GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Pontimonas salivibrio CL-TW6

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_104914115.1 C3B54_RS08500 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_002950575.1:WP_104914115.1
          Length = 707

 Score =  384 bits (986), Expect = e-111
 Identities = 194/323 (60%), Positives = 249/323 (77%)

Query: 5   LFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGL 64
           +FE  LL+RA+++  HIVLPEG DDRI+ AA  LL + +  +T+LGD  +I+ RA+ELG+
Sbjct: 379 MFEYDLLERAKSDLKHIVLPEGSDDRIIRAAATLLARGVVRLTLLGDEQEIRSRASELGV 438

Query: 65  HLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGDADGM 124
            L  A +++P  +   E FA ++  LR+ K +T+++AR+I+ D+S+FGTMMVH   ADGM
Sbjct: 439 SLEGANVLSPFDEGLRERFAAEYFRLREHKGMTVEQARDIVVDVSFFGTMMVHLALADGM 498

Query: 125 VSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEI 184
           VSGA NTTAHTI PSFQIIKT P  SVVSS+F M L  R+  +GDCAV P PTAE+L +I
Sbjct: 499 VSGAVNTTAHTITPSFQIIKTTPGVSVVSSVFFMCLADRVLVYGDCAVVPEPTAEELADI 558

Query: 185 AVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDA 244
           A  +A+TAAQFGI+PRVA+LSYSTG SG G++V++   A A  R+L P+L ++GP+Q+DA
Sbjct: 559 AAGAAQTAAQFGIEPRVAMLSYSTGESGRGTEVEKVRTATALLRKLRPDLPIEGPIQYDA 618

Query: 245 AVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNKPVND 304
           A +P VAR KMPDSDVAG+A VF+FPDL  GN  YK  QR+  A+A+GP+LQGLNKPVND
Sbjct: 619 AAEPTVARTKMPDSDVAGRATVFVFPDLNTGNNTYKAVQRSAGAIAIGPVLQGLNKPVND 678

Query: 305 LSRGATVPDIVNTVAITAIQAGG 327
           LSRGATV DIVNTVAITAIQA G
Sbjct: 679 LSRGATVRDIVNTVAITAIQAQG 701


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: 589
Number of extensions: 22
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: 707
Length adjustment: 34
Effective length of query: 295
Effective length of database: 673
Effective search space:   198535
Effective search space used:   198535
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_104914115.1 C3B54_RS08500 (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.2271083.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-123  398.1   0.0   2.2e-123  397.6   0.0    1.2  1  NCBI__GCF_002950575.1:WP_104914115.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002950575.1:WP_104914115.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.6   0.0  2.2e-123  2.2e-123       1     304 []     395     696 ..     395     696 .. 0.99

  Alignments for each domain:
  == domain 1  score: 397.6 bits;  conditional E-value: 2.2e-123
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEgs+ r+++Aaa+l+ +++++ +ll++++e+ + +a+e+  +l+  +v  p     +e+++ +++ +r 
  NCBI__GCF_002950575.1:WP_104914115.1 395 IVLPEGSDDRIIRAAATLLARGVVRLTLLGDEQEIRS-RASELGVSLEGANVLSPFDEGLRERFAAEYFRLRE 466
                                           8****************************99988877.9*************99999999************* PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                           hkG+t ++ar+ + D + +++++v+l  adg+vsGav+tta+t+ p++qiikt++gv++vssvf+m++ ++vl
  NCBI__GCF_002950575.1:WP_104914115.1 467 HKGMTVEQARDIVVDVSFFGTMMVHLALADGMVSGAVNTTAHTITPSFQIIKTTPGVSVVSSVFFMCLADRVL 539
                                           ************************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           v++DCav+++P+aeeLA+iA  +a++a ++g +ep+va+lsyst+ sg+g evekv+ A+++l++ +pdl ++
  NCBI__GCF_002950575.1:WP_104914115.1 540 VYGDCAVVPEPTAEELADIAAGAAQTAAQFG-IEPRVAMLSYSTGESGRGTEVEKVRTATALLRKLRPDLPIE 611
                                           *******************************.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           G++q+DaA  ++va+ k+p+s vag+a+vfvFPdL++Gn++Yk+vqR+a+a aiGP+lqGl+kPvnDLsRGa+
  NCBI__GCF_002950575.1:WP_104914115.1 612 GPIQYDAAAEPTVARTKMPDSDVAGRATVFVFPDLNTGNNTYKAVQRSAGAIAIGPVLQGLNKPVNDLSRGAT 684
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                           v divn+v+ita
  NCBI__GCF_002950575.1:WP_104914115.1 685 VRDIVNTVAITA 696
                                           **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (707 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: 00:00:00.00
# Mc/sec: 24.04
//
[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:

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