Alignments for a candidate for pta in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Desulfobulbus mediterraneus DSM 13871

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_028585908.1 G494_RS0119815 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000429965.1:WP_028585908.1
          Length = 706

 Score =  343 bits (879), Expect = 1e-98
 Identities = 179/329 (54%), Positives = 237/329 (72%), Gaps = 4/329 (1%)

Query: 1   MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60
           ++  +FE  L+++A ++  HIVLPEG   R+L AA  +L + I D+T+LG   +I  +A 
Sbjct: 371 ITPRMFEYSLVEKASSDRQHIVLPEGLGQRMLQAADIILRRGIADLTLLGRKDEIATKAA 430

Query: 61  ELGLHLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGD 120
           +LG+++  A +++P+   R EEF E + E+RK K +  D AR+ M D +YFGTMMVH G 
Sbjct: 431 KLGINIEGATVIDPVESNRYEEFVETYFEIRKHKGIVRDVARDRMSDPTYFGTMMVHKGL 490

Query: 121 ADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQ 180
           ADGMVSG+  TTA TI+P+F+ +KT P  SVVSSIF+M  + R+ AFGDCAV PNP A Q
Sbjct: 491 ADGMVSGSVTTTAQTIRPAFEFVKTKPHVSVVSSIFIMCFQSRVLAFGDCAVVPNPDARQ 550

Query: 181 LGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVD--- 237
           L EIA+ SA+TA  F I+PRVA+LSYSTG SG G DV++ ++A A AR+L  E  +D   
Sbjct: 551 LAEIALSSAETARIFNIEPRVAMLSYSTGISGSGQDVEKVVEATAIARQLMEERGLDFPL 610

Query: 238 -GPLQFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQ 296
            GPLQ+DAA D  VA+ K P+S VAG+A VF+FPDL  GN  YK  QR  +A+A+GP+LQ
Sbjct: 611 EGPLQYDAAFDLEVAKVKSPESVVAGRATVFVFPDLNTGNNTYKAVQRAANAVAMGPVLQ 670

Query: 297 GLNKPVNDLSRGATVPDIVNTVAITAIQA 325
           GLNKPVNDLSRG TV DIV+TVA+TA+QA
Sbjct: 671 GLNKPVNDLSRGCTVLDIVDTVALTALQA 699


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: 521
Number of extensions: 22
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: 706
Length adjustment: 34
Effective length of query: 295
Effective length of database: 672
Effective search space:   198240
Effective search space used:   198240
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_028585908.1 G494_RS0119815 (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.18361.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-122  393.3   0.1   5.9e-122  392.8   0.1    1.2  1  lcl|NCBI__GCF_000429965.1:WP_028585908.1  G494_RS0119815 phosphate acetylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028585908.1  G494_RS0119815 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.8   0.1  5.9e-122  5.9e-122       1     304 []     391     696 ..     391     696 .. 0.97

  Alignments for each domain:
  == domain 1  score: 392.8 bits;  conditional E-value: 5.9e-122
                                 TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 
                                               ivlPEg  +r+l+Aa ++++++ia+ +ll++k+e+ + ka+++ ++++  +v+dp  s+  e++ve+++
  lcl|NCBI__GCF_000429965.1:WP_028585908.1 391 IVLPEGLGQRMLQAADIILRRGIADLTLLGRKDEIAT-KAAKLGINIEGATVIDPVESNRYEEFVETYF 458
                                               8****************************99888877.9****************************** PP

                                 TIGR00651  70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfi 138
                                               e rkhkG+ +  ar+ + D++++++++v++g adg+vsG+v tta+t+rpa++ +kt++ v++vss+fi
  lcl|NCBI__GCF_000429965.1:WP_028585908.1 459 EIRKHKGIVRDVARDRMSDPTYFGTMMVHKGLADGMVSGSVTTTAQTIRPAFEFVKTKPHVSVVSSIFI 527
                                               ********************************************************************* PP

                                 TIGR00651 139 mekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvk 207
                                               m+ +++vl f+DCav+++P+a++LAeiAl+sa++a+ ++ +ep+va+lsyst+ sg+g++vekv+eA++
  lcl|NCBI__GCF_000429965.1:WP_028585908.1 528 MCFQSRVLAFGDCAVVPNPDARQLAEIALSSAETARIFN-IEPRVAMLSYSTGISGSGQDVEKVVEATA 595
                                               **************************************9.****************************8 PP

                                 TIGR00651 208 ilk....ekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaea 272
                                               i++    e+  d+ l+G+lq+DaA+  +va+ k pes vag+a+vfvFPdL++Gn++Yk+vqR a+a a
  lcl|NCBI__GCF_000429965.1:WP_028585908.1 596 IARqlmeERGLDFPLEGPLQYDAAFDLEVAKVKSPESVVAGRATVFVFPDLNTGNNTYKAVQRAANAVA 664
                                               86533338999********************************************************** PP

                                 TIGR00651 273 iGPilqGlakPvnDLsRGasvedivnvviita 304
                                               +GP+lqGl+kPvnDLsRG++v div +v++ta
  lcl|NCBI__GCF_000429965.1:WP_028585908.1 665 MGPVLQGLNKPVNDLSRGCTVLDIVDTVALTA 696
                                               *****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (706 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 19.24
//
[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 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