Alignments for a candidate for deoD in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Halomonas desiderata SP1

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate WP_086510571.1 BZY95_RS14220 purine-nucleoside phosphorylase

Query= BRENDA::P0ABP8
         (239 letters)



>NCBI__GCF_002151265.1:WP_086510571.1
          Length = 242

 Score =  336 bits (862), Expect = 2e-97
 Identities = 164/237 (69%), Positives = 196/237 (82%)

Query: 1   MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60
           MATPHI  E G FAD VLMPGDPLRAK+IAETFLEDAREV +VR MLGFTG Y+GR ISV
Sbjct: 1   MATPHIQGERGIFADTVLMPGDPLRAKHIAETFLEDAREVTSVRNMLGFTGRYRGRDISV 60

Query: 61  MGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIR 120
           MGHGMGIPS SIY KELITD+GV+++IRVGSCGAV   V +RDVVIG+GA TDS VNR R
Sbjct: 61  MGHGMGIPSVSIYAKELITDYGVQRLIRVGSCGAVRDDVAVRDVVIGLGASTDSAVNRTR 120

Query: 121 FKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVE 180
           F  HDFAAIADF++ R+AVDAA A G+  +VGNLFS DLFY+P  E+F +M++YGI+GVE
Sbjct: 121 FMGHDFAAIADFELTRHAVDAAAAQGVPVKVGNLFSTDLFYNPQAELFTLMKRYGIVGVE 180

Query: 181 MEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGD 237
           MEAAG+YGVAAEFG +A+TICTVSDHI   E   +  R+ +FN+M+++AL++VL  D
Sbjct: 181 MEAAGLYGVAAEFGGRAMTICTVSDHILKGESLPSEARERSFNEMVEVALDAVLRDD 237


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: 233
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: 242
Length adjustment: 23
Effective length of query: 216
Effective length of database: 219
Effective search space:    47304
Effective search space used:    47304
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_086510571.1 BZY95_RS14220 (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.12765.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-110  354.8   0.0   1.1e-110  354.6   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510571.1  BZY95_RS14220 purine-nucleoside 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510571.1  BZY95_RS14220 purine-nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.6   0.0  1.1e-110  1.1e-110       1     230 [.       5     234 ..       5     236 .. 0.99

  Alignments for each domain:
  == domain 1  score: 354.6 bits;  conditional E-value: 1.1e-110
                                 TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiy 69 
                                               hi+ ++g +ad+vl+pGdPlrak+iae+fleda+ev+ vr+mlgftG+y+g+ isvmGhGmGips+siy
  lcl|NCBI__GCF_002151265.1:WP_086510571.1   5 HIQGERGIFADTVLMPGDPLRAKHIAETFLEDAREVTSVRNMLGFTGRYRGRDISVMGHGMGIPSVSIY 73 
                                               9******************************************************************** PP

                                 TIGR00107  70 skelikeyevkkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaa 138
                                               +keli++y+v+++irvGsCGa+r +v ++dv+i+l+astds vnr rf+ +d+aaiadfel+++a++aa
  lcl|NCBI__GCF_002151265.1:WP_086510571.1  74 AKELITDYGVQRLIRVGSCGAVRDDVAVRDVVIGLGASTDSAVNRTRFMGHDFAAIADFELTRHAVDAA 142
                                               ********************************************************************* PP

                                 TIGR00107 139 kkkgldvkvGnvfsadlfystdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthe 207
                                                ++g++vkvGn+fs+dlfy+++ e + l+++yg+++vemeaa+ly+vaae+g +a+t++tvsdh++  e
  lcl|NCBI__GCF_002151265.1:WP_086510571.1 143 AAQGVPVKVGNLFSTDLFYNPQAELFTLMKRYGIVGVEMEAAGLYGVAAEFGGRAMTICTVSDHILKGE 211
                                               ********************************************************************* PP

                                 TIGR00107 208 altaeerqktfkdmielalesvs 230
                                                l++e r ++f++m+e+al++v+
  lcl|NCBI__GCF_002151265.1:WP_086510571.1 212 SLPSEARERSFNEMVEVALDAVL 234
                                               ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (232 nodes)
Target sequences:                          1  (242 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 7.82
//
[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 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