLSYSSGASGTGEDVEKVRTATELVRQNRKDIKVEG 609

Query: 239 PLQFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGL 298
           P+Q+DAAVDP   ++KMPDS+VAGQA+V IFPDL  GN  YK  QR   A+A+GP+LQGL
Sbjct: 610 PIQYDAAVDPLTGKQKMPDSEVAGQASVLIFPDLNTGNNTYKAVQRETGAIAIGPMLQGL 669

Query: 299 NKPVNDLSRGATVPDIVNTVAITAIQA 325
           NKPVNDLSRG TV DI NTV ITAIQA
Sbjct: 670 NKPVNDLSRGCTVDDIFNTVVITAIQA 696


Lambda     K      H
   0.318    0.134    0.386 

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: 537
Number of extensions: 24
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: 329
Length of database: 698
Length adjustment: 33
Effective length of query: 296
Effective length of database: 665
Effective search space:   196840
Effective search space used:   196840
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_008623525.1 C943_RS01285 (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.2151942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-127  410.9   0.0   3.9e-127  409.9   0.0    1.5  1  NCBI__GCF_000330725.2:WP_008623525.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330725.2:WP_008623525.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.9   0.0  3.9e-127  3.9e-127       1     304 []     390     693 ..     390     693 .. 0.98

  Alignments for each domain:
  == domain 1  score: 409.9 bits;  conditional E-value: 3.9e-127
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEg +er+lkAa  l++++i++ +ll+n ++++ + +  +++l+  +++++dp+ s   e+y+++l+e+r
  NCBI__GCF_000330725.2:WP_008623525.1 390 IVLPEGIDERILKAADRLVRQGIVNVTLLGNLNDITGTiNRLGLQLTQDNCQIIDPHDSIFFEDYAQTLFELR 462
                                           8*********************************999545556666667899*****999************* PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k k + ++ ar+ ++D +++++++v++g+adg+vsGa +tta+t+rpalq ikt++g++lvss+f+m+++++v
  NCBI__GCF_000330725.2:WP_008623525.1 463 KGKNMPLEVARDLMTDVSYFGTMMVHKGHADGMVSGAMHTTAHTIRPALQFIKTKPGISLVSSIFFMCLPDRV 535
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                            vf+DCa++++P+aeeLAeiA++sa++a ++g +ep+va+lsys+++sg ge+vekv+ A++++++ + d+++
  NCBI__GCF_000330725.2:WP_008623525.1 536 TVFGDCAININPTAEELAEIAISSADTATKFG-IEPRVAMLSYSSGASGTGEDVEKVRTATELVRQNRKDIKV 607
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           +G++q+DaA+ +   ++k+p+sevag+a v++FPdL++Gn++Yk+vqR+++a aiGP+lqGl+kPvnDLsRG+
  NCBI__GCF_000330725.2:WP_008623525.1 608 EGPIQYDAAVDPLTGKQKMPDSEVAGQASVLIFPDLNTGNNTYKAVQRETGAIAIGPMLQGLNKPVNDLSRGC 680
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+di+n+v+ita
  NCBI__GCF_000330725.2:WP_008623525.1 681 TVDDIFNTVVITA 693
                                           ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (698 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: 39.83
//
[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