Alignments for a candidate for deoA in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Desulfobulbus mediterraneus DSM 13871

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate WP_028584428.1 G494_RS0109965 thymidine phosphorylase

Query= BRENDA::Q7CP66
         (440 letters)



>NCBI__GCF_000429965.1:WP_028584428.1
          Length = 444

 Score =  526 bits (1355), Expect = e-154
 Identities = 265/438 (60%), Positives = 331/438 (75%)

Query: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60
           M+L QEIIRKKRDG  LS  EI FF+ G+ D++ISEGQIAALAM I+F  M+  E + LT
Sbjct: 1   MYLPQEIIRKKRDGAPLSRAEIDFFVQGLSDDSISEGQIAALAMAIYFQGMSPDEAIDLT 60

Query: 61  MAMRDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHT 120
           MAMRDSGTVL+W    L+GP+VDKHSTGGVGD+ SL+L PM+AACGGYVPMISGRGLGHT
Sbjct: 61  MAMRDSGTVLEWADQELDGPVVDKHSTGGVGDLVSLVLAPMIAACGGYVPMISGRGLGHT 120

Query: 121 GGTLDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180
           GGTLDKL+AIPG+D  PD +RFR+++++VGVAIIGQT  LAPAD+R YA RD+TATV+SI
Sbjct: 121 GGTLDKLDAIPGYDTSPDISRFRQVVKEVGVAIIGQTGELAPADRRLYAIRDVTATVESI 180

Query: 181 PLITGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240
           PLIT SILAKKLA GLD LVMDVK G+GAFM     +  LA +IV VANGAG RT+A+LT
Sbjct: 181 PLITASILAKKLAAGLDGLVMDVKTGNGAFMANQAEAGQLARSIVSVANGAGCRTSAILT 240

Query: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKL 300
            M+QVLA+SAG  +EVREAV++L G  RN RL  V MAL  E+L+   +A D  + R KL
Sbjct: 241 RMDQVLAASAGTGLEVREAVRYLRGADRNSRLHQVNMALATELLVLAGIAVDAGKGREKL 300

Query: 301 QAVLDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALG 360
           +AVLD+G+AAE+F +MVAA  GPSDF+E  + YL    + + VY+   G + AMDTRALG
Sbjct: 301 EAVLDSGRAAELFAQMVAALGGPSDFIERIESYLEPTEIIRPVYSPMAGVVQAMDTRALG 360

Query: 361 MAVVSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAA 420
           M VV+MGGGR  AS  +DY VG ++M  LG+  D  RPLA++HA+ E  + EA +A++ A
Sbjct: 361 MVVVAMGGGRCSASAALDYGVGLSEMISLGEQADAHRPLALVHARSEQQFLEAEQAIRRA 420

Query: 421 IILDDKAPASTPSVYRRI 438
           +++   AP   P +  RI
Sbjct: 421 MVIGSAAPLQQPQLVERI 438


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: 577
Number of extensions: 19
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: 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_028584428.1 G494_RS0109965 (thymidine phosphorylase)
to HMM TIGR02643 (deoA: thymidine phosphorylase (EC 2.4.2.4))

# 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/TIGR02643.hmm
# target sequence database:        /tmp/gapView.29762.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02643  [M=437]
Accession:   TIGR02643
Description: T_phosphoryl: thymidine 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-210  685.2  10.4   2.3e-210  684.9  10.4    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028584428.1  G494_RS0109965 thymidine phospho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028584428.1  G494_RS0109965 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.9  10.4  2.3e-210  2.3e-210       2     437 .]       3     438 ..       2     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 684.9 bits;  conditional E-value: 2.3e-210
                                 TIGR02643   2 lpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvld 70 
                                               lpqeiirkkrdg+ ls +ei  fv+g++dds+segqiaalama+yf+g++ de++ lt+amrdsG+vl+
  lcl|NCBI__GCF_000429965.1:WP_028584428.1   3 LPQEIIRKKRDGAPLSRAEIDFFVQGLSDDSISEGQIAALAMAIYFQGMSPDEAIDLTMAMRDSGTVLE 71 
                                               9******************************************************************** PP

                                 TIGR02643  71 wkdldlngPvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdee 139
                                               w d++l+gPvvdkhstGGvGd+vsl+laP++aacGgyvPmisGrGlGhtGGtldkl+aiPGyd+ Pd +
  lcl|NCBI__GCF_000429965.1:WP_028584428.1  72 WADQELDGPVVDKHSTGGVGDLVSLVLAPMIAACGGYVPMISGRGLGHTGGTLDKLDAIPGYDTSPDIS 140
                                               ********************************************************************* PP

                                 TIGR02643 140 lfrkvvkdvGvaiiGqtadlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGa 208
                                               +fr+vvk+vGvaiiGqt++laPad+rlyairdvtatvesiplitasil+kklaaGld+lv+dvk GnGa
  lcl|NCBI__GCF_000429965.1:WP_028584428.1 141 RFRQVVKEVGVAIIGQTGELAPADRRLYAIRDVTATVESIPLITASILAKKLAAGLDGLVMDVKTGNGA 209
                                               ********************************************************************* PP

                                 TIGR02643 209 fmesleeseelarslvevangaGvrttalitdmnqalasaaGnavevreavdfltGekrdkrleevtla 277
                                               fm +++e+ +lars+v+vangaG rt+a++t m+q+la +aG  +evreav++l+G+ r++rl++v +a
  lcl|NCBI__GCF_000429965.1:WP_028584428.1 210 FMANQAEAGQLARSIVSVANGAGCRTSAILTRMDQVLAASAGTGLEVREAVRYLRGADRNSRLHQVNMA 278
                                               ********************************************************************* PP

                                 TIGR02643 278 laaellvsgklaadeaeaeakleavlesGraaerfarmvaalgGPadfvekpekylakaaiakavkaar 346
                                               la+ellv +++a d+ +++ kleavl+sGraae fa+mvaalgGP+df+e+ e yl  ++i+++v+   
  lcl|NCBI__GCF_000429965.1:WP_028584428.1 279 LATELLVLAGIAVDAGKGREKLEAVLDSGRAAELFAQMVAALGGPSDFIERIESYLEPTEIIRPVYSPM 347
                                               ********************************************************************* PP

                                 TIGR02643 347 egylseidtrelGlavvalGGGrrkaddkldlsvGltdllelGekvekeeplavvhaadeedaeeaaka 415
                                               +g ++++dtr+lG++vva+GGGr  a+  ld+ vGl+++++lGe+ ++++pla+vha++e+++ ea +a
  lcl|NCBI__GCF_000429965.1:WP_028584428.1 348 AGVVQAMDTRALGMVVVAMGGGRCSASAALDYGVGLSEMISLGEQADAHRPLALVHARSEQQFLEAEQA 416
                                               ********************************************************************* PP

                                 TIGR02643 416 vkkalkiadeaPeeakvvleri 437
                                               +++a+ i+++aP +++ ++eri
  lcl|NCBI__GCF_000429965.1:WP_028584428.1 417 IRRAMVIGSAAPLQQPQLVERI 438
                                               ***************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (437 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.39
//
[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