Alignments for a candidate for deoD in Desulfovibrio vulgaris Hildenborough JW710

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Desulfovibrio vulgaris Hildenborough JW710

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 207714 DVU2230 purine nucleoside phosphorylase (TIGR)

Query= SwissProt::P77834
         (274 letters)



>FitnessBrowser__DvH:207714
          Length = 274

 Score =  248 bits (634), Expect = 8e-71
 Identities = 135/269 (50%), Positives = 165/269 (61%), Gaps = 2/269 (0%)

Query: 2   NRTAIEQAAQFLKEKFPT--SPQIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEG 59
           N   ++ AAQ ++   P   SP++G++LG+GLG LA+ +   + IPY  +P FP STV  
Sbjct: 3   NPEKVQIAAQAVRTALPQGFSPRVGIVLGTGLGALANAVTSPVAIPYESLPGFPRSTVAS 62

Query: 60  HAGQLVYGQLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNES 119
           HAG  + G L GA VV+ QGR H YEGY  + V   VRVM ALG   L++TNAAG +N  
Sbjct: 63  HAGSFLCGFLGGAPVVLQQGRCHLYEGYQPEDVCMGVRVMAALGAATLVITNAAGALNPQ 122

Query: 120 FEPGDLMIISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVR 179
           F+ GDLM I+DHIN  G  PL GPN  A G RFPDMS  Y+  L QLA   A  +G+R+ 
Sbjct: 123 FDAGDLMCITDHINFTGRTPLAGPNHDAWGPRFPDMSAPYAPGLVQLAMREAGQLGIRLE 182

Query: 180 EGVYVANTGPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGI 239
            GVYV   GP  ETPAE RM R +G DAVGMSTV EVI ARH GM+VLGISC+SN     
Sbjct: 183 RGVYVGVHGPQMETPAETRMFRTLGADAVGMSTVLEVIAARHLGMKVLGISCLSNKNLPD 242

Query: 240 LDQPLTHDEVIETTEKVKADFLRFVKAIV 268
             +    +EVI           R V AIV
Sbjct: 243 CMEEAPLEEVIRVAGMAGERLTRLVAAIV 271


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: 230
Number of extensions: 8
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: 274
Length adjustment: 25
Effective length of query: 249
Effective length of database: 249
Effective search space:    62001
Effective search space used:    62001
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 207714 DVU2230 (purine nucleoside phosphorylase (TIGR))
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.1799692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
      5e-94  300.4   0.0    5.8e-94  300.2   0.0    1.0  1  FitnessBrowser__DvH:207714  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__DvH:207714  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.2   0.0   5.8e-94   5.8e-94       2     248 ..      26     271 ..      25     272 .. 0.97

  Alignments for each domain:
  == domain 1  score: 300.2 bits;  conditional E-value: 5.8e-94
                   TIGR01700   2 iaiilGsGlGelaekvedavildyseiPefpestveGhkGklvfGklegkkvvilqGrfhlyegydlakvtfPvrvlkllGve 84 
                                 ++i+lG+GlG la+ v+ +v ++y+ +P fp+stv  h+G ++ G l+g +vv+ qGr hlyegy+ + v++ vrv+ +lG  
  FitnessBrowser__DvH:207714  26 VGIVLGTGLGALANAVTSPVAIPYESLPGFPRSTVASHAGSFLCGFLGGAPVVLQQGRCHLYEGYQPEDVCMGVRVMAALGAA 108
                                 89********************************************************************************* PP

                   TIGR01700  85 alvvtnaaGgintefkvGdlmlikdhinllalnPliGpneekfGarfpdmsdaydkelrqkakeiakelditlkeGvyvavtG 167
                                 +lv+tnaaG++n++f +Gdlm i+dhin+ ++ Pl Gpn++  G+rfpdms  y + l q+a   a +l+i+l++Gvyv+v G
  FitnessBrowser__DvH:207714 109 TLVITNAAGALNPQFDAGDLMCITDHINFTGRTPLAGPNHDAWGPRFPDMSAPYAPGLVQLAMREAGQLGIRLERGVYVGVHG 191
                                 *********************************************************************************** PP

                   TIGR01700 168 PsyetpaevrllkklGadavGmstvpevivarhcGlrvlglslitnkaagildaelsdheevlevakkakekleklvsalv 248
                                 P+ etpae+r++++lGadavGmstv evi+arh G++vlg+s+++nk      +e+   eev++va +a e+l++lv+a+v
  FitnessBrowser__DvH:207714 192 PQMETPAETRMFRTLGADAVGMSTVLEVIAARHLGMKVLGISCLSNKNLPDCMEEAP-LEEVIRVAGMAGERLTRLVAAIV 271
                                 ***********************************************9855545554.89******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (249 nodes)
Target sequences:                          1  (274 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: 21.59
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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