Alignments for a candidate for deoA in Rhodanobacter denitrificans 2APBS1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Rhodanobacter denitrificans 2APBS1

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate WP_015448446.1 R2APBS1_RS14135 thymidine phosphorylase

Query= BRENDA::P07650
         (440 letters)



>NCBI__GCF_000230695.2:WP_015448446.1
          Length = 444

 Score =  379 bits (972), Expect = e-109
 Identities = 196/429 (45%), Positives = 272/429 (63%), Gaps = 2/429 (0%)

Query: 4   AQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAM 63
           A  +IR KRDG  L   ++R    GI     SEGQIAA AM + +  M+ PE    T+A+
Sbjct: 6   ATGLIRCKRDGGQLDASQLRAVAQGIGSGAWSEGQIAAFAMAVAWRGMSTPECRQFTLAL 65

Query: 64  RDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHTGGT 123
           RDSG  L W   HL GP +DKHSTGGVGD  SL+L P++AACGGY+PMISGRGLGHTGGT
Sbjct: 66  RDSGQCLRWD--HLPGPTLDKHSTGGVGDGVSLLLAPLLAACGGYVPMISGRGLGHTGGT 123

Query: 124 LDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLI 183
           LDKLES+ G+D+ P   R R+++++VG AI+GQ   L PAD+R YA RD+TATVD   L+
Sbjct: 124 LDKLESLAGYDVHPSTARLRQVVEEVGCAIVGQGDELVPADRRLYAVRDVTATVDVADLM 183

Query: 184 TASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDMN 243
            ASIL+KKLA G   LV+D+K G+GA +P    + ALA  ++ VA G+G+    + +DM+
Sbjct: 184 VASILSKKLAGGARVLVLDIKTGNGAQLPGMAAARALAGRMLAVAEGSGLDLRVVYSDMD 243

Query: 244 QVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKLQAV 303
           Q+L   AGNA+E+R  +  L     NPRL  +T+ L   +L +G LA D  +A  +L+  
Sbjct: 244 QLLGREAGNALELRAVLDLLCSRGDNPRLLSLTLELAAALLCTGGLADDRNDAERRLRRA 303

Query: 304 LDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALGMAV 363
           LD G+AAE F RMV A  GP D ++    +L  A + + V +   G+V  +D RALG AV
Sbjct: 304 LDTGEAAERFARMVVALGGPADLLQRADVHLARAPIQREVRSPGSGYVVAVDVRALGQAV 363

Query: 364 VAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAAIKL 423
           V +GGGR +    +D++VG  ++   G  V+  +PLA+IHA+  ++ +   + V  A ++
Sbjct: 364 VELGGGRSRPGQALDHAVGLAEVLGCGSAVEAGQPLAIIHARRADDAEAVQRRVACAFRI 423

Query: 424 ADKAPESTP 432
             + P S P
Sbjct: 424 TSEMPPSRP 432


Lambda     K      H
   0.318    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: 466
Number of extensions: 16
Number of successful extensions: 2
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: 444
Length adjustment: 32
Effective length of query: 408
Effective length of database: 412
Effective search space:   168096
Effective search space used:   168096
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 WP_015448446.1 R2APBS1_RS14135 (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.2695496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-135  437.8   0.0   2.2e-135  437.6   0.0    1.0  1  NCBI__GCF_000230695.2:WP_015448446.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015448446.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.6   0.0  2.2e-135  2.2e-135       3     416 ..       8     423 ..       6     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 437.6 bits;  conditional E-value: 2.2e-135
                             TIGR02644   3 eiiekKrdgkklseeeinflingytkgeiadyQisallmaiyfkgldkeEtlalTkamvesGevldlselkki 75 
                                            +i+ Krdg +l++ +++++ +g+ +g+ ++ Qi+a++ma+ ++g+++ E+ ++T a+++sG+ l + +l+++
  NCBI__GCF_000230695.2:WP_015448446.1   8 GLIRCKRDGGQLDASQLRAVAQGIGSGAWSEGQIAAFAMAVAWRGMSTPECRQFTLALRDSGQCLRWDHLPGP 80 
                                           69*********************************************************************** PP

                             TIGR02644  76 kvDKHStGGvGDkvsLvlaPlvaalgvkvaklSGRgLghTGGTlDKLesipGfktelseeefieivkkvglai 148
                                           + DKHStGGvGD vsL+laPl+aa+g +v+++SGRgLghTGGTlDKLes+ G++++ s+++++++v++vg+ai
  NCBI__GCF_000230695.2:WP_015448446.1  81 TLDKHSTGGVGDGVSLLLAPLLAACGGYVPMISGRGLGHTGGTLDKLESLAGYDVHPSTARLRQVVEEVGCAI 153
                                           ************************************************************************* PP

                             TIGR02644 149 igqtkdlapaDkklYalRdvtgTvdslpLiasSilsKKlaagadalvlDvkvGkGaFmktleeakeLakelve 221
                                           +gq+++l+paD++lYa+Rdvt+Tvd   L+++SilsKKla ga+ lvlD+k+G+Ga +  ++ a++La ++ +
  NCBI__GCF_000230695.2:WP_015448446.1 154 VGQGDELVPADRRLYAVRDVTATVDVADLMVASILSKKLAGGARVLVLDIKTGNGAQLPGMAAARALAGRMLA 226
                                           ************************************************************************* PP

                             TIGR02644 222 igkkagrkvvalltdmnepLgkaiGNalEvkeavevLkge.gpadlkelvlalaaemlllaklakteeeakek 293
                                           ++++ g  ++++++dm++ Lg+ +GNalE++ ++++L  + ++ +l  l+l+laa +l + +la+++++a+++
  NCBI__GCF_000230695.2:WP_015448446.1 227 VAEGSGLDLRVVYSDMDQLLGREAGNALELRAVLDLLCSRgDNPRLLSLTLELAAALLCTGGLADDRNDAERR 299
                                           **************************************995555***************************** PP

                             TIGR02644 294 leevlesgkalekfkefveaqgGdle.vlkeekklakakkkeevkaeksgvieeidaeelgliavelgaGRak 365
                                           l+++l++g+a+e+f+++v a gG+++ + +++ +la+a  ++ev++  sg++  +d ++lg ++velg+GR++
  NCBI__GCF_000230695.2:WP_015448446.1 300 LRRALDTGEAAERFARMVVALGGPADlLQRADVHLARAPIQREVRSPGSGYVVAVDVRALGQAVVELGGGRSR 372
                                           **************************44556678999************************************ PP

                             TIGR02644 366 kedkidleaGielekkvgdkvkkgdllltlyssdeekaeeaakalkkaiki 416
                                             + +d+++G++     g  v++g++l+ +++++ ++ae+++++++ a++i
  NCBI__GCF_000230695.2:WP_015448446.1 373 PGQALDHAVGLAEVLGCGSAVEAGQPLAIIHARRADDAEAVQRRVACAFRI 423
                                           ******************************************999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (444 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: 32.49
//
[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