GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoA in Rhodococcus qingshengii djl-6-2

Align Pyrimidine-nucleoside phosphorylase; PYNP; Py-NPase; EC 2.4.2.2 (characterized)
to candidate WP_050654871.1 C1M55_RS10330 thymidine phosphorylase

Query= SwissProt::P77836
         (433 letters)



>NCBI__GCF_002893965.1:WP_050654871.1
          Length = 431

 Score =  358 bits (918), Expect = e-103
 Identities = 199/411 (48%), Positives = 267/411 (64%), Gaps = 14/411 (3%)

Query: 4   VDLIEKKRDGHALTKEEIQFIIEGYTKGDIPDYQMSALAMAIFFRGMNEEETAELTMAMV 63
           V +I  KRDG  L+  EI +I++ +T+G + D QMSALAMAI+FRGM+  ET   T AM+
Sbjct: 5   VSIIGAKRDGRELSGTEIDWIVQAFTEGVVGDEQMSALAMAIYFRGMSRAETGRWTEAMI 64

Query: 64  HSGDTIDLSRIEGIKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDK 123
            SG  +D S +    VDKHSTGGVGD  TL L PLVA+ G+ V ++SGRGLGHTGGT+DK
Sbjct: 65  ESGGRMDFSDLPLPTVDKHSTGGVGDKITLPLAPLVAACGLAVPQLSGRGLGHTGGTLDK 124

Query: 124 LESVPGFHVEITNDEFIDLVNKNKIAVV--GQSGNLTPADKKLYALRDVTATVNSIPLIA 181
           LE++PG+  E+T  E +D+++  KI  V      NL PADKKLYALRDVT TV SIPLIA
Sbjct: 125 LEAIPGWRAELTATEMVDILSDPKIGAVICAAGANLAPADKKLYALRDVTGTVESIPLIA 184

Query: 182 SSIMSKKIAAGADAIVLDVKTGVGAFMKDLNDAKALAKAMVDIGNRVGRKTMAIISDMSQ 241
           SSIMSKKIA G  A+VLDVK G GAFMKDL DA+ LA+ MV++GN  G +T A+I+ M  
Sbjct: 185 SSIMSKKIAEGTGALVLDVKVGSGAFMKDLGDARELARTMVELGNDAGVRTSALITGMDT 244

Query: 242 PLGYAIGNALEVKEAIDTLKGEGPEDFQELCLVLGSHMVYLAEKASSLEEARHMLEKAMK 301
           PLG   GNALEV+E+++ L G GP D  EL LVL   M+  A     ++ A       + 
Sbjct: 245 PLGLTAGNALEVRESVEVLAGGGPSDVVELTLVLAREML-SAAGIDGIDPA-----DKLS 298

Query: 302 DGSALQTFKTFLAAQGGDASVVDDPSKLPQAKYIIELEAKEDGYVSEIVADAVGTAAMWL 361
           DG+A+  ++  +AAQGGD       + LP A++   + A  DG ++ + A AVG AA  L
Sbjct: 299 DGTAMDRWRAMIAAQGGDPH-----ATLPTARHSDVVTADRDGVLTRLDAMAVGIAAWKL 353

Query: 362 GAGRATKESTIDLAVGLVLRKKVGDAVKKGESLVTIYSNR-EQVDDVKQKL 411
           GAGR  +   +    G+ +  K GD V+ G+ L+T++++  E+ D  ++ L
Sbjct: 354 GAGRERQGEAVQAGAGIEMHAKPGDVVRAGQKLMTLHTDTPERFDAARRSL 404


