Alignments for a candidate for pta in Aquimarina agarilytica ZC1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Aquimarina agarilytica ZC1

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_010181310.1 KQA_RS0211605 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000255455.1:WP_010181310.1
          Length = 697

 Score =  357 bits (916), Expect = e-103
 Identities = 178/327 (54%), Positives = 236/327 (72%), Gaps = 2/327 (0%)

Query: 1   MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60
           ++  +F+  LLKRA+ +   IVLPEG D+RI+ A  +LL   + D+ +LG+ VKIK +A 
Sbjct: 368 VTPRMFQYNLLKRAQTQRKRIVLPEGYDERIIRATSRLLASGVVDVILLGNEVKIKNKAV 427

Query: 61  ELGL--HLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHN 118
           +LG+   L    +++P+  P  +++ +   ELRK K+V +D AR++M D+SYFGTMM++ 
Sbjct: 428 KLGVPFDLKRMTIIDPVNSPHFDDYVQTLYELRKHKNVNMDMARDLMADVSYFGTMMIYK 487

Query: 119 GDADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTA 178
           G ADGMVSGA NTT HTI+P+ Q IKT P ASVVSS+F M L GR+  FGDCA+NPNP A
Sbjct: 488 GHADGMVSGAVNTTQHTIRPALQFIKTKPTASVVSSVFFMCLEGRVSIFGDCAINPNPNA 547

Query: 179 EQLGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDG 238
            QL EIA+ SA TA  FGI+ ++A+LSYS+G+SG G DVD+  +A    +    +L ++G
Sbjct: 548 AQLAEIAIASADTAVNFGIEAKIAMLSYSSGDSGKGVDVDKVREATKIVKEKRTDLKIEG 607

Query: 239 PLQFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGL 298
           P+Q+DAAVD  V + K+P+S+VAGQA+V IFPDL  GN  YK  QR   ALA+GP+LQGL
Sbjct: 608 PIQYDAAVDYAVGKSKLPNSEVAGQASVLIFPDLNTGNNTYKAVQRETGALAIGPMLQGL 667

Query: 299 NKPVNDLSRGATVPDIVNTVAITAIQA 325
           NKPVNDLSRG TV DI NTV ITAIQA
Sbjct: 668 NKPVNDLSRGCTVADIYNTVIITAIQA 694


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: 494
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: 697
Length adjustment: 33
Effective length of query: 296
Effective length of database: 664
Effective search space:   196544
Effective search space used:   196544
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_010181310.1 KQA_RS0211605 (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.3278791.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-127  411.1   0.6   2.6e-127  410.5   0.6    1.3  1  NCBI__GCF_000255455.1:WP_010181310.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000255455.1:WP_010181310.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.5   0.6  2.6e-127  2.6e-127       1     304 []     388     691 ..     388     691 .. 0.99

  Alignments for each domain:
  == domain 1  score: 410.5 bits;  conditional E-value: 2.6e-127
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEg +er+++A + l+ +++++ +ll+n+ +++++    +v  +l++++++dp  s++ ++yv++lye+r
  NCBI__GCF_000255455.1:WP_010181310.1 388 IVLPEGYDERIIRATSRLLASGVVDVILLGNEVKIKNKaVKLGVPFDLKRMTIIDPVNSPHFDDYVQTLYELR 460
                                           8*****************************9999988745678999*************************** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           khk v++ +ar+ + D ++++++++++g+adg+vsGav+tt++t+rpalq ikt+++ ++vssvf+m++e +v
  NCBI__GCF_000255455.1:WP_010181310.1 461 KHKNVNMDMARDLMADVSYFGTMMIYKGHADGMVSGAVNTTQHTIRPALQFIKTKPTASVVSSVFFMCLEGRV 533
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                            +f+DCa++++Pna +LAeiA+ sa++a ++g +e k+a+lsys++ sgkg +v+kv+eA+ki+kek++dl++
  NCBI__GCF_000255455.1:WP_010181310.1 534 SIFGDCAINPNPNAAQLAEIAIASADTAVNFG-IEAKIAMLSYSSGDSGKGVDVDKVREATKIVKEKRTDLKI 605
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           +G++q+DaA+   v ++k p+sevag+a v++FPdL++Gn++Yk+vqR+++a aiGP+lqGl+kPvnDLsRG+
  NCBI__GCF_000255455.1:WP_010181310.1 606 EGPIQYDAAVDYAVGKSKLPNSEVAGQASVLIFPDLNTGNNTYKAVQRETGALAIGPMLQGLNKPVNDLSRGC 678
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v di+n+viita
  NCBI__GCF_000255455.1:WP_010181310.1 679 TVADIYNTVIITA 691
                                           ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (697 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 35.19
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources