Alignments for a candidate for pta in Desulfovibrio vulgaris Hildenborough JW710

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Desulfovibrio vulgaris Hildenborough JW710

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 208543 DVU3029 phosphate acetyltransferase (TIGR)

Query= metacyc::GIO2-991-MONOMER
         (792 letters)



>FitnessBrowser__DvH:208543
          Length = 704

 Score =  477 bits (1228), Expect = e-139
 Identities = 296/724 (40%), Positives = 426/724 (58%), Gaps = 40/724 (5%)

Query: 61  DTLFLSDISLVGQRTPLLLGFFNYFERHLPHVGFFEPIAAEALASSELRIDRHVELVYKV 120
           + L+++       ++ ++LG      R +  V FF PI  +A  S+++R D  + L+ + 
Sbjct: 3   NNLYITATESKSGKSAVVLGMMQLLLRDVRKVAFFRPIINQA--STDVR-DHDINLILRH 59

Query: 121 FNLKGDVRAMTGVQDAEAARMIANGQHSELLDKIYSQYASYKEGQDLVLVEGPGPLMGGT 180
           F L             +A  +I NGQH+ LLD I  +Y   ++  D VL EG   L    
Sbjct: 60  FGLDIAYEDTYAYSLQDARELINNGQHATLLDNILKKYKKLEDAYDFVLCEGTDFLGKDA 119

Query: 181 ----ELDAQIAAALNAPVLMTMTGQPNATVADYYNRAMVKRQVFLD----HHVEVLGLVM 232
               EL+A IAA L  PV++   GQ  A         +   Q+ +D      ++V+  V+
Sbjct: 120 AFEFELNADIAANLGCPVMVVANGQQKAA-----RELIASTQLTIDLLDEKGLDVVTAVI 174

Query: 233 NG--LPRQSHAILSGQLRDKFAAAGLPFAGAIPTDIMLRNVRLDEVQTAMGAQRLYGDSL 290
           N   +       +   L  K   +       +P +  L    +++V+  +GAQ LYG   
Sbjct: 175 NRATVTEAEREEIIKSLECKVNCSNPLAVYVLPEESTLGKPTMNDVKKWLGAQVLYGHGR 234

Query: 291 LTDVEFDDVVVASQRLEELLEILAERPMGRPLVVTSADRLDIVLGLLAAQLSVSGPGVAG 350
           L D   DD ++A+ ++   L+ +++      LV+T  DR DI+L  LA++LS + P ++G
Sbjct: 235 L-DTLVDDYIIAAMQIGNFLDYVSQGC----LVITPGDRSDIILSSLASRLSTAYPDISG 289

Query: 351 ILLTQAGSARSGRNYARDTIDRIFAGLSSSGLYKGSLLPVLVTDMPLRDAIRKLDNLDAA 410
           +LLT  G      N     + R+  G      + G  +P+L         I+ L+ L   
Sbjct: 290 LLLT--GGLEPAAN-----VHRLIEG------WTGVPIPILSVKDHTYKTIQTLNELYGK 336

Query: 411 ILPSSTRKISQCKRLFEQYVDANAVVARLQNMVRPNRMTPKMFMHTLKSMCNATPQHIVL 470
           I P + RKI+    LFE+++D++ + +RL N  + +R+TPKMF   L          IVL
Sbjct: 337 IEPDNDRKINTALALFERHIDSSELGSRLINR-KSSRITPKMFEFNLIEKAKRNRMRIVL 395

Query: 471 PESEDKRVLAAAADVVQRGLAKITLLGDPTTILAEAAKLGLDLSGCNIHNPNTSDRFDKY 530
           PE  ++R+L AA  +V+R +A I LLGD  T+ +    LGLD+ G  I  PN S +FD+Y
Sbjct: 396 PEGAEERILRAADILVRREVADIILLGDANTVGSRIGDLGLDMDGVQIVQPNLSPKFDEY 455

Query: 531 VDMLVEARKKKGMTREVAADTLHGDVNFFATMMIVAGDADGMVSGAVHTTASTVRPALQV 590
           V    E RKKKG++ E A D ++ D  +F TMM+  GDADGMVSGA++TTA T+RPA + 
Sbjct: 456 VAAYHECRKKKGISMEQARDMMN-DPTYFGTMMVHKGDADGMVSGAINTTAHTIRPAFEF 514

Query: 591 LKS-PDTPLVSSVFIMCLPDRVVVYGDCAVNVNPSAADLAQIAITSNDTAAAFGIEPRVA 649
           +K+ P   +VSSVF+MCL DRV+V+GDCAVN NP+A  LA+IAI+++ TA  FG++PRVA
Sbjct: 515 IKTKPGVSIVSSVFLMCLKDRVLVFGDCAVNPNPTAEQLAEIAISASHTARIFGVDPRVA 574

Query: 650 MLSYSTLGSGSGPDVQKVSEAVAIVKQRRPDIKVEGPIQYDAAIDPKVAAVKVQGLSEVA 709
           MLSYST  SG G DV+KV EA  I K+R P++ +EGP+QYDAAID  VA  K+ G S VA
Sbjct: 575 MLSYSTGSSGKGADVEKVIEATRIAKERAPELLLEGPLQYDAAIDMDVARTKLPG-STVA 633

Query: 710 GKATVFIFPDLNTGNNTYKAVQQSTGAIAMGPVMQGLLRPVNDLSRGCTVPDIINTICVT 769
           G+ATVFIFPDLNTGNNTYKAVQ++ GA+A+GPV+QGL +PVNDLSRGCTV DI+NT+ +T
Sbjct: 634 GQATVFIFPDLNTGNNTYKAVQRAAGAVAIGPVLQGLNKPVNDLSRGCTVADIVNTVAIT 693

Query: 770 SIQA 773
           +IQA
Sbjct: 694 AIQA 697


Lambda     K      H
   0.320    0.134    0.376 

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: 1191
Number of extensions: 62
Number of successful extensions: 10
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: 792
Length of database: 704
Length adjustment: 40
Effective length of query: 752
Effective length of database: 664
Effective search space:   499328
Effective search space used:   499328
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: 55 (25.8 bits)

Align candidate 208543 DVU3029 (phosphate acetyltransferase (TIGR))
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.2996092.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
   2.4e-131  423.7   0.1   3.3e-131  423.2   0.1    1.2  1  FitnessBrowser__DvH:208543  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__DvH:208543  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.2   0.1  3.3e-131  3.3e-131       1     304 []     393     694 ..     393     694 .. 0.99

  Alignments for each domain:
  == domain 1  score: 423.2 bits;  conditional E-value: 3.3e-131
                   TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkGvtekear 83 
                                 ivlPEg eer+l+Aa +l+++++a+ +ll++ +++ + ++ ++ l++  v++++p++s++ ++yv +++e rk+kG+++++ar
  FitnessBrowser__DvH:208543 393 IVLPEGAEERILRAADILVRREVADIILLGDANTVGS-RIGDLGLDMDGVQIVQPNLSPKFDEYVAAYHECRKKKGISMEQAR 474
                                 8************************999999887777.9******************************************** PP

                   TIGR00651  84 eqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCavavdPnaeeLAeiA 166
                                 ++++D++++++++v++g adg+vsGa +tta+t+rpa++ ikt++gv++vssvf+m+++++vlvf+DCav+++P+ae+LAeiA
  FitnessBrowser__DvH:208543 475 DMMNDPTYFGTMMVHKGDADGMVSGAINTTAHTIRPAFEFIKTKPGVSIVSSVFLMCLKDRVLVFGDCAVNPNPTAEQLAEIA 557
                                 *********************************************************************************** PP

                   TIGR00651 167 lqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvf 249
                                 +++ ++a+ +g  +p+va+lsyst++sgkg++vekv eA++i+ke++p+lll+G+lq+DaA+  +va+ k p s+vag+a+vf
  FitnessBrowser__DvH:208543 558 ISASHTARIFG-VDPRVAMLSYSTGSSGKGADVEKVIEATRIAKERAPELLLEGPLQYDAAIDMDVARTKLPGSTVAGQATVF 639
                                 ***********.*********************************************************************** PP

                   TIGR00651 250 vFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                 +FPdL++Gn++Yk+vqR a+a aiGP+lqGl+kPvnDLsRG++v divn+v+ita
  FitnessBrowser__DvH:208543 640 IFPDLNTGNNTYKAVQRAAGAVAIGPVLQGLNKPVNDLSRGCTVADIVNTVAITA 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.88
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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