Alignments for a candidate for deoD in Clostridium kluyveri DSM 555

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Clostridium kluyveri DSM 555

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_012102003.1 CKL_RS07905 purine-nucleoside phosphorylase

Query= SwissProt::P77834
         (274 letters)



>NCBI__GCF_000016505.1:WP_012102003.1
          Length = 272

 Score =  324 bits (830), Expect = 1e-93
 Identities = 154/266 (57%), Positives = 207/266 (77%)

Query: 6   IEQAAQFLKEKFPTSPQIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEGHAGQLV 65
           +++  +++      +P+IG+ILGSGLG +A+EIE+     Y++IP+FPVSTVEGH  + V
Sbjct: 7   VKETVEYINSNIKATPKIGIILGSGLGDMAEEIEKPRICKYNEIPHFPVSTVEGHKNRFV 66

Query: 66  YGQLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNESFEPGDL 125
            G L G  V+ MQGRFHYYEGYS ++VTFP+RVMK LGVE  IVTNAAGGVN++++ G+L
Sbjct: 67  IGNLGGKYVIAMQGRFHYYEGYSMEEVTFPIRVMKKLGVEMFIVTNAAGGVNKNYKSGEL 126

Query: 126 MIISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVREGVYVA 185
           M+I+DHIN  G NPLIG N    G RFPDMSEAY K L ++AK+ A  + +++++GVYV 
Sbjct: 127 MLINDHINLSGQNPLIGQNLEDFGTRFPDMSEAYDKELIKVAKNAALQLNIQLQQGVYVY 186

Query: 186 NTGPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGILDQPLT 245
            +GP+YETPAEI M+RV+GGDAVGMSTVPEVI A H+GM+V+GISCI+NMAAGIL QPL+
Sbjct: 187 MSGPSYETPAEINMLRVLGGDAVGMSTVPEVITANHSGMKVMGISCITNMAAGILRQPLS 246

Query: 246 HDEVIETTEKVKADFLRFVKAIVRNM 271
           H+EVI+T+  V  +F   ++ I+R +
Sbjct: 247 HEEVIKTSSMVSENFKLLLRKILREL 272


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: 272
Number of extensions: 6
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: 274
Length of database: 272
Length adjustment: 25
Effective length of query: 249
Effective length of database: 247
Effective search space:    61503
Effective search space used:    61503
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_012102003.1 CKL_RS07905 (purine-nucleoside phosphorylase)
to HMM TIGR01700 (purine nucleoside phosphorylase I, inosine and guanosine-specific (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/TIGR01700.hmm
# target sequence database:        /tmp/gapView.16255.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01700  [M=249]
Accession:   TIGR01700
Description: PNPH: purine nucleoside phosphorylase I, inosine and guanosine-specific
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-117  375.2   1.9     8e-117  375.0   1.9    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012102003.1  CKL_RS07905 purine-nucleoside ph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012102003.1  CKL_RS07905 purine-nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.0   1.9    8e-117    8e-117       1     248 [.      23     269 ..      23     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 375.0 bits;  conditional E-value: 8e-117
                                 TIGR01700   1 diaiilGsGlGelaekvedavildyseiPefpestveGhkGklvfGklegkkvvilqGrfhlyegydla 69 
                                               +i+iilGsGlG +ae++e++ i +y+eiP+fp stveGhk ++v+G+l+gk v+++qGrfh+yegy+++
  lcl|NCBI__GCF_000016505.1:WP_012102003.1  23 KIGIILGSGLGDMAEEIEKPRICKYNEIPHFPVSTVEGHKNRFVIGNLGGKYVIAMQGRFHYYEGYSME 91 
                                               699****************************************************************** PP

                                 TIGR01700  70 kvtfPvrvlkllGvealvvtnaaGgintefkvGdlmlikdhinllalnPliGpneekfGarfpdmsday 138
                                               +vtfP+rv+k+lGve+++vtnaaGg+n ++k G+lmli+dhinl ++nPliG n e+fG+rfpdms+ay
  lcl|NCBI__GCF_000016505.1:WP_012102003.1  92 EVTFPIRVMKKLGVEMFIVTNAAGGVNKNYKSGELMLINDHINLSGQNPLIGQNLEDFGTRFPDMSEAY 160
                                               ********************************************************************* PP

                                 TIGR01700 139 dkelrqkakeiakelditlkeGvyvavtGPsyetpaevrllkklGadavGmstvpevivarhcGlrvlg 207
                                               dkel++ ak+ a +l+i+l++Gvyv ++GPsyetpae+++l+ lG+davGmstvpevi a+h+G++v+g
  lcl|NCBI__GCF_000016505.1:WP_012102003.1 161 DKELIKVAKNAALQLNIQLQQGVYVYMSGPSYETPAEINMLRVLGGDAVGMSTVPEVITANHSGMKVMG 229
                                               ********************************************************************* PP

                                 TIGR01700 208 lslitnkaagildaelsdheevlevakkakekleklvsalv 248
                                               +s+itn+aagil + ls heev++++ +++e+++ l+ +++
  lcl|NCBI__GCF_000016505.1:WP_012102003.1 230 ISCITNMAAGILRQPLS-HEEVIKTSSMVSENFKLLLRKIL 269
                                               *****************.***************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (249 nodes)
Target sequences:                          1  (272 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.46
//
[ok]

This GapMind analysis is from Sep 24 2021. 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