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.27938.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: 9.14
//
[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