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_028584418.1 G494_RS0109915 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000429965.1:WP_028584418.1
          Length = 701

 Score =  354 bits (909), Expect = e-102
 Identities = 173/324 (53%), Positives = 238/324 (73%)

Query: 2   SAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATE 61
           S ++FE  LLKRAR+    IVLPEG+++RIL AA  L+ +D  DI +LG P +I+ + +E
Sbjct: 371 SPKMFEFGLLKRARSHKQLIVLPEGEEERILKAAEILIHRDAVDIILLGRPKEIRSKISE 430

Query: 62  LGLHLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGDA 121
            GL L    ++ P   P  +++A  + +LR+ K +T D AR++M  +++FGTMMV+ G A
Sbjct: 431 FGLSLEGVEIIEPTASPHFDDYAATYFQLRRHKGITADNARDVMSGVNHFGTMMVYKGHA 490

Query: 122 DGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQL 181
           DGMVSGA ++T  T++PS + +KT P ++++SS+F M L  R+ A+ DCAVNP P+AEQL
Sbjct: 491 DGMVSGAVHSTLQTVRPSLEFVKTKPGSTIMSSVFFMCLEDRVLAYADCAVNPRPSAEQL 550

Query: 182 GEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQ 241
            EIA+ ++KTA+ FGI P VA+LSYS+G+SG G +VD+  +A   A+   PEL ++GP+Q
Sbjct: 551 AEIAIETSKTASLFGIKPLVAMLSYSSGSSGRGEEVDKVKEATRIAQERAPELLLEGPIQ 610

Query: 242 FDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNKP 301
           +DAAVD  VAR KMP+S VAG+A VFIFPDL  GN  YK  QR+  A+A+GPI+QGLN+P
Sbjct: 611 YDAAVDAEVARTKMPESKVAGRATVFIFPDLNTGNNTYKAVQRSAGAVAIGPIMQGLNRP 670

Query: 302 VNDLSRGATVPDIVNTVAITAIQA 325
           VNDLSRG  +PDIVNTVAITAIQA
Sbjct: 671 VNDLSRGCLIPDIVNTVAITAIQA 694


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: 517
Number of extensions: 25
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: 701
Length adjustment: 34
Effective length of query: 295
Effective length of database: 667
Effective search space:   196765
Effective search space used:   196765
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_028584418.1 G494_RS0109915 (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.27823.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-127  411.5   0.0   1.6e-127  411.1   0.0    1.2  1  lcl|NCBI__GCF_000429965.1:WP_028584418.1  G494_RS0109915 phosphate acetylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028584418.1  G494_RS0109915 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.1   0.0  1.6e-127  1.6e-127       1     304 []     390     691 ..     390     691 .. 0.99

  Alignments for each domain:
  == domain 1  score: 411.1 bits;  conditional E-value: 1.6e-127
                                 TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 
                                               ivlPEg+eer+lkAa++l++++ ++ +ll++ +e+ + k++e+ l+l+ v++++p+ s++ ++y+ +++
  lcl|NCBI__GCF_000429965.1:WP_028584418.1 390 IVLPEGEEERILKAAEILIHRDAVDIILLGRPKEIRS-KISEFGLSLEGVEIIEPTASPHFDDYAATYF 457
                                               8******************************999988.******************************* PP

                                 TIGR00651  70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfi 138
                                               ++r+hkG+t  +ar+ +   + +++++v++g+adg+vsGav++t +t+rp+l+ +kt++g+ ++ssvf+
  lcl|NCBI__GCF_000429965.1:WP_028584418.1 458 QLRRHKGITADNARDVMSGVNHFGTMMVYKGHADGMVSGAVHSTLQTVRPSLEFVKTKPGSTIMSSVFF 526
                                               ********************************************************************* PP

                                 TIGR00651 139 mekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvk 207
                                               m++e++vl +aDCav++ P+ae+LAeiA+++ k+a  +g ++p va+lsys+++sg+geev+kvkeA++
  lcl|NCBI__GCF_000429965.1:WP_028584418.1 527 MCLEDRVLAYADCAVNPRPSAEQLAEIAIETSKTASLFG-IKPLVAMLSYSSGSSGRGEEVDKVKEATR 594
                                               **************************************9.***************************** PP

                                 TIGR00651 208 ilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPi 276
                                               i++e++p+lll+G++q+DaA+ ++va+ k+pes+vag+a+vf+FPdL++Gn++Yk+vqR+a+a aiGPi
  lcl|NCBI__GCF_000429965.1:WP_028584418.1 595 IAQERAPELLLEGPIQYDAAVDAEVARTKMPESKVAGRATVFIFPDLNTGNNTYKAVQRSAGAVAIGPI 663
                                               ********************************************************************* PP

                                 TIGR00651 277 lqGlakPvnDLsRGasvedivnvviita 304
                                               +qGl++PvnDLsRG+++ divn+v+ita
  lcl|NCBI__GCF_000429965.1:WP_028584418.1 664 MQGLNRPVNDLSRGCLIPDIVNTVAITA 691
                                               **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (701 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.81
//
[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