GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoD in Escherichia coli BW25113

Align Purine nucleoside phosphorylase 2; Inosine-guanosine phosphorylase; Purine nucleoside phosphorylase II; PNP II; Xanthosine phosphorylase; EC 2.4.2.1 (characterized)
to candidate 16506 b2407 purine nucleoside phosphorylase (NCBI)

Query= SwissProt::P45563
         (277 letters)



>lcl|FitnessBrowser__Keio:16506 b2407 purine nucleoside
           phosphorylase (NCBI)
          Length = 277

 Score =  553 bits (1425), Expect = e-162
 Identities = 277/277 (100%), Positives = 277/277 (100%)

Query: 1   MSQVQFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVS 60
           MSQVQFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVS
Sbjct: 1   MSQVQFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVS 60

Query: 61  TVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGS 120
           TVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGS
Sbjct: 61  TVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGS 120

Query: 121 LRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEG 180
           LRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEG
Sbjct: 121 LRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEG 180

Query: 181 FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNM 240
           FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNM
Sbjct: 181 FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNM 240

Query: 241 AEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
           AEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA
Sbjct: 241 AEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277


Lambda     K      H
   0.323    0.139    0.410 

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: 443
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: 277
Length of database: 277
Length adjustment: 25
Effective length of query: 252
Effective length of database: 252
Effective search space:    63504
Effective search space used:    63504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate 16506 b2407 (purine nucleoside phosphorylase (NCBI))
to HMM TIGR01699 (xapA: xanthosine phosphorylase (EC 2.4.2.1))

# 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/TIGR01699.hmm
# target sequence database:        /tmp/gapView.31410.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01699  [M=248]
Accession:   TIGR01699
Description: XAPA: xanthosine phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.8e-168  541.9   1.0   1.1e-167  541.7   1.0    1.0  1  lcl|FitnessBrowser__Keio:16506  b2407 purine nucleoside phosphor


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16506  b2407 purine nucleoside phosphorylase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  541.7   1.0  1.1e-167  1.1e-167       1     248 []      27     274 ..      27     274 .. 1.00

  Alignments for each domain:
  == domain 1  score: 541.7 bits;  conditional E-value: 1.1e-167
                       TIGR01699   1 rvafilgsglgdlvdqiendvaisyedlpgfpvssvhghagelvlgdlqgvpvvcmkgrghfyegkgmsimtdavrtfk 79 
                                     rvafilgsglg+l+dqien+vaisye+lpgfpvs+vhghagelvlg+lqgvpvvcmkgrghfyeg+gm+imtda+rtfk
  lcl|FitnessBrowser__Keio:16506  27 RVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFK 105
                                     79***************************************************************************** PP

                       TIGR01699  80 llgcellfctnaagslrpevlagslvalkdhintmpgtplvglnddrfgerffslanaydkelradlakvakeediplt 158
                                     llgcellfctnaagslrpev+agslvalkdhintmpgtp+vglnddrfgerffslanayd+e+ra+l+kvakee++plt
  lcl|FitnessBrowser__Keio:16506 106 LLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLT 184
                                     ******************************************************************************* PP

                       TIGR01699 159 egvfvsylgpnfetaaeirmmqiiggdvvgmsvvpevlsaahcdlkvvalsaitnlaeglsdvklsheqtlkaaklakv 237
                                     egvfvsy+gpnfetaaeirmmqiiggdvvgmsvvpev+sa+hcdlkvva+saitn+aeglsdvklsh+qtl+aa+l+k+
  lcl|FitnessBrowser__Keio:16506 185 EGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQ 263
                                     ******************************************************************************* PP

                       TIGR01699 238 nfiklieaflk 248
                                     nfi+li++fl+
  lcl|FitnessBrowser__Keio:16506 264 NFINLICGFLR 274
                                     *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (277 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: 00:00:00.01
# Mc/sec: 6.67
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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