Alignments for a candidate for pta in Microbacterium profundi Shh49

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Microbacterium profundi Shh49

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_033106600.1 JF52_RS0110650 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000763375.1:WP_033106600.1
          Length = 708

 Score =  390 bits (1002), Expect = e-113
 Identities = 195/323 (60%), Positives = 248/323 (76%)

Query: 5   LFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGL 64
           +FE  L++RARA+   IVLPEG+DDRIL AA  L+ +D+ D+TILGD  +I+ RATELG+
Sbjct: 379 MFEYGLIERARADRKRIVLPEGEDDRILRAASSLIARDVADLTILGDESEIRARATELGI 438

Query: 65  HLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGDADGM 124
            ++ A +++P     +E FAE++A LR  K VT+ +A + + D+SYFGT+MVH G ADGM
Sbjct: 439 DISAAQIISPTDPSYIERFAEEYARLRAHKGVTLSQAADTVTDVSYFGTLMVHLGLADGM 498

Query: 125 VSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEI 184
           VSGA +TTAHTI+PSF+IIKT P   VVSS+FLM L  R+  +GDCAV P+PT+ QL +I
Sbjct: 499 VSGATHTTAHTIRPSFEIIKTRPGVEVVSSVFLMALADRVLVYGDCAVIPDPTSTQLADI 558

Query: 185 AVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDA 244
           A+ SA+TA QFGI+PRVA+LSYSTG SG G+DV++  +A A  R   PEL VDGP+Q+DA
Sbjct: 559 AISSAQTARQFGIEPRVAMLSYSTGESGTGADVEKVREATALVRERAPELPVDGPIQYDA 618

Query: 245 AVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNKPVND 304
           A D  VA+ KMPDS VAG+A VF+FPDL  GN  YK  QR+  A+A+GP+LQGLNKP+ND
Sbjct: 619 AADAAVAKAKMPDSAVAGRATVFVFPDLNTGNNTYKAVQRSAGAVAIGPVLQGLNKPIND 678

Query: 305 LSRGATVPDIVNTVAITAIQAGG 327
           LSRGA V DIVNTVAITAIQA G
Sbjct: 679 LSRGALVDDIVNTVAITAIQAQG 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: 631
Number of extensions: 17
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: 708
Length adjustment: 34
Effective length of query: 295
Effective length of database: 674
Effective search space:   198830
Effective search space used:   198830
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_033106600.1 JF52_RS0110650 (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.562905.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-128  413.2   0.1     5e-128  412.8   0.1    1.2  1  NCBI__GCF_000763375.1:WP_033106600.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000763375.1:WP_033106600.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.8   0.1    5e-128    5e-128       1     304 []     395     696 ..     395     696 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.8 bits;  conditional E-value: 5e-128
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEg++ r+l+Aa++l+ +++a+ ++l++++e+ + +a+e+ ++++  +++ p+    ie+++e++  +r 
  NCBI__GCF_000763375.1:WP_033106600.1 395 IVLPEGEDDRILRAASSLIARDVADLTILGDESEIRA-RATELGIDISAAQIISPTDPSYIERFAEEYARLRA 466
                                           8****************************99988877.99**************99999************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                           hkGvt+++a+++++D +++++l+v+lg adg+vsGa +tta+t+rp+++iikt++gv++vssvf+m++ ++vl
  NCBI__GCF_000763375.1:WP_033106600.1 467 HKGVTLSQAADTVTDVSYFGTLMVHLGLADGMVSGATHTTAHTIRPSFEIIKTRPGVEVVSSVFLMALADRVL 539
                                           ************************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           v++DCav++dP++ +LA+iA++sa++a+++g +ep+va+lsyst+ sg g++vekv+eA+++++e++p+l +d
  NCBI__GCF_000763375.1:WP_033106600.1 540 VYGDCAVIPDPTSTQLADIAISSAQTARQFG-IEPRVAMLSYSTGESGTGADVEKVREATALVRERAPELPVD 611
                                           *******************************.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           G++q+DaA  + va+ k+p+s+vag+a+vfvFPdL++Gn++Yk+vqR+a+a aiGP+lqGl+kP+nDLsRGa+
  NCBI__GCF_000763375.1:WP_033106600.1 612 GPIQYDAAADAAVAKAKMPDSAVAGRATVFVFPDLNTGNNTYKAVQRSAGAVAIGPVLQGLNKPINDLSRGAL 684
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                           v+divn+v+ita
  NCBI__GCF_000763375.1:WP_033106600.1 685 VDDIVNTVAITA 696
                                           **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (708 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: 30.17
//
[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