GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Weissella oryzae SG25

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_027699422.1 TT13_RS07580 phosphate acetyltransferase

Query= metacyc::MONOMER-13062
         (328 letters)



>NCBI__GCF_000691805.2:WP_027699422.1
          Length = 324

 Score =  406 bits (1044), Expect = e-118
 Identities = 212/324 (65%), Positives = 253/324 (78%)

Query: 1   MDLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALN 60
           M+LFE L +KI ++   LVFPEGED RI  AA RLA + L  P+LLG  +EI  TA +  
Sbjct: 1   MELFEQLSAKILNQGKILVFPEGEDVRIQGAAIRLAANGLVKPILLGVASEIAATAASHG 60

Query: 61  VSLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVD 120
             L  IEI+D    P +  + MV+A+VERR GKT A  AA+WLKD NYFGT +VY+   D
Sbjct: 61  FDLSSIEIIDPAQYPSDKFEAMVEALVERRNGKTDAVTAAKWLKDVNYFGTMLVYLGQAD 120

Query: 121 GMVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLA 180
           GMVSGA HPTGDTVRPALQI+KTKPG + ISG+FVMQK DQRY+FAD AINI+ +   +A
Sbjct: 121 GMVSGATHPTGDTVRPALQIVKTKPGSSRISGAFVMQKADQRYIFADAAINIDIDAQTMA 180

Query: 181 EIAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQF 240
           EIAV+S +TA++F IDP+VA+LSFST GSAK+P+V+KV  ATKLAQ   P + IDGE+QF
Sbjct: 181 EIAVQSAQTAKVFGIDPKVAMLSFSTKGSAKAPQVDKVAEATKLAQVAAPELLIDGELQF 240

Query: 241 DAAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPV 300
           DAAFV +VA AK  +SKVAG A VFVFP+LQSGNIGYKIAQR+GGFEAIGP+LQGL KP+
Sbjct: 241 DAAFVESVAAAKAPNSKVAGQANVFVFPDLQSGNIGYKIAQRLGGFEAIGPVLQGLAKPI 300

Query: 301 SDLSRGCNAEDVYKVSIITATQAL 324
           SDLSRG N EDVYKV+IITA QAL
Sbjct: 301 SDLSRGANEEDVYKVAIITAAQAL 324


Lambda     K      H
   0.315    0.133    0.369 

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: 340
Number of extensions: 7
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: 328
Length of database: 324
Length adjustment: 28
Effective length of query: 300
Effective length of database: 296
Effective search space:    88800
Effective search space used:    88800
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: 48 (23.1 bits)

Align candidate WP_027699422.1 TT13_RS07580 (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.2191886.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-115  371.1   0.9   2.9e-115  370.9   0.9    1.0  1  NCBI__GCF_000691805.2:WP_027699422.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691805.2:WP_027699422.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.9   0.9  2.9e-115  2.9e-115       1     304 []      18     320 ..      18     320 .. 0.97

  Alignments for each domain:
  == domain 1  score: 370.9 bits;  conditional E-value: 2.9e-115
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvsk..diekyverlyek 71 
                                           +v+PEg++ r+  Aa+ la +++++++ll+  +e+ + +a++   +l++++++dp  ++  + e  ve+l+e+
  NCBI__GCF_000691805.2:WP_027699422.1  18 LVFPEGEDVRIQGAAIRLAANGLVKPILLGVASEIAA-TAASHGFDLSSIEIIDPAQYPsdKFEAMVEALVER 89 
                                           69*************************9999888887.78888999999***999987522689********* PP

                             TIGR00651  72 rkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeee 144
                                           r  k  +  +a++ l+D ++++++lv+lg+adg+vsGa + t +t+rpalqi+kt++g++ +s+ f+m+k ++
  NCBI__GCF_000691805.2:WP_027699422.1  90 RNGK-TDAVTAAKWLKDVNYFGTMLVYLGQADGMVSGATHPTGDTVRPALQIVKTKPGSSRISGAFVMQKADQ 161
                                           ****.8999999************************************************************* PP

                             TIGR00651 145 vlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdll 217
                                           +++faD a+++d +a+ +AeiA+qsa++ak +g ++pkva+ls+stkgs+k+ +v+kv+eA+k+++  +p+ll
  NCBI__GCF_000691805.2:WP_027699422.1 162 RYIFADAAINIDIDAQTMAEIAVQSAQTAKVFG-IDPKVAMLSFSTKGSAKAPQVDKVAEATKLAQVAAPELL 233
                                           *********************************.*************************************** PP

                             TIGR00651 218 ldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRG 290
                                           +dGelqfDaA+ve+va+ kap+s+vag+anvfvFPdL++GnigYki+qRl+++eaiGP+lqGlakP++DLsRG
  NCBI__GCF_000691805.2:WP_027699422.1 234 IDGELQFDAAFVESVAAAKAPNSKVAGQANVFVFPDLQSGNIGYKIAQRLGGFEAIGPVLQGLAKPISDLSRG 306
                                           ************************************************************************* PP

                             TIGR00651 291 asvedivnvviita 304
                                           a+ ed+++v+iita
  NCBI__GCF_000691805.2:WP_027699422.1 307 ANEEDVYKVAIITA 320
                                           ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (324 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.23
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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