Alignments for a candidate for deoA in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Desulfitobacterium hafniense DCB-2

Align Pyrimidine-nucleoside phosphorylase; PYNP; Py-NPase; EC 2.4.2.2 (characterized)
to candidate WP_015944606.1 DHAF_RS17205 pyrimidine-nucleoside phosphorylase

Query= SwissProt::P39142
         (433 letters)



>NCBI__GCF_000021925.1:WP_015944606.1
          Length = 430

 Score =  479 bits (1233), Expect = e-140
 Identities = 248/412 (60%), Positives = 310/412 (75%)

Query: 1   MRMVDIIIKKQNGKELTTEEIQFFVNGYTDGSIPDYQASALAMAIFFQDMSDRERADLTM 60
           MR+VDII KK+ G+ LT EEI+FFV GY  G IPDYQ +AL MAI+FQ M+D E ADLTM
Sbjct: 1   MRVVDIINKKKKGEALTKEEIEFFVQGYVKGEIPDYQIAALYMAIYFQGMNDEEIADLTM 60

Query: 61  AMVNSGETIDLSAIEGIKVDKHSTGGVGDTTTLVLAPLVAALDVPVAKMSGRGLGHTGGT 120
           A VNSGETIDLS I G+KVDKHSTGGVGD  +L++ PLVA+L +PVAKMSGRGLGHTGGT
Sbjct: 61  AYVNSGETIDLSGIPGVKVDKHSTGGVGDKISLIVIPLVASLGIPVAKMSGRGLGHTGGT 120

Query: 121 IDKLEAIMGFHVELTKDEFIKLVNRDKVAVIGQSGNLTPADKKLYALRDVTGTVNSIPLI 180
           IDKLEAI GF   L+  EFI  VN   +AV+GQ+ NLTPADK  YALRDVTGTV+SIPLI
Sbjct: 121 IDKLEAIQGFRTALSTGEFIANVNNHGMAVVGQTANLTPADKLTYALRDVTGTVDSIPLI 180

Query: 181 ASSIMSKKIAAGADAIVLDVKTGAGAFMKTEEDAAELAKAMVRIGNNVGRQTMAVISDMS 240
           A SIMSKKIA+GADAIVLDVK G+GAFMK+  +A +LA+ MV+IG ++ R+T+A+I+DM+
Sbjct: 181 AGSIMSKKIASGADAIVLDVKVGSGAFMKSLPEAKKLAECMVQIGKSLKRRTIAIITDMN 240

Query: 241 QPLGFAIGNALEVKEAIDTLKGEGPEDLHELVLTLGSQMVVLAKKADTLDEARAKLEEVM 300
           QPLG  +GNA E+KE ID LKG+G ED   + LT+ S M + +          A+L++V+
Sbjct: 241 QPLGHEVGNANEIKEIIDVLKGKGAEDETRIALTIASYMAIASGNYHDFQSTYAELQQVI 300

Query: 301 KNGKALEKFKDFLKNQGGDSSIVDDPSKLPQAAYQIDVPAKEAGVVSEIVADEIGVAAML 360
            +GKA+EK K+ +  QGG+  IV +PS+LPQA + I+V A  AG +S I A++IG+ AML
Sbjct: 301 ASGKAVEKLKELISIQGGNPQIVHEPSQLPQAKHHIEVLANHAGYISSIDAEQIGLVAML 360

Query: 361 LGAGRATKEDEIDLAVGIMLRKKVGDKVEKGEPLVTLYANRENVDEVIAKVY 412
           LGAGR  K+D ID A G+ L KKVGD V+  EPL  L+ N E V+  + K Y
Sbjct: 361 LGAGRKKKDDPIDYAAGVTLLKKVGDYVDLDEPLCILHTNLEYVEADVLKAY 412


Lambda     K      H
   0.314    0.133    0.355 

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: 551
Number of extensions: 26
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: 433
Length of database: 430
Length adjustment: 32
Effective length of query: 401
Effective length of database: 398
Effective search space:   159598
Effective search space used:   159598
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_015944606.1 DHAF_RS17205 (pyrimidine-nucleoside phosphorylase)
to HMM TIGR02644 (pdp: pyrimidine-nucleoside phosphorylase (EC 2.4.2.2))

