Alignments for a candidate for pta in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Desulfovibrio vulgaris Miyazaki F

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate 8501128 DvMF_1864 phosphate acetyltransferase (RefSeq)

Query= SwissProt::P77844
         (329 letters)



>FitnessBrowser__Miya:8501128
          Length = 704

 Score =  388 bits (996), Expect = e-112
 Identities = 194/321 (60%), Positives = 246/321 (76%)

Query: 5   LFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGL 64
           +FE  L++RA+     IVLPEG ++RIL AA  L  +++ DI +LGD  K+  + +ELG+
Sbjct: 377 MFEFNLIERAKQNRMRIVLPEGVEERILRAADILARREVADIILLGDADKVGAKVSELGI 436

Query: 65  HLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGDADGM 124
            L+   ++ P   P+ EE+A+ + ELRK K V+I+ AR+ M D++YFGTMMVH GDA+GM
Sbjct: 437 ALDGVQIIQPNLSPKFEEYAQAYFELRKHKGVSIERARDTMNDVTYFGTMMVHKGDAEGM 496

Query: 125 VSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEI 184
           VSG+ NTTAHTI+P+F+ IKT P  S+VSS+FLM L+ R+ AFGDCAVNPNPTAEQL EI
Sbjct: 497 VSGSINTTAHTIRPAFEFIKTKPGFSIVSSVFLMCLKDRVLAFGDCAVNPNPTAEQLAEI 556

Query: 185 AVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDA 244
           A+ SA TA  FGI+PRVA+LSYSTG+SG G+DV++ I+A   A+   PEL ++GPLQ+DA
Sbjct: 557 AINSAHTARIFGIEPRVAMLSYSTGSSGKGADVEKVIEATRIAKERAPELLLEGPLQYDA 616

Query: 245 AVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNKPVND 304
           A+D  VAR K+P S VAGQA VFIFPDL  GN  YK  QR   A+A+GP+LQGLNKPVND
Sbjct: 617 AIDMDVARTKLPGSQVAGQATVFIFPDLNTGNNTYKAVQRAAGAVAIGPVLQGLNKPVND 676

Query: 305 LSRGATVPDIVNTVAITAIQA 325
           LSRG TVPDIVNTVAITAIQA
Sbjct: 677 LSRGCTVPDIVNTVAITAIQA 697


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: 600
Number of extensions: 18
Number of successful extensions: 1
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: 704
Length adjustment: 34
Effective length of query: 295
Effective length of database: 670
Effective search space:   197650
Effective search space used:   197650
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 8501128 DvMF_1864 (phosphate acetyltransferase (RefSeq))
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.19756.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.7e-133  429.0   0.1   7.7e-133  428.6   0.1    1.2  1  lcl|FitnessBrowser__Miya:8501128  DvMF_1864 phosphate acetyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501128  DvMF_1864 phosphate acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.6   0.1  7.7e-133  7.7e-133       1     304 []     393     694 ..     393     694 .. 0.99

  Alignments for each domain:
  == domain 1  score: 428.6 bits;  conditional E-value: 7.7e-133
                         TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkGv 77 
                                       ivlPEg eer+l+Aa +la++++a+ +ll++ +++ + k++e+ ++l  v++++p++s++ e+y+++++e+rkhkGv
  lcl|FitnessBrowser__Miya:8501128 393 IVLPEGVEERILRAADILARREVADIILLGDADKVGA-KVSELGIALDGVQIIQPNLSPKFEEYAQAYFELRKHKGV 468
                                       8************************999999888777.9************************************** PP

                         TIGR00651  78 tekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCava 154
                                       + ++ar++++D +++++++v++g a+g+vsG+ +tta+t+rpa++ ikt++g+++vssvf+m+++++vl f+DCav+
  lcl|FitnessBrowser__Miya:8501128 469 SIERARDTMNDVTYFGTMMVHKGDAEGMVSGSINTTAHTIRPAFEFIKTKPGFSIVSSVFLMCLKDRVLAFGDCAVN 545
                                       ***************************************************************************** PP

                         TIGR00651 155 vdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlvek 231
                                       ++P+ae+LAeiA++sa++a+ +g +ep+va+lsyst++sgkg++vekv eA++i+ke++p+lll+G+lq+DaA+  +
  lcl|FitnessBrowser__Miya:8501128 546 PNPTAEQLAEIAINSAHTARIFG-IEPRVAMLSYSTGSSGKGADVEKVIEATRIAKERAPELLLEGPLQYDAAIDMD 621
                                       ***********************.***************************************************** PP

                         TIGR00651 232 vaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                       va+ k p s+vag+a+vf+FPdL++Gn++Yk+vqR a+a aiGP+lqGl+kPvnDLsRG++v divn+v+ita
  lcl|FitnessBrowser__Miya:8501128 622 VARTKLPGSQVAGQATVFIFPDLNTGNNTYKAVQRAAGAVAIGPVLQGLNKPVNDLSRGCTVPDIVNTVAITA 694
                                       ***********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (704 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: 00:00:00.01
# Mc/sec: 20.81
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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