Alignments for a candidate for pta in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Pseudomonas putida KT2440

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate PP_0774 PP_0774 Phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>FitnessBrowser__Putida:PP_0774
          Length = 695

 Score = 1054 bits (2726), Expect = 0.0
 Identities = 544/699 (77%), Positives = 608/699 (86%), Gaps = 9/699 (1%)

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

Query: 61  GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120
           G+  P PL LA VERMLGDGQLDELLEEII LYQ+A    DVV+VEGMVPTRHASYAARV
Sbjct: 61  GIKPPVPLSLAHVERMLGDGQLDELLEEIIRLYQQACVGNDVVVVEGMVPTRHASYAARV 120

Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180
           N HLAKSLDAEVILVSAPENE L+EL+ R+E+QAQLFGGPRDPKVLGVILNKVR      
Sbjct: 121 NLHLAKSLDAEVILVSAPENEVLSELSGRVELQAQLFGGPRDPKVLGVILNKVR------ 174

Query: 181 NAEDGVADFARRLTEHSPLLR-DDFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239
             ++ +ADFA RL EHSPLLR +DFRL+GCIP+Q ELNA RTRD+A+LL A+V+NAGDYE
Sbjct: 175 -TDESMADFATRLREHSPLLRGNDFRLLGCIPYQPELNAPRTRDVAELLGAQVLNAGDYE 233

Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299
           QRR+ KI++CAR V NTV LL  G LVVTPGDRDDIILA SLAA+NGVPLAGLLL SD  
Sbjct: 234 QRRMSKIIICARTVANTVPLLTSGTLVVTPGDRDDIILAVSLAAINGVPLAGLLLTSDSK 293

Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359
           PD RI+ LCRGALQ GLP+LSV+TGSYDTA  LN +N+EIPVDDRERAE +T+FVA H+D
Sbjct: 294 PDVRILGLCRGALQAGLPILSVSTGSYDTANQLNSLNREIPVDDRERAEFITDFVASHLD 353

Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419
             WL QRCGTPRELRLSP  FRYQ++QRAQ+A KRIVLPEG+EP  VQAAAICQARGIAR
Sbjct: 354 AAWLHQRCGTPRELRLSPAVFRYQLIQRAQQANKRIVLPEGAEPLLVQAAAICQARGIAR 413

Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479
           CVLLAKPE+V AVA+AQGI LP GLEI+DP+L+R RYVEPMVELRK K LNAPMAEQQLE
Sbjct: 414 CVLLAKPEDVDAVARAQGITLPPGLEILDPELIRGRYVEPMVELRKSKNLNAPMAEQQLE 473

Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539
           D VV+ TMMLALDEVDGLVSG +H+TA+TIRPALQLIKTAPG +LVSSVFFML P+QVLV
Sbjct: 474 DPVVIGTMMLALDEVDGLVSGLVHSTANTIRPALQLIKTAPGSSLVSSVFFMLFPEQVLV 533

Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599
           YGDC +NP PSA++LAEIA QSAASAQAFGI  RVAMISYS+ DS S  +V+KVREATRL
Sbjct: 534 YGDCVMNPHPSAAELAEIAQQSAASAQAFGIAPRVAMISYSS-DSASDEEVEKVREATRL 592

Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659
           A++   +LLIDGPLQYDAAA  ++ R+ AP SPVAG+ATVF+FPDLNTGNTT+KAVQRSA
Sbjct: 593 AQDAAQELLIDGPLQYDAAANPAIARELAPASPVAGRATVFVFPDLNTGNTTHKAVQRSA 652

Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           D VS+GPMLQGLRKPVNDL RGA V+DIV+TIALTAIQA
Sbjct: 653 DGVSLGPMLQGLRKPVNDLPRGAQVDDIVHTIALTAIQA 691


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: 1387
Number of extensions: 56
Number of successful extensions: 4
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: 695
Length adjustment: 39
Effective length of query: 665
Effective length of database: 656
Effective search space:   436240
Effective search space used:   436240
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 PP_0774 PP_0774 (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.1113.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.3e-113  363.4   0.0   6.9e-113  363.1   0.0    1.1  1  lcl|FitnessBrowser__Putida:PP_0774  PP_0774 Phosphate acetyltransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0774  PP_0774 Phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.1   0.0  6.9e-113  6.9e-113       1     304 []     389     688 ..     389     688 .. 0.97

  Alignments for each domain:
  == domain 1  score: 363.1 bits;  conditional E-value: 6.9e-113
                           TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkh 74 
                                         ivlPEg e+ +++Aaa+++ ++ia++vll++ e++ ++ +a+++ l  g +++ dp++   + +yve ++e+rk 
  lcl|FitnessBrowser__Putida:PP_0774 389 IVLPEGAEPLLVQAAAICQARGIARCVLLAKPEDVDAVaRAQGITLPPG-LEILDPELI--RGRYVEPMVELRKS 460
                                         8***********************************9977888888766.677788888..79************ PP

                           TIGR00651  75 kGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfa 149
                                         k ++  +a++ql+D+v++++++++l+e+dglvsG v++ta+t+rpalq+ikt++g++lvssvf+m  +e+vlv++
  lcl|FitnessBrowser__Putida:PP_0774 461 KNLNAPMAEQQLEDPVVIGTMMLALDEVDGLVSGLVHSTANTIRPALQLIKTAPGSSLVSSVFFMLFPEQVLVYG 535
                                         *************************************************************************** PP

                           TIGR00651 150 DCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqf 224
                                         DC ++++P+a eLAeiA qsa+sa+++g + p+va++sys+  s+++eevekv+eA++++++ + +ll+dG+lq+
  lcl|FitnessBrowser__Putida:PP_0774 536 DCVMNPHPSAAELAEIAQQSAASAQAFG-IAPRVAMISYSSD-SASDEEVEKVREATRLAQDAAQELLIDGPLQY 608
                                         ****************************.***********86.7899**************************** PP

                           TIGR00651 225 DaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnv 299
                                         DaA  + +a++ ap s+vag+a+vfvFPdL++Gn++ k+vqR+ad  ++GP+lqGl+kPvnDL RGa+v+div++
  lcl|FitnessBrowser__Putida:PP_0774 609 DAAANPAIARELAPASPVAGRATVFVFPDLNTGNTTHKAVQRSADGVSLGPMLQGLRKPVNDLPRGAQVDDIVHT 683
                                         *************************************************************************** PP

                           TIGR00651 300 viita 304
                                         +++ta
  lcl|FitnessBrowser__Putida:PP_0774 684 IALTA 688
                                         ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (695 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: 00:00:00.01
# Mc/sec: 19.42
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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