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.17713.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.81
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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:

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