Alignments for a candidate for deoD in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Oceanisphaera arctica V1-41

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate WP_104486399.1 UN63_RS08780 purine-nucleoside phosphorylase

Query= BRENDA::P0ABP8
         (239 letters)



>NCBI__GCF_002936955.1:WP_104486399.1
          Length = 238

 Score =  360 bits (925), Expect = e-104
 Identities = 177/236 (75%), Positives = 203/236 (86%)

Query: 1   MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60
           MATPHI AE GDFAD VLMPGDPLRAKYIA+TFL D R+VN VR MLGFTGTYKGR ISV
Sbjct: 1   MATPHIKAERGDFADTVLMPGDPLRAKYIADTFLSDVRQVNQVRNMLGFTGTYKGRAISV 60

Query: 61  MGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIR 120
           MGHGMGIPS SIY KELIT+FGV  +IRVGSCGAV   V LRDVVIG+GA TDS+VNRIR
Sbjct: 61  MGHGMGIPSVSIYAKELITEFGVNTLIRVGSCGAVRDDVALRDVVIGLGASTDSRVNRIR 120

Query: 121 FKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVE 180
           F +HDFAA+ADF++V  AV  AKA  +  +VGN+FSADLFYSP  E+F++M++YGILGVE
Sbjct: 121 FMEHDFAALADFELVSQAVATAKACKVPVKVGNIFSADLFYSPQPELFELMKRYGILGVE 180

Query: 181 MEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLG 236
           MEAAG+YGVAAE+GA+ALTICTVSDHI  HE  +A ERQT+FNDM+++ALESVLLG
Sbjct: 181 MEAAGLYGVAAEYGARALTICTVSDHILRHEALSADERQTSFNDMMEVALESVLLG 236


Lambda     K      H
   0.322    0.138    0.401 

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: 265
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: 239
Length of database: 238
Length adjustment: 23
Effective length of query: 216
Effective length of database: 215
Effective search space:    46440
Effective search space used:    46440
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 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate WP_104486399.1 UN63_RS08780 (purine-nucleoside phosphorylase)
to HMM TIGR00107 (deoD: purine nucleoside 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/TIGR00107.hmm
# target sequence database:        /tmp/gapView.2721405.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00107  [M=232]
Accession:   TIGR00107
Description: deoD: purine nucleoside 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-120  385.7   0.1     4e-120  385.5   0.1    1.0  1  NCBI__GCF_002936955.1:WP_104486399.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002936955.1:WP_104486399.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.5   0.1    4e-120    4e-120       1     230 [.       5     234 ..       5     236 .. 0.99

  Alignments for each domain:
  == domain 1  score: 385.5 bits;  conditional E-value: 4e-120
                             TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskel 73 
                                           hi+a++gd+ad+vl+pGdPlrakyia++fl d+++vn+vr+mlgftG+ykg+ isvmGhGmGips+siy+kel
  NCBI__GCF_002936955.1:WP_104486399.1   5 HIKAERGDFADTVLMPGDPLRAKYIADTFLSDVRQVNQVRNMLGFTGTYKGRAISVMGHGMGIPSVSIYAKEL 77 
                                           9************************************************************************ PP

                             TIGR00107  74 ikeyevkkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvk 146
                                           i+e++v+++irvGsCGa+r +v l+dv+i+l+astds+vnr+rf+e+d+aa+adfelv +a+ +ak+ +++vk
  NCBI__GCF_002936955.1:WP_104486399.1  78 ITEFGVNTLIRVGSCGAVRDDVALRDVVIGLGASTDSRVNRIRFMEHDFAALADFELVSQAVATAKACKVPVK 150
                                           ************************************************************************* PP

                             TIGR00107 147 vGnvfsadlfystdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfk 219
                                           vGn+fsadlfys++ e ++l+++yg+l+vemeaa+ly+vaae+g++alt++tvsdh++ heal+a+erq++f+
  NCBI__GCF_002936955.1:WP_104486399.1 151 VGNIFSADLFYSPQPELFELMKRYGILGVEMEAAGLYGVAAEYGARALTICTVSDHILRHEALSADERQTSFN 223
                                           ************************************************************************* PP

                             TIGR00107 220 dmielalesvs 230
                                           dm+e+alesv+
  NCBI__GCF_002936955.1:WP_104486399.1 224 DMMEVALESVL 234
                                           *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (232 nodes)
Target sequences:                          1  (238 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: 20.78
//
[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:

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