# 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/TIGR02644.hmm
# target sequence database:        /tmp/gapView.739.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02644  [M=417]
Accession:   TIGR02644
Description: Y_phosphoryl: pyrimidine-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-176  571.4   7.5   6.3e-176  571.1   7.5    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015944606.1  DHAF_RS17205 pyrimidine-nucleosi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015944606.1  DHAF_RS17205 pyrimidine-nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.1   7.5  6.3e-176  6.3e-176       2     402 ..       4     404 ..       3     414 .. 0.98

  Alignments for each domain:
  == domain 1  score: 571.1 bits;  conditional E-value: 6.3e-176
                                 TIGR02644   2 veiiekKrdgkklseeeinflingytkgeiadyQisallmaiyfkgldkeEtlalTkamvesGevldls 70 
                                               v+ii+kK++g++l++eei+f+++gy+kgei+dyQi+al maiyf+g+++eE+++lT+a+v+sGe++dls
  lcl|NCBI__GCF_000021925.1:WP_015944606.1   4 VDIINKKKKGEALTKEEIEFFVQGYVKGEIPDYQIAALYMAIYFQGMNDEEIADLTMAYVNSGETIDLS 72 
                                               89******************************************************************* PP

                                 TIGR02644  71 elkkikvDKHStGGvGDkvsLvlaPlvaalgvkvaklSGRgLghTGGTlDKLesipGfktelseeefie 139
                                                ++++kvDKHStGGvGDk+sL++ Plva+lg++vak+SGRgLghTGGT+DKLe+i+Gf+t ls+ efi+
  lcl|NCBI__GCF_000021925.1:WP_015944606.1  73 GIPGVKVDKHSTGGVGDKISLIVIPLVASLGIPVAKMSGRGLGHTGGTIDKLEAIQGFRTALSTGEFIA 141
                                               ********************************************************************* PP

                                 TIGR02644 140 ivkkvglaiigqtkdlapaDkklYalRdvtgTvdslpLiasSilsKKlaagadalvlDvkvGkGaFmkt 208
                                               +v+++g+a++gqt++l+paDk  YalRdvtgTvds+pLia Si+sKK+a+gada+vlDvkvG+GaFmk+
  lcl|NCBI__GCF_000021925.1:WP_015944606.1 142 NVNNHGMAVVGQTANLTPADKLTYALRDVTGTVDSIPLIAGSIMSKKIASGADAIVLDVKVGSGAFMKS 210
                                               ********************************************************************* PP

                                 TIGR02644 209 leeakeLakelveigkkagrkvvalltdmnepLgkaiGNalEvkeavevLkgegpadlkelvlalaaem 277
                                               l eak+La+ +v+igk+++r+++a++tdmn+pLg+ +GNa+E+ke ++vLkg+g +d + ++l++a+ m
  lcl|NCBI__GCF_000021925.1:WP_015944606.1 211 LPEAKKLAECMVQIGKSLKRRTIAIITDMNQPLGHEVGNANEIKEIIDVLKGKGAEDETRIALTIASYM 279
                                               ********************************************************************* PP

                                 TIGR02644 278 lllaklakteeeakekleevlesgkalekfkefveaqgGdlevlkeekklakakkkeevkaeksgviee 346
                                                 +++  ++ + + ++l++v++sgka+ek+ke++++qgG++++++e ++l++ak+++ev a+++g+i++
  lcl|NCBI__GCF_000021925.1:WP_015944606.1 280 AIASGNYHDFQSTYAELQQVIASGKAVEKLKELISIQGGNPQIVHEPSQLPQAKHHIEVLANHAGYISS 348
                                               ********************************************************************* PP

                                 TIGR02644 347 idaeelgliavelgaGRakkedkidleaGielekkvgdkvkkgdllltlyssdeek 402
                                               idae++gl+a+ lgaGR+kk+d+id++aG++l kkvgd+v+ +++l+ l+++ e  
  lcl|NCBI__GCF_000021925.1:WP_015944606.1 349 IDAEQIGLVAMLLGAGRKKKDDPIDYAAGVTLLKKVGDYVDLDEPLCILHTNLEYV 404
                                               ***************************************************96544 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (430 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: 00:00:00.02
# Mc/sec: 8.93
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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