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.6430.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: 19.02
//
[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:

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