Alignments for a candidate for deoA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Sinorhizobium meliloti 1021

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate SMc04122 SMc04122 thymidine phosphorylase

Query= BRENDA::P07650
         (440 letters)



>FitnessBrowser__Smeli:SMc04122
          Length = 440

 Score =  444 bits (1143), Expect = e-129
 Identities = 237/436 (54%), Positives = 297/436 (68%), Gaps = 2/436 (0%)

Query: 3   LAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMA 62
           L QEIIRKKRDG  L   EI  FI G+ D ++SEGQ AA AM ++F  M   E V+LT+A
Sbjct: 4   LPQEIIRKKRDGDRLDPAEIAGFIAGVTDGSVSEGQAAAFAMAVWFSGMNRDECVALTLA 63

Query: 63  MRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHTGG 122
           MRDSG  LDW  L    PIVDKHSTGGVGD  SLML P+VAACG  +PMISGRGLGHTGG
Sbjct: 64  MRDSGETLDWSDLAR--PIVDKHSTGGVGDNVSLMLAPIVAACGAAVPMISGRGLGHTGG 121

Query: 123 TLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPL 182
           TLDKLESIPG+DI P    FR +  +VG AIIGQT+ LAPADKR YA RD+TATVDS+PL
Sbjct: 122 TLDKLESIPGYDIQPSPELFRRVADEVGCAIIGQTADLAPADKRLYAIRDVTATVDSVPL 181

Query: 183 ITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