Alignments for a candidate for pta in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Desulfobacter vibrioformis DSM 8776

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_035238512.1 Q366_RS09670 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000745975.1:WP_035238512.1
          Length = 702

 Score =  393 bits (1010), Expect = e-114
 Identities = 198/326 (60%), Positives = 249/326 (76%), Gaps = 1/326 (0%)

Query: 1   MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60
           ++ ++FE  L+++A+ +  HIVLPEG  DRIL AA  LL +  CDITILG    ++ R  
Sbjct: 370 ITPQMFEYSLIEKAKKDRQHIVLPEGSSDRILKAADILLRRSFCDITILGRSEAVERRVK 429

Query: 61  ELGLHLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGD 120
           ELGL+L+ A ++ P   P L+++A+ + ELRK K VT+D AR+ M D SYFGTMMVH G+
Sbjct: 430 ELGLNLSQARIIQPDASPWLDDYAQTYFELRKHKGVTLDMARDTMTDPSYFGTMMVHKGN 489

Query: 121 ADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQ 180
           ADGMVSG+ NTTAHTI P+FQIIKT P +S+VSS+FLM L+ R+  FGDCAVN NPTA Q
Sbjct: 490 ADGMVSGSVNTTAHTILPAFQIIKTRPGSSIVSSVFLMCLKDRVLVFGDCAVNTNPTASQ 549

Query: 181 LGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPL 240
           L EIAV+SA TA+ FGI+PRVA+LSYSTG+SG G+DVD+ I A A AR   P+L ++GP+
Sbjct: 550 LAEIAVISAGTASIFGIEPRVAMLSYSTGSSGTGADVDKVIQATAMAREKAPDLPIEGPI 609

Query: 241 QFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGH-ALAVGPILQGLN 299
           Q+DAA+DP VA  K+PDS VAG+A VFIFPDL  GN  YK  QR     +A+GP+LQGL 
Sbjct: 610 QYDAAIDPAVAMTKLPDSQVAGRATVFIFPDLNTGNNTYKAVQRASEKTVAIGPVLQGLK 669

Query: 300 KPVNDLSRGATVPDIVNTVAITAIQA 325
           +P+NDLSRG TVPDIVNTVAITAIQA
Sbjct: 670 RPINDLSRGCTVPDIVNTVAITAIQA 695


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: 586
Number of extensions: 21
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: 702
Length adjustment: 34
Effective length of query: 295
Effective length of database: 668
Effective search space:   197060
Effective search space used:   197060
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_035238512.1 Q366_RS09670 (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.2268350.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   2.5e-127  410.5   0.0    1.2  1  NCBI__GCF_000745975.1:WP_035238512.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745975.1:WP_035238512.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.5   0.0  2.5e-127  2.5e-127       1     304 []     390     692 ..     390     692 .. 0.99

  Alignments for each domain:
  == domain 1  score: 410.5 bits;  conditional E-value: 2.5e-127
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEgs+ r+lkAa +l+++   + ++l+++e++++ ++ke+ l+l++ ++++pd s+ +++y+++++e+rk
  NCBI__GCF_000745975.1:WP_035238512.1 390 IVLPEGSSDRILKAADILLRRSFCDITILGRSEAVER-RVKELGLNLSQARIIQPDASPWLDDYAQTYFELRK 461
                                           8******************************999999.9********************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                           hkGvt+ +ar++++D++++++++v++g+adg+vsG+v+tta+t+ pa+qiikt++g+++vssvf+m+++++vl
  NCBI__GCF_000745975.1:WP_035238512.1 462 HKGVTLDMARDTMTDPSYFGTMMVHKGNADGMVSGSVNTTAHTILPAFQIIKTRPGSSIVSSVFLMCLKDRVL 534
                                           ************************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           vf+DCav+ +P+a +LAeiA+ sa +a  +g +ep+va+lsyst++sg g++v+kv +A+++++ek+pdl ++
  NCBI__GCF_000745975.1:WP_035238512.1 535 VFGDCAVNTNPTASQLAEIAVISAGTASIFG-IEPRVAMLSYSTGSSGTGADVDKVIQATAMAREKAPDLPIE 606
                                           ******************************9.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRlad.aeaiGPilqGlakPvnDLsRGa 291
                                           G++q+DaA+ + va  k p+s+vag+a+vf+FPdL++Gn++Yk+vqR ++   aiGP+lqGl++P+nDLsRG+
  NCBI__GCF_000745975.1:WP_035238512.1 607 GPIQYDAAIDPAVAMTKLPDSQVAGRATVFIFPDLNTGNNTYKAVQRASEkTVAIGPVLQGLKRPINDLSRGC 679
                                           ***********************************************986268******************** PP

                             TIGR00651 292 svedivnvviita 304
                                           +v divn+v+ita
  NCBI__GCF_000745975.1:WP_035238512.1 680 TVPDIVNTVAITA 692
                                           ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (702 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: 44.51
//
[ok]

This GapMind analysis is from Apr 09 2024. 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