Alignments for a candidate for pta in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Pseudomonas fluorescens FW300-N1B4

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate Pf1N1B4_1055 Phosphate acetyltransferase (EC 2.3.1.8)

Query= SwissProt::P77844
         (329 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055
          Length = 422

 Score =  266 bits (681), Expect = 5e-76
 Identities = 143/330 (43%), Positives = 206/330 (62%), Gaps = 5/330 (1%)

Query: 1   MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60
           +S  +F   L++RA+A +  IVLPEG +   + AA     + I    +L  P  ++  A 
Sbjct: 92  LSPAVFRYQLIQRAQAANKRIVLPEGSEPLTVQAAAICQARGIARCVLLAKPADVEAVAR 151

Query: 61  ELGLHLNTAYLVNPLTDPRL--EEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHN 118
             G+ L        + DP L  E + E    LRK+KS+    A + ++D    GTMM+  
Sbjct: 152 AQGIELPPGL---EILDPDLIRERYVEPMVALRKTKSLNAPMAEQQLEDTVVIGTMMLAL 208

Query: 119 GDADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTA 178
            + DG+VSG  ++TA+TI+P+ Q+IKT P  ++VSS+F M+    +  +GDC +NP+P+A
Sbjct: 209 DEVDGLVSGVIHSTANTIRPALQLIKTAPGCTLVSSVFFMLFPEEVLVYGDCVMNPHPSA 268

Query: 179 EQLGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDG 238
            +L EIA+ SA +AA FGI PRVA++SYS+G S  G +V++  +A   A      L +DG
Sbjct: 269 SELAEIALQSADSAAAFGITPRVAMISYSSGESASGEEVEKVREATLLAHEQQNSLLIDG 328

Query: 239 PLQFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGL 298
           PLQ+DAA +  VAR+  P+S VAG+A VF+FPDL  GN  +K  QR+   +++GP+LQGL
Sbjct: 329 PLQYDAAANETVARQLAPNSQVAGRATVFVFPDLNTGNTTHKAVQRSADCVSLGPMLQGL 388

Query: 299 NKPVNDLSRGATVPDIVNTVAITAIQAGGR 328
            KPVNDL RGA V DIV T+A+TAIQA  R
Sbjct: 389 RKPVNDLPRGAQVDDIVYTIALTAIQAANR 418


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: 332
Number of extensions: 9
Number of successful extensions: 2
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: 422
Length adjustment: 30
Effective length of query: 299
Effective length of database: 392
Effective search space:   117208
Effective search space used:   117208
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: 49 (23.5 bits)

Align candidate Pf1N1B4_1055 (Phosphate acetyltransferase (EC 2.3.1.8))
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.4872.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.5e-118  380.9   0.0   3.2e-118  380.6   0.0    1.1  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055  Phosphate acetyltransferase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055  Phosphate acetyltransferase (EC 2.3.1.8)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.6   0.0  3.2e-118  3.2e-118       1     304 []     112     412 ..     112     412 .. 0.98

  Alignments for each domain:
  == domain 1  score: 380.6 bits;  conditional E-value: 3.2e-118
                                      TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiek 63 
                                                    ivlPEgse+ +++Aaa+++ ++ia++vll++ ++++++ +a++++l  g +++ dpd+   +e+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 112 IVLPEGSEPLTVQAAAICQARGIARCVLLAKPADVEAVaRAQGIELPPG-LEILDPDLI--RER 172
                                                    8************************************978999999876.678889998..8** PP

                                      TIGR00651  64 yverlyekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktl 127
                                                    yve ++ +rk+k ++  +a++ql+D+v++++++++l+e+dglvsG  ++ta+t+rpalq+ikt+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 173 YVEPMVALRKTKSLNAPMAEQQLEDTVVIGTMMLALDEVDGLVSGVIHSTANTIRPALQLIKTA 236
                                                    **************************************************************** PP

                                      TIGR00651 128 egvklvssvfimekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystk 191
                                                    +g  lvssvf+m  +eevlv++DC ++++P+a eLAeiAlqsa+sa ++g + p+va++sys++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 237 PGCTLVSSVFFMLFPEEVLVYGDCVMNPHPSASELAEIALQSADSAAAFG-ITPRVAMISYSSG 299
                                                    **************************************************.************* PP

                                      TIGR00651 192 gsgkgeevekvkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLd 255
                                                     s++geevekv+eA+ +++e++  ll+dG+lq+DaA  e+va++ ap+s+vag+a+vfvFPdL+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 300 ESASGEEVEKVREATLLAHEQQNSLLIDGPLQYDAAANETVARQLAPNSQVAGRATVFVFPDLN 363
                                                    **************************************************************** PP

                                      TIGR00651 256 aGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                                    +Gn++ k+vqR+ad  ++GP+lqGl+kPvnDL RGa+v+div+++++ta
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 364 TGNTTHKAVQRSADCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTA 412
                                                    ***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (422 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: 00:00:00.01
# Mc/sec: 12.43
//
[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:

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