Alignments for a candidate for pta in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Sedimenticola selenatireducens DSM 17993

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_029132548.1 A3GO_RS0105465 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>NCBI__GCF_000428045.1:WP_029132548.1
          Length = 702

 Score =  431 bits (1109), Expect = e-125
 Identities = 278/711 (39%), Positives = 398/711 (55%), Gaps = 33/711 (4%)

Query: 1   MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60
           + + +IA    G G + I LG++  L     +VGFF+PI    P + G +  + L+++ +
Sbjct: 2   LRSIYIAGAEPGSGKSVIVLGVMEMLTALTKRVGFFRPII---PENGGSDDLTHLISQRY 58

Query: 61  GLDTPKPLPLAQVER----MLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASY 116
           G+D P        +     +L +G+  ELL++I++ Y+      D+V+  G       + 
Sbjct: 59  GIDLPASALYGCTDETARNLLAEGRYAELLKQIMAKYKLVEQQVDMVVCAG-TDFSDVTS 117

Query: 117 AARVNFH--LAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVR 174
           A  ++F+  LA +L   ++ V      +  E  D + +  +     R  ++L  I+N+V 
Sbjct: 118 AMELDFNADLANNLGCLLMPVIKGYGRSAHETVDAVRVLEESLNN-RGCELLAAIVNRV- 175

Query: 175 GEADAANAEDGVADFARRLTEHSPLLRDDFRLIGCIPWQDELNAARTRDIADLLSARVIN 234
              D  N +  +A+         P           +P    L      +IA  LS   ++
Sbjct: 176 ---DPENIDQVIAELTVSSIPTLPFY--------VLPEHRTLEKPTVGEIARSLSIACLS 224

Query: 235 AGDYEQ--RRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGV--PLA 290
            GD E   + V    + A  VPN +  ++   LV+TPGDR DIIL    A ++     +A
Sbjct: 225 -GDQESLNQEVSHYKVAAMEVPNFLDNIQEDSLVITPGDRSDIILTTLAADVSSSYPKIA 283

Query: 291 GLLLCSDFPPDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEI-PVDDRERAER 349
           GLLL     P P++  L  G  +  L +LS    ++ TA  +N +   I P DDR+ A  
Sbjct: 284 GLLLTGGLTPAPQVTRLLEGLTKSRLAILSAPWDTFCTALKVNEVEGSILPSDDRKIAAA 343

Query: 350 VTEFVAGHIDFEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAA 409
           +   V  HI+ E L  R    R  R +P  F Y+++QRA+   K IVLPEG + R ++AA
Sbjct: 344 LG-IVEKHINAEELTARISVGRTHRKTPLMFEYEMIQRAKSVRKHIVLPEGFDERILRAA 402

Query: 410 AICQARGIARCVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLV--RQRYVEPMVELRKGK 467
            I   R +    LL   E++Q      G+ L +G++ IDP     RQ + +   +LR+ K
Sbjct: 403 EILLLREVVDITLLGSEEKIQQRISQLGLNL-QGVKTIDPRTSPWRQTFADTYFKLRQHK 461

Query: 468 GLNAPMAEQQLEDSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSS 527
           G++  MA   + D     TMM+     DG+VSGA HTT  TIRPA ++I+T PG +LVSS
Sbjct: 462 GISEQMAYDAMADVSYFGTMMIHHGHADGMVSGAAHTTQHTIRPAFEIIRTKPGCSLVSS 521

Query: 528 VFFMLLPDQVLVYGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSG 587
           VFFM L D+VLVYGDCA+NP+P+A+ LA+IA+ SA +A  FGI  RVAM+SYSTG SG G
Sbjct: 522 VFFMCLEDKVLVYGDCAINPNPNAAQLADIAISSAGTAAMFGIEPRVAMLSYSTGVSGKG 581

Query: 588 VDVDKVREATRLAREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNT 647
            DV+ VR+A  +AR  RPDL ++GP+QYDAA    V R K P S VAGQATVFIFPDLNT
Sbjct: 582 DDVESVRDAVAIARRLRPDLKLEGPIQYDAAIDPGVARSKMPESEVAGQATVFIFPDLNT 641

Query: 648 GNTTYKAVQRSADCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           GN TYKAVQRSA+ V++GP++QGL +PVNDLSRG  V DIV T+A+TAIQA
Sbjct: 642 GNNTYKAVQRSANAVAIGPVIQGLNRPVNDLSRGCTVTDIVNTVAITAIQA 692


Lambda     K      H
   0.319    0.136    0.388 

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: 1049
Number of extensions: 35
Number of successful extensions: 4
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: 704
Length of database: 702
Length adjustment: 39
Effective length of query: 665
Effective length of database: 663
Effective search space:   440895
Effective search space used:   440895
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_029132548.1 A3GO_RS0105465 (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.1168851.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-129  415.8   0.0   8.4e-129  415.3   0.0    1.2  1  NCBI__GCF_000428045.1:WP_029132548.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000428045.1:WP_029132548.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.3   0.0  8.4e-129  8.4e-129       1     304 []     388     689 ..     388     689 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.3 bits;  conditional E-value: 8.4e-129
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEg +er+l+Aa++l+ +++++ +ll+++e++++ +++++ l+l+ v+ +dp++s+ +++++++++++r+
  NCBI__GCF_000428045.1:WP_029132548.1 388 IVLPEGFDERILRAAEILLLREVVDITLLGSEEKIQQ-RISQLGLNLQGVKTIDPRTSPWRQTFADTYFKLRQ 459
                                           8******************************999999.9********************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                           hkG++e++a +++ D +++++++++ g+adg+vsGa++tt++t+rpa++ii+t++g +lvssvf+m++e++vl
  NCBI__GCF_000428045.1:WP_029132548.1 460 HKGISEQMAYDAMADVSYFGTMMIHHGHADGMVSGAAHTTQHTIRPAFEIIRTKPGCSLVSSVFFMCLEDKVL 532
                                           ************************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           v++DCa++++Pna +LA+iA++sa +a ++g +ep+va+lsyst+ sgkg++ve v++Av+i++  +pdl+l+
  NCBI__GCF_000428045.1:WP_029132548.1 533 VYGDCAINPNPNAAQLADIAISSAGTAAMFG-IEPRVAMLSYSTGVSGKGDDVESVRDAVAIARRLRPDLKLE 604
                                           *******************************.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           G++q+DaA+ + va++k+pesevag+a+vf+FPdL++Gn++Yk+vqR+a+a aiGP++qGl++PvnDLsRG++
  NCBI__GCF_000428045.1:WP_029132548.1 605 GPIQYDAAIDPGVARSKMPESEVAGQATVFIFPDLNTGNNTYKAVQRSANAVAIGPVIQGLNRPVNDLSRGCT 677
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                           v divn+v+ita
  NCBI__GCF_000428045.1:WP_029132548.1 678 VTDIVNTVAITA 689
                                           **********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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.96
//
[ok]

This GapMind analysis is from Sep 24 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