Lambda     K      H
   0.315    0.133    0.361 

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: 494
Number of extensions: 29
Number of successful extensions: 4
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: 431
Length adjustment: 32
Effective length of query: 401
Effective length of database: 399
Effective search space:   159999
Effective search space used:   159999
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_050654871.1 C1M55_RS10330 (thymidine 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.1968806.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-168  546.5   0.2   2.2e-168  546.3   0.2    1.0  1  NCBI__GCF_002893965.1:WP_050654871.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050654871.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.3   0.2  2.2e-168  2.2e-168       2     410 ..       5     404 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 546.3 bits;  conditional E-value: 2.2e-168
                             TIGR02644   2 veiiekKrdgkklseeeinflingytkgeiadyQisallmaiyfkgldkeEtlalTkamvesGevldlselkk 74 
                                           v+ii  Krdg++ls +ei+++++++t+g + d+Q+sal+maiyf+g++++Et ++T+am+esG ++d+s+l+ 
  NCBI__GCF_002893965.1:WP_050654871.1   5 VSIIGAKRDGRELSGTEIDWIVQAFTEGVVGDEQMSALAMAIYFRGMSRAETGRWTEAMIESGGRMDFSDLPL 77 
                                           789********************************************************************** PP

                             TIGR02644  75 ikvDKHStGGvGDkvsLvlaPlvaalgvkvaklSGRgLghTGGTlDKLesipGfktelseeefieivkk..vg 145
                                           ++vDKHStGGvGDk++L+laPlvaa+g++v++lSGRgLghTGGTlDKLe+ipG+++el+  e+++i+++  +g
  NCBI__GCF_002893965.1:WP_050654871.1  78 PTVDKHSTGGVGDKITLPLAPLVAACGLAVPQLSGRGLGHTGGTLDKLEAIPGWRAELTATEMVDILSDpkIG 150
                                           *******************************************************************965599 PP

                             TIGR02644 146 laiigqtkdlapaDkklYalRdvtgTvdslpLiasSilsKKlaagadalvlDvkvGkGaFmktleeakeLake 218
                                           ++i++++++lapaDkklYalRdvtgTv+s+pLiasSi+sKK+a+g+ alvlDvkvG+GaFmk+l +a+eLa++
  NCBI__GCF_002893965.1:WP_050654871.1 151 AVICAAGANLAPADKKLYALRDVTGTVESIPLIASSIMSKKIAEGTGALVLDVKVGSGAFMKDLGDARELART 223
                                           9************************************************************************ PP

                             TIGR02644 219 lveigkkagrkvvalltdmnepLgkaiGNalEvkeavevLkgegpadlkelvlalaaemlllaklakteeeak 291
                                           +ve+g++ag++++al+t m++pLg ++GNalEv+e+vevL+g gp+d++el+l la+eml +a+++       
  NCBI__GCF_002893965.1:WP_050654871.1 224 MVELGNDAGVRTSALITGMDTPLGLTAGNALEVRESVEVLAGGGPSDVVELTLVLAREMLSAAGIDG------ 290
                                           ******************************************************************8...... PP

                             TIGR02644 292 ekleevlesgkalekfkefveaqgGdlevlkeekklakakkkeevkaeksgvieeidaeelgliavelgaGRa 364
                                            + +++l++g+a+++++++++aqgGd+     +++l++a+++  v+a+++gv++++da+++g++a++lgaGR+
  NCBI__GCF_002893965.1:WP_050654871.1 291 IDPADKLSDGTAMDRWRAMIAAQGGDP-----HATLPTARHSDVVTADRDGVLTRLDAMAVGIAAWKLGAGRE 358
                                           788999********************8.....6789************************************* PP

                             TIGR02644 365 kkedkidleaGielekkvgdkvkkgdllltlyssdeekaeeaakal 410
                                           ++ + ++  aGie+++k gd v++g++l+tl+++++e++++a++ l
  NCBI__GCF_002893965.1:WP_050654871.1 359 RQGEAVQAGAGIEMHAKPGDVVRAGQKLMTLHTDTPERFDAARRSL 404
                                           **************************************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (431 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: 00:00:00.01
# Mc/sec: 17.34
//
[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:

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:

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:

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:

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