Alignments for a candidate for pta in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Cupriavidus basilensis 4G11

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate RR42_RS33690 RR42_RS33690 phosphate acetyltransferase

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



>FitnessBrowser__Cup4G11:RR42_RS33690
          Length = 346

 Score =  303 bits (776), Expect = 4e-87
 Identities = 157/330 (47%), Positives = 226/330 (68%)

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

Query: 61  LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDG 120
           +D++  +++DP TS  T + AR  + LR+ KGMT+E++ + V  PL FA + ++ G+ DG
Sbjct: 61  IDLAGMDVIDPATSALTPSLARKLFALREKKGMTLEEARREVLKPLCFANLMVRLGHADG 120

Query: 121 MVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPT 180
            V+GAVHTT D++R  +Q+I   P  K+VS FF+M++ +  +  +G L+F+DC +  +P 
Sbjct: 121 SVAGAVHTTADVVRTAIQVIGIHPAFKLVSSFFLMMLCEPFHALKGGLIFSDCGLVVDPG 180

Query: 181 SDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAI 240
           + ELA+IA+  A++A+ L    P+VAMLSFST GSA+   VDKV  A  + +  RP LAI
Sbjct: 181 AAELAEIAMAAADSAQNLLMDAPRVAMLSFSTSGSARHAAVDKVVQATRLVQAQRPALAI 240

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

Query: 301 GFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330
           G  KP NDLSRGCS++D+  V+A+T VQAQ
Sbjct: 301 GLQKPANDLSRGCSADDVFYVIAVTAVQAQ 330


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: 294
Number of extensions: 8
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: 346
Length adjustment: 28
Effective length of query: 305
Effective length of database: 318
Effective search space:    96990
Effective search space used:    96990
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 RR42_RS33690 RR42_RS33690 (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.20764.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-111  358.3   0.4   2.3e-111  358.1   0.4    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS33690  RR42_RS33690 phosphate acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS33690  RR42_RS33690 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.1   0.4  2.3e-111  2.3e-111       1     304 []      18     326 ..      18     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 358.1 bits;  conditional E-value: 2.3e-111
                                 TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 
                                               ivl E++++r+l+Aa+  a+++ia+ vl+++ +++ + +a++ +++l+ + v+dp +s  + +++ +l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS33690  18 IVLCEAEDPRILQAAQRAAHEGIARIVLVGDAARIRQ-AAASEDIDLAGMDVIDPATSALTPSLARKLF 85 
                                               89**********************9999999988888.7888899************************ PP

                                 TIGR00651  70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfi 138
                                                +r +kG+t++ear+++  ++ +a l+v+lg+adg v+Gav+tta+++r+a+q+i+ ++++klvss+f+
  lcl|FitnessBrowser__Cup4G11:RR42_RS33690  86 ALREKKGMTLEEARREVLKPLCFANLMVRLGHADGSVAGAVHTTADVVRTAIQVIGIHPAFKLVSSFFL 154
                                               ********************************************************************* PP

                                 TIGR00651 139 mekee......evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevek 201
                                               m + e      + l+f+DC ++vdP a eLAeiA+ +a+sa++l  + p+va+ls+st gs++ ++v+k
  lcl|FitnessBrowser__Cup4G11:RR42_RS33690 155 MMLCEpfhalkGGLIFSDCGLVVDPGAAELAEIAMAAADSAQNLLMDAPRVAMLSFSTSGSARHAAVDK 223
                                               **99999999999******************************************************** PP

                                 TIGR00651 202 vkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRlada 270
                                               v++A+++++ ++p l++dG++q+DaA+v+++a kk+ +s+v+g+anv+vFP+L+aGnigYk+++R+++a
  lcl|FitnessBrowser__Cup4G11:RR42_RS33690 224 VVQATRLVQAQRPALAIDGDVQLDAAIVAEIASKKIEHSKVEGRANVLVFPSLEAGNIGYKLAERVGGA 292
                                               ********************************************************************* PP

                                 TIGR00651 271 eaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                               +aiGP+lqGl+kP nDLsRG+s++d+++v+++ta
  lcl|FitnessBrowser__Cup4G11:RR42_RS33690 293 KAIGPLLQGLQKPANDLSRGCSADDVFYVIAVTA 326
                                               ********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (346 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: 7.06
//
[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