GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Bacillus altitudinis 41KF2b

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_008343597.1 BA79_RS09250 phosphate acetyltransferase

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



>NCBI__GCF_000691145.1:WP_008343597.1
          Length = 323

 Score =  379 bits (973), Expect = e-110
 Identities = 186/323 (57%), Positives = 246/323 (76%), Gaps = 2/323 (0%)

Query: 2   DLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALNV 61
           D+F +++ K+  + +K+VFPEG DERI++A  +LA+  +  P+++G + E++  A  L +
Sbjct: 3   DIFSTVQEKVAGKGVKIVFPEGMDERILTAVQKLADGKVLQPIVVGKKEEVEAKAKELGL 62

Query: 62  SLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVDG 121
           +LDG+++ D     G   + +VQA VERRKGK T +QA + L D NYFGT +VY    DG
Sbjct: 63  TLDGVDVYDPHTYEGF--EDLVQAFVERRKGKATEEQARKALLDENYFGTMLVYKGLADG 120

Query: 122 MVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLAE 181
           +VSGAAH T DTVRPALQIIKTK GV   SG F+M +G+++Y+FADCAINI P+   LAE
Sbjct: 121 LVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEEQYVFADCAINIAPDSQDLAE 180

Query: 182 IAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQFD 241
           IA+ES  TA++FDI+PRVA+LSFST GSAKS E +KV  A ++A+E  P + +DGE QFD
Sbjct: 181 IAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETDKVSEAVRIAKEKAPELVLDGEFQFD 240

Query: 242 AAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPVS 301
           AAFVP+VA  K  DS + G A+VFVFP L++GNIGYKIAQR+G FEA+GPILQGLN+PV+
Sbjct: 241 AAFVPSVAAKKAPDSVIKGDASVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGLNQPVN 300

Query: 302 DLSRGCNAEDVYKVSIITATQAL 324
           DLSRGCNAEDVY +++ITA QAL
Sbjct: 301 DLSRGCNAEDVYNLALITAAQAL 323


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: 330
Number of extensions: 14
Number of successful extensions: 2
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: 323
Length adjustment: 28
Effective length of query: 300
Effective length of database: 295
Effective search space:    88500
Effective search space used:    88500
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_008343597.1 BA79_RS09250 (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.3641604.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-136  439.9   0.3   3.2e-136  439.7   0.3    1.0  1  NCBI__GCF_000691145.1:WP_008343597.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_008343597.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.7   0.3  3.2e-136  3.2e-136       1     304 []      19     319 ..      19     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: 439.7 bits;  conditional E-value: 3.2e-136
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           iv+PEg++er+l A+++la+ k+++++++++kee+++ kake+ l+l  v v+dp+++++ e++v++++e+rk
  NCBI__GCF_000691145.1:WP_008343597.1  19 IVFPEGMDERILTAVQKLADGKVLQPIVVGKKEEVEA-KAKELGLTLDGVDVYDPHTYEGFEDLVQAFVERRK 90 
                                           8**************************9999888887.*********************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                            k +te++ar++l De++++++lv++g adglvsGa+++ta+t+rpalqiikt+egvk +s+vfim+++ee++
  NCBI__GCF_000691145.1:WP_008343597.1  91 GK-ATEEQARKALLDENYFGTMLVYKGLADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEEQY 162
                                           **.99******************************************************************** PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           vfaDCa++++P++++LAeiA++sa++ak+++ +ep+va+ls+stkgs+k++e++kv eAv+i+kek+p+l+ld
  NCBI__GCF_000691145.1:WP_008343597.1 163 VFADCAINIAPDSQDLAEIAIESANTAKMFD-IEPRVAMLSFSTKGSAKSDETDKVSEAVRIAKEKAPELVLD 234
                                           ******************************9.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           Ge+qfDaA+v++va+kkap+s ++g+a vfvFP+L+aGnigYki+qRl+++ea+GPilqGl++PvnDLsRG++
  NCBI__GCF_000691145.1:WP_008343597.1 235 GEFQFDAAFVPSVAAKKAPDSVIKGDASVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGLNQPVNDLSRGCN 307
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                           +ed++n+++ita
  NCBI__GCF_000691145.1:WP_008343597.1 308 AEDVYNLALITA 319
                                           **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (323 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: 16.19
//
[ok]

This GapMind analysis is from Sep 24 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