Alignments for a candidate for deoA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Dinoroseobacter shibae DFL-12

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate 3607414 Dshi_0828 pyrimidine-nucleoside phosphorylase (RefSeq)

Query= BRENDA::Q7CP66
         (440 letters)



>FitnessBrowser__Dino:3607414
          Length = 435

 Score =  383 bits (983), Expect = e-111
 Identities = 209/420 (49%), Positives = 276/420 (65%), Gaps = 3/420 (0%)

Query: 4   AQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAM 63
           A+ +I   RDG  +  E++R F  G+   T+S+ Q  A AM +    +    RV+LT AM
Sbjct: 3   ARTVIAAVRDGAPVVAEDLRAFARGLASGTVSDAQAGAFAMAVLLRGLGDAGRVALTQAM 62

Query: 64  RDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHTGGT 123
           RDSG VL W   +L GP++DKHSTGG+GD  SL+L P +AACG YVPMISGRGLGHTGGT
Sbjct: 63  RDSGDVLAW---DLPGPVLDKHSTGGIGDTVSLLLAPALAACGAYVPMISGRGLGHTGGT 119

Query: 124 LDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLI 183
           LDKLEA+ G+     ++  R ++ + G AI+G T  +APAD+R YA RD+TATV+SI LI
Sbjct: 120 LDKLEALEGYRTDISEDALRAVVAETGCAIVGATGQIAPADRRLYAIRDVTATVESIDLI 179

Query: 184 TGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDMN 243
           T SIL+KKLA GL  LV+DVK GSGAF+     +  LA+A+V  ANGAG  T ALLTDM+
Sbjct: 180 TASILSKKLAAGLGGLVLDVKCGSGAFLTDPAAARDLAQALVRTANGAGCPTWALLTDMD 239

Query: 244 QVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKLQAV 303
           + LAS+AGNA+EV E ++ L G+  +PRL   T+AL   +L  G LA D A+  A++ A 
Sbjct: 240 ESLASAAGNALEVAEVLRILRGDATSPRLRAATVALGGALLALGGLADDPADGAARIDAT 299

Query: 304 LDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALGMAV 363
           L +G+AAEVF RMVAA  GP D V      LP A + + V A   G ++A D +ALG AV
Sbjct: 300 LRDGRAAEVFARMVAALGGPRDVVATGLAGLPEAPVVREVPAPAAGVLTACDAKALGWAV 359

Query: 364 VSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAAIIL 423
           VS+GGGR+  +D +D +VG +D+A LG  +    P+A +HA  E +   A   V+AA  L
Sbjct: 360 VSLGGGRQVETDPVDPAVGLSDIAPLGTRVVRGEPIARVHAAREEAADRAVAEVQAAFTL 419


Lambda     K      H
   0.319    0.134    0.377 

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: 525
Number of extensions: 26
Number of successful extensions: 3
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: 440
Length of database: 435
Length adjustment: 32
Effective length of query: 408
Effective length of database: 403
Effective search space:   164424
Effective search space used:   164424
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: 51 (24.3 bits)

Align candidate 3607414 Dshi_0828 (pyrimidine-nucleoside phosphorylase (RefSeq))
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.27164.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-140  454.8   0.0   1.5e-140  454.6   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607414  Dshi_0828 pyrimidine-nucleoside 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607414  Dshi_0828 pyrimidine-nucleoside phosphorylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.6   0.0  1.5e-140  1.5e-140       3     416 ..       5     419 ..       3     420 .. 0.98

  Alignments for each domain:
  == domain 1  score: 454.6 bits;  conditional E-value: 1.5e-140
                         TIGR02644   3 eiiekKrdgkklseeeinflingytkgeiadyQisallmaiyfkgldkeEtlalTkamvesGevldlselkkikvDK 79 
                                       ++i   rdg  + +e+++++ +g+++g+++d Q+ a++ma++++gl ++  +alT+am++sG+vl + +l++++ DK
  lcl|FitnessBrowser__Dino:3607414   5 TVIAAVRDGAPVVAEDLRAFARGLASGTVSDAQAGAFAMAVLLRGLGDAGRVALTQAMRDSGDVLAW-DLPGPVLDK 80 
                                       5899999***********************************************************9.69******* PP

                         TIGR02644  80 HStGGvGDkvsLvlaPlvaalgvkvaklSGRgLghTGGTlDKLesipGfktelseeefieivkkvglaiigqtkdla 156
                                       HStGG+GD+vsL+laP +aa+g++v+++SGRgLghTGGTlDKLe+++G++t++se+ ++++v ++g+ai+g+t ++a
  lcl|FitnessBrowser__Dino:3607414  81 HSTGGIGDTVSLLLAPALAACGAYVPMISGRGLGHTGGTLDKLEALEGYRTDISEDALRAVVAETGCAIVGATGQIA 157
                                       ***************************************************************************** PP

                         TIGR02644 157 paDkklYalRdvtgTvdslpLiasSilsKKlaagadalvlDvkvGkGaFmktleeakeLakelveigkkagrkvval 233
                                       paD++lYa+Rdvt+Tv+s+ Li++SilsKKlaag   lvlDvk+G+GaF+++++ a++La++lv+ +++ag  + al
  lcl|FitnessBrowser__Dino:3607414 158 PADRRLYAIRDVTATVESIDLITASILSKKLAAGLGGLVLDVKCGSGAFLTDPAAARDLAQALVRTANGAGCPTWAL 234
                                       ***************************************************************************** PP

                         TIGR02644 234 ltdmnepLgkaiGNalEvkeavevLkge.gpadlkelvlalaaemlllaklakteeeakekleevlesgkalekfke 309
                                       ltdm+e L++a+GNalEv+e++ +L+g+  + +l+  ++al+  +l+l +la++ +++ +++  +l++g+a+e f++
  lcl|FitnessBrowser__Dino:3607414 235 LTDMDESLASAAGNALEVAEVLRILRGDaTSPRLRAATVALGGALLALGGLADDPADGAARIDATLRDGRAAEVFAR 311
                                       ****************************6666********************************************* PP

                         TIGR02644 310 fveaqgGdle.vlkeekklakakkkeevkaeksgvieeidaeelgliavelgaGRakkedkidleaGielekkvgdk 385
                                       +v+a gG+ + v +  + l++a  ++ev a  +gv++ +da++lg ++v+lg+GR+ ++d++d+++G++  +  g +
  lcl|FitnessBrowser__Dino:3607414 312 MVAALGGPRDvVATGLAGLPEAPVVREVPAPAAGVLTACDAKALGWAVVSLGGGRQVETDPVDPAVGLSDIAPLGTR 388
                                       **********66677899*********************************************************** PP

                         TIGR02644 386 vkkgdllltlyssdeekaeeaakalkkaiki 416
                                       v +g++++++++ +ee a++a +++++a+++
  lcl|FitnessBrowser__Dino:3607414 389 VVRGEPIARVHAAREEAADRAVAEVQAAFTL 419
                                       **********************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (435 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: 00:00:00.01
# Mc/sec: 12.21
//
[ok]

This GapMind analysis is from Sep 17 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