Alignments for a candidate for pta in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Burkholderia phytofirmans PsJN

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate BPHYT_RS21700 BPHYT_RS21700 phosphotransacetylase

Query= metacyc::PTACLOS-MONOMER
         (333 letters)



>FitnessBrowser__BFirm:BPHYT_RS21700
          Length = 344

 Score =  316 bits (810), Expect = 5e-91
 Identities = 166/333 (49%), Positives = 230/333 (69%)

Query: 1   MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60
           M  I  I E A++   RI+L+E E+ R L AA +  +EG+A ++LVGD  +I+E A+  +
Sbjct: 1   MKAINRIIEQARRSPMRIVLSEAEDPRVLQAAQRATREGIARILLVGDATRIREAAAGFD 60

Query: 61  LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDG 120
           +D+S  E++DP TS    +YA + + LR  KGMT+E++ K + +PL FA + ++ G+ DG
Sbjct: 61  VDLSGMELVDPATSALASSYADELFALRSKKGMTLEQARKEILNPLCFANLMVRLGHADG 120

Query: 121 MVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPT 180
            VSGAV+TT D++R  +QII  AP  K+VS FF+M++ +  +  +G L+F+DCA+   P 
Sbjct: 121 SVSGAVNTTADVVRTAIQIIGIAPSFKLVSSFFLMMLCEPFHTLKGGLIFSDCALVVEPD 180

Query: 181 SDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAI 240
           + +LA+IA+  A++AR L   EP+VAMLSFST GSA    VDKV NA  I ++ RP LAI
Sbjct: 181 AAQLAEIAMAAADSARSLLMDEPRVAMLSFSTSGSAHHAAVDKVVNATHIVQERRPHLAI 240

Query: 241 DGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQ 300
           DG++QLDAAI SE+A  K   S V G+ANVLVFP L+ GNIGYKL +R   AKAIGP+ Q
Sbjct: 241 DGDVQLDAAIVSEIALRKVKHSQVEGHANVLVFPSLEAGNIGYKLAERIGGAKAIGPLLQ 300

Query: 301 GFAKPINDLSRGCSSEDIVNVVAITVVQAQRGI 333
           G  KP NDLSRGCS++DI  V A+T VQAQ  +
Sbjct: 301 GLRKPANDLSRGCSADDIYYVTAVTAVQAQAAL 333


Lambda     K      H
   0.316    0.134    0.374 

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: 287
Number of extensions: 12
Number of successful extensions: 1
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: 333
Length of database: 344
Length adjustment: 28
Effective length of query: 305
Effective length of database: 316
Effective search space:    96380
Effective search space used:    96380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS21700 BPHYT_RS21700 (phosphotransacetylase)
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.681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   8.5e-118  379.2   0.2   9.8e-118  379.0   0.2    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS21700  BPHYT_RS21700 phosphotransacetyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS21700  BPHYT_RS21700 phosphotransacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.0   0.2  9.8e-118  9.8e-118       1     304 []      18     326 ..      18     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 379.0 bits;  conditional E-value: 9.8e-118
                                TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlye 70 
                                              ivl E++++rvl+Aa+  ++++ia+  l+++  ++ + +a++++ +l+ ++++dp +s    +y+++l+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS21700  18 IVLSEAEDPRVLQAAQRATREGIARILLVGDATRIRE-AAAGFDVDLSGMELVDPATSALASSYADELFA 86 
                                              8**********************98777776666666.9******************************* PP

                                TIGR00651  71 krkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfime 140
                                              +r +kG+t+++ar+++ +++ +a l+v+lg+adg vsGav+tta+++r+a+qii+ ++++klvss+f+m 
  lcl|FitnessBrowser__BFirm:BPHYT_RS21700  87 LRSKKGMTLEQARKEILNPLCFANLMVRLGHADGSVSGAVNTTADVVRTAIQIIGIAPSFKLVSSFFLMM 156
                                              ********************************************************************** PP

                                TIGR00651 141 kee......evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvke 204
                                              + e      + l+f+DCa++v+P+a +LAeiA+ +a+sa+sl  +ep+va+ls+st gs++ ++v+kv++
  lcl|FitnessBrowser__BFirm:BPHYT_RS21700 157 LCEpfhtlkGGLIFSDCALVVEPDAAQLAEIAMAAADSARSLLMDEPRVAMLSFSTSGSAHHAAVDKVVN 226
                                              99999999999*********************************************************** PP

                                TIGR00651 205 AvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiG 274
                                              A++i++e++p l++dG++q+DaA+v+++a +k+++s+v+g+anv+vFP+L+aGnigYk+++R+++a+aiG
  lcl|FitnessBrowser__BFirm:BPHYT_RS21700 227 ATHIVQERRPHLAIDGDVQLDAAIVSEIALRKVKHSQVEGHANVLVFPSLEAGNIGYKLAERIGGAKAIG 296
                                              ********************************************************************** PP

                                TIGR00651 275 PilqGlakPvnDLsRGasvedivnvviita 304
                                              P+lqGl+kP nDLsRG+s++di++v+++ta
  lcl|FitnessBrowser__BFirm:BPHYT_RS21700 297 PLLQGLRKPANDLSRGCSADDIYYVTAVTA 326
                                              ****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (344 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.47
//
[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