Alignments for a candidate for deoD in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Cereibacter sphaeroides ATCC 17029

Align Purine nucleoside phosphorylase 1; PNP 1; Inosine phosphorylase; Inosine-guanosine phosphorylase; Purine nucleoside phosphorylase I; PNP I; Pu-NPase I; EC 2.4.2.1 (characterized)
to candidate WP_011840662.1 RSPH17029_RS04490 purine-nucleoside phosphorylase

Query= SwissProt::P77834
         (274 letters)



>NCBI__GCF_000015985.1:WP_011840662.1
          Length = 266

 Score =  213 bits (541), Expect = 5e-60
 Identities = 112/243 (46%), Positives = 156/243 (64%), Gaps = 5/243 (2%)

Query: 6   IEQAAQFLKEKFPTSP-QIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEGHAGQL 64
           +E+ A  ++ +    P ++GL+LGSGLG LA+ +E  + +PY ++  FP + V GH  +L
Sbjct: 3   VERLASLIRARAGHQPVRLGLVLGSGLGHLAEAVE-GVSLPYEELAGFPEAGVSGHQPRL 61

Query: 65  VYGQLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNESFEPGD 124
           V G LEG  V V  GR HYYE  +   +  P+ V+K LG E LI TNAAG +     PG 
Sbjct: 62  VVGDLEGVRVAVFGGRAHYYESGNPAAMRVPLAVLKHLGAEALIATNAAGSLRADLPPGS 121

Query: 125 LMIISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVREGVYV 184
           LM++SDHIN  G NPLIG    A   RF  M++A+   LR   +  A   G+ + EG+Y 
Sbjct: 122 LMLLSDHINLSGANPLIGEPSEA---RFVPMTDAHDPGLRARLRAAAEAAGVPLGEGIYA 178

Query: 185 ANTGPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGILDQPL 244
             +GP++ETPAEIRM RV+G DAVGMSTVPEVI+AR  G++V  IS ++NM AG+ D+ +
Sbjct: 179 WFSGPSFETPAEIRMARVLGADAVGMSTVPEVILARFLGLKVAAISTVTNMGAGLSDEAI 238

Query: 245 THD 247
           +H+
Sbjct: 239 SHE 241


Lambda     K      H
   0.319    0.137    0.388 

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: 216
Number of extensions: 11
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: 274
Length of database: 266
Length adjustment: 25
Effective length of query: 249
Effective length of database: 241
Effective search space:    60009
Effective search space used:    60009
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_011840662.1 RSPH17029_RS04490 (purine-nucleoside phosphorylase)
to HMM TIGR01698 (purine nucleotide 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/TIGR01698.hmm
# target sequence database:        /tmp/gapView.4027534.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01698  [M=245]
Accession:   TIGR01698
Description: PUNP: purine nucleotide 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-104  334.3   5.7   2.4e-104  334.1   5.7    1.0  1  NCBI__GCF_000015985.1:WP_011840662.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015985.1:WP_011840662.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.1   5.7  2.4e-104  2.4e-104       2     244 ..      21     262 ..      20     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 334.1 bits;  conditional E-value: 2.4e-104
                             TIGR01698   2 laivlGsGlgalvealaetvelpyaeiPGfsapavaGhagrllrvrigdrsvlvlegrthayegkdvravvvp 74 
                                           l++vlGsGlg l+ea+ e v+lpy+e+ Gf+ ++v+Gh  rl+ +++ + +v+v++gr+h+ye+++ +a++vp
  NCBI__GCF_000015985.1:WP_011840662.1  21 LGLVLGSGLGHLAEAV-EGVSLPYEELAGFPEAGVSGHQPRLVVGDLEGVRVAVFGGRAHYYESGNPAAMRVP 92 
                                           79*************9.679***************************************************** PP

                             TIGR01698  75 vraaraiGaelliltnaaGslreelgaGslvlladhinltarsPliGlesderfvdltdaydprlrigleela 147
                                           ++ ++ +Gae li tnaaGslr++l++Gsl+ll+dhinl++++PliG++s++rfv +tda+dp+lr++l ++a
  NCBI__GCF_000015985.1:WP_011840662.1  93 LAVLKHLGAEALIATNAAGSLRADLPPGSLMLLSDHINLSGANPLIGEPSEARFVPMTDAHDPGLRARLRAAA 165
                                           ************************************************************************* PP

                             TIGR01698 148 ervdlplaeGvyaqfsGPsyetPaevrmarilGadlvGmstvletilarflGlevlavslvtnlaaGitgeel 220
                                           e+ ++pl eG+ya+fsGPs+etPae+rmar+lGad+vGmstv+e+ilarflGl+v+a+s vtn+ aG++ e +
  NCBI__GCF_000015985.1:WP_011840662.1 166 EAAGVPLGEGIYAWFSGPSFETPAEIRMARVLGADAVGMSTVPEVILARFLGLKVAAISTVTNMGAGLSDEAI 238
                                           ************************************************************************* PP

                             TIGR01698 221 shaevkavaaaagtrlaalladli 244
                                           sh+ +ka+a++++++l +ll +++
  NCBI__GCF_000015985.1:WP_011840662.1 239 SHEHTKAMAPLGAAKLETLLREFL 262
                                           ********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (245 nodes)
Target sequences:                          1  (266 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: 4.73
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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