GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Pseudomonas simiae WCS417

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate GFF734 PS417_03730 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>FitnessBrowser__WCS417:GFF734
          Length = 699

 Score = 1082 bits (2797), Expect = 0.0
 Identities = 555/699 (79%), Positives = 615/699 (87%), Gaps = 8/699 (1%)

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

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

Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180
           N HLAKSLDAEVILVSAPENE LTEL+ R+E+QAQLFGGP+DPKVLGVILNKVR      
Sbjct: 121 NLHLAKSLDAEVILVSAPENEVLTELSGRVELQAQLFGGPKDPKVLGVILNKVR------ 174

Query: 181 NAEDGVADFARRLTEHSPLLRD-DFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239
             ++ +  F+ RL EHSPLLR  DFRL+GCIP+Q ELNA RTRD+ADL+ A+++NAGDYE
Sbjct: 175 -TDESMEAFSARLKEHSPLLRSGDFRLLGCIPYQPELNAPRTRDVADLMGAQILNAGDYE 233

Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299
            RR+ KI++CAR + NTV+LLKPGVLVVTPGDRDDIILA SLAA+NGVPLAGLLL SD  
Sbjct: 234 TRRMTKIIICARTMRNTVELLKPGVLVVTPGDRDDIILAVSLAAINGVPLAGLLLTSDTL 293

Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359
           PDPRIMELCRGA Q GLPVLSV+TGSYDTA  LN +NKEIP+DDRERAE +T+FVA H+D
Sbjct: 294 PDPRIMELCRGAFQAGLPVLSVSTGSYDTANQLNSLNKEIPIDDRERAEIITDFVASHLD 353

Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419
             WL QRCGTPRE+RLSP  FRYQ++QRAQ A KRIVLPEGSEP TVQAAAICQARGIAR
Sbjct: 354 ARWLHQRCGTPREMRLSPAVFRYQLIQRAQAANKRIVLPEGSEPLTVQAAAICQARGIAR 413

Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479
           CVLLAKP +V+AVA+AQGI LPEGLEI+DPDL+RQRYVEPMV LRK K LNAPMAEQQLE
Sbjct: 414 CVLLAKPADVEAVARAQGIELPEGLEILDPDLIRQRYVEPMVALRKSKSLNAPMAEQQLE 473

Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539
           D+VV+ATMMLALDEVDGLVSG IH+TA+TIRPALQLIKTAPG  LVSSVFFML P+QVLV
Sbjct: 474 DTVVIATMMLALDEVDGLVSGVIHSTANTIRPALQLIKTAPGCTLVSSVFFMLFPEQVLV 533

Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599
           YGDC +NP PSA++LAEIA+QSA SA AFGI  RVAMISYS+GDS SG +V+KVREAT L
Sbjct: 534 YGDCVMNPHPSAAELAEIALQSADSAAAFGITPRVAMISYSSGDSASGEEVEKVREATLL 593

Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659
           A EQ+  LLIDGPLQYDAAA  +V RQ APNS VAG+ATVF+FPDLNTGNTT+KAVQRSA
Sbjct: 594 AHEQQSSLLIDGPLQYDAAANENVARQLAPNSQVAGKATVFVFPDLNTGNTTHKAVQRSA 653

Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           DCVS+GPMLQGLRKPVNDL RGA V+DIVYTIALTAIQA
Sbjct: 654 DCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTAIQA 692


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: 1389
Number of extensions: 56
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: 699
Length adjustment: 39
Effective length of query: 665
Effective length of database: 660
Effective search space:   438900
Effective search space used:   438900
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 GFF734 PS417_03730 (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.23709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.4e-118  380.1   0.1   5.9e-118  379.7   0.1    1.2  1  lcl|FitnessBrowser__WCS417:GFF734  PS417_03730 phosphate acetyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF734  PS417_03730 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.7   0.1  5.9e-118  5.9e-118       1     304 []     389     689 ..     389     689 .. 0.98

  Alignments for each domain:
  == domain 1  score: 379.7 bits;  conditional E-value: 5.9e-118
                          TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkhk 75 
                                        ivlPEgse+ +++Aaa+++ ++ia++vll++ ++++++ +a++++l  g +++ dpd+   +++yve ++ +rk k
  lcl|FitnessBrowser__WCS417:GFF734 389 IVLPEGSEPLTVQAAAICQARGIARCVLLAKPADVEAVaRAQGIELPEG-LEILDPDLI--RQRYVEPMVALRKSK 461
                                        8************************************978999998765.788899999..89************* PP

                          TIGR00651  76 GvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDC 151
                                         ++  +a++ql+D+v++a+++++l+e+dglvsG  ++ta+t+rpalq+ikt++g  lvssvf+m  +e+vlv++DC
  lcl|FitnessBrowser__WCS417:GFF734 462 SLNAPMAEQQLEDTVVIATMMLALDEVDGLVSGVIHSTANTIRPALQLIKTAPGCTLVSSVFFMLFPEQVLVYGDC 537
                                        **************************************************************************** PP

                          TIGR00651 152 avavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaA 227
                                         ++++P+a eLAeiAlqsa+sa ++g + p+va++sys++ s++geevekv+eA+ +++e+++ ll+dG+lq+DaA
  lcl|FitnessBrowser__WCS417:GFF734 538 VMNPHPSAAELAEIALQSADSAAAFG-ITPRVAMISYSSGDSASGEEVEKVREATLLAHEQQSSLLIDGPLQYDAA 612
                                        **************************.************************************************* PP

                          TIGR00651 228 lvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviit 303
                                          e+va++ ap+s+vagka+vfvFPdL++Gn++ k+vqR+ad  ++GP+lqGl+kPvnDL RGa+v+div+++++t
  lcl|FitnessBrowser__WCS417:GFF734 613 ANENVARQLAPNSQVAGKATVFVFPDLNTGNTTHKAVQRSADCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALT 688
                                        ***************************************************************************9 PP

                          TIGR00651 304 a 304
                                        a
  lcl|FitnessBrowser__WCS417:GFF734 689 A 689
                                        6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (699 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: 14.30
//
[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