Alignments for a candidate for pta in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Pseudomonas fluorescens GW456-L13

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate PfGW456L13_4990 Phosphate acetyltransferase (EC 2.3.1.8)

Query= SwissProt::Q9I5A5
         (704 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990
          Length = 706

 Score = 1080 bits (2792), Expect = 0.0
 Identities = 556/699 (79%), Positives = 616/699 (88%), Gaps = 8/699 (1%)

Query: 1   MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60
           M TFFIAPT FGVGLTSISLGL+R LERAGLKVGFFKPIAQ HPGD GPERS+ELVARTH
Sbjct: 8   MQTFFIAPTDFGVGLTSISLGLVRTLERAGLKVGFFKPIAQPHPGDTGPERSTELVARTH 67

Query: 61  GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120
           GL  P+PL LA VERMLGDGQLDELLEEII+LYQ+AA  KDV+IVEGMVPTR ASYAARV
Sbjct: 68  GLKPPQPLGLAHVERMLGDGQLDELLEEIITLYQQAAIGKDVLIVEGMVPTRSASYAARV 127

Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180
           N HLAKSLDAEVILVSAPENE LTEL+ R+E+QAQLFGGP+DPKVLGVILNKV+      
Sbjct: 128 NLHLAKSLDAEVILVSAPENEVLTELSGRVELQAQLFGGPKDPKVLGVILNKVK------ 181

Query: 181 NAEDGVADFARRLTEHSPLLRD-DFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239
             E+ +  FA RL EHSPLLR  DFRL+GCIP+Q ELNA RTRD+ADL+ A+V+NAGDYE
Sbjct: 182 -TEESMEAFATRLKEHSPLLRSGDFRLLGCIPFQPELNAPRTRDVADLMGAQVLNAGDYE 240

Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299
            RR+ KI++CAR + NTV+LLKPGVLVVTPGDRDDIILA SLAA+NGVPLAGLLL SD  
Sbjct: 241 TRRMTKIIICARTMRNTVELLKPGVLVVTPGDRDDIILAVSLAALNGVPLAGLLLTSDTL 300

Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359
           PDPRIM+LCRGALQ GLPVLSV+TGSYDTA  LN +NKEIP+DDRERAE +T+F+AGH+D
Sbjct: 301 PDPRIMDLCRGALQAGLPVLSVSTGSYDTANLLNGLNKEIPIDDRERAEIITDFIAGHLD 360

Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419
             WL QRCGTPRE+RLSP  FRYQ++QRAQ A KRIVLPEGSEP TVQAAAICQARGIAR
Sbjct: 361 ANWLHQRCGTPREMRLSPAVFRYQLIQRAQAANKRIVLPEGSEPLTVQAAAICQARGIAR 420

Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479
           CVLLAKPE+VQAVA+AQGI LP GLEIIDPDL+R+RYVEPMV LRK K LNAPMAEQQLE
Sbjct: 421 CVLLAKPEDVQAVARAQGIELPPGLEIIDPDLIRERYVEPMVALRKSKSLNAPMAEQQLE 480

Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539
           D+VV+ TMMLALDEVDGLVSG I+TTA+TIRPALQLIKTAPG  LVSSVFFML P++VLV
Sbjct: 481 DTVVIGTMMLALDEVDGLVSGVINTTANTIRPALQLIKTAPGCTLVSSVFFMLFPEEVLV 540

Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599
           YGDC +NP PSAS+LAEIA+QSA SA AFGI  RVAMISYS+G+S SG +V+KVREAT L
Sbjct: 541 YGDCVMNPHPSASELAEIALQSADSAAAFGITPRVAMISYSSGESASGEEVEKVREATLL 600

Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659
           A EQ+  LLIDGPLQYDAAA  SV RQ APNS VAG+ATV++FPDLNTGNTT+KAVQRSA
Sbjct: 601 AHEQQHSLLIDGPLQYDAAANESVARQLAPNSQVAGRATVYVFPDLNTGNTTHKAVQRSA 660

Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           DCVS+GPMLQGLRKPVNDL RGA V+DIVYTIALTAIQA
Sbjct: 661 DCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTAIQA 699


Lambda     K      H
   0.319    0.136    0.388 

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: 1413
Number of extensions: 54
Number of successful extensions: 3
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: 704
Length of database: 706
Length adjustment: 39
Effective length of query: 665
Effective length of database: 667
Effective search space:   443555
Effective search space used:   443555
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate PfGW456L13_4990 (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.13882.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.1e-118  382.1   0.0   1.5e-118  381.6   0.0    1.2  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990  Phosphate acetyltransferase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990  Phosphate acetyltransferase (EC 2.3.1.8)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.6   0.0  1.5e-118  1.5e-118       1     304 []     396     696 ..     396     696 .. 0.98

  Alignments for each domain:
  == domain 1  score: 381.6 bits;  conditional E-value: 1.5e-118
                                               TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvved 54 
                                                             ivlPEgse+ +++Aaa+++ ++ia++vll++ e+++++ +a++++l  g ++++d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 396 IVLPEGSEPLTVQAAAICQARGIARCVLLAKPEDVQAVaRAQGIELPPG-LEIID 449
                                                             8************************************978999999876.67788 PP

                                               TIGR00651  55 pdvskdiekyverlyekrkhkGvtekeareqlrDevslaallvelgeadglvsGa 109
                                                             pd+   +e+yve ++ +rk k ++  +a++ql+D+v++++++++l+e+dglvsG 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 450 PDLI--RERYVEPMVALRKSKSLNAPMAEQQLEDTVVIGTMMLALDEVDGLVSGV 502
                                                             8888..8************************************************ PP

                                               TIGR00651 110 vsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCavavdPnaeeLAe 164
                                                              +tta+t+rpalq+ikt++g  lvssvf+m  +eevlv++DC ++++P+a eLAe
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 503 INTTANTIRPALQLIKTAPGCTLVSSVFFMLFPEEVLVYGDCVMNPHPSASELAE 557
                                                             ******************************************************* PP

                                               TIGR00651 165 iAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                                             iAlqsa+sa ++g + p+va++sys++ s++geevekv+eA+ +++e++  ll+d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 558 IALQSADSAAAFG-ITPRVAMISYSSGESASGEEVEKVREATLLAHEQQHSLLID 611
                                                             *************.***************************************** PP

                                               TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiG 274
                                                             G+lq+DaA  e+va++ ap+s+vag+a+v+vFPdL++Gn++ k+vqR+ad  ++G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 612 GPLQYDAAANESVARQLAPNSQVAGRATVYVFPDLNTGNTTHKAVQRSADCVSLG 666
                                                             ******************************************************* PP

                                               TIGR00651 275 PilqGlakPvnDLsRGasvedivnvviita 304
                                                             P+lqGl+kPvnDL RGa+v+div+++++ta
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 667 PMLQGLRKPVNDLPRGAQVDDIVYTIALTA 696
                                                             ****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (706 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: 14.20
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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