Alignments for a candidate for pta in Pseudomonas simiae WCS417

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.1551.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.98
//
[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:

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