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.7624.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.80
//
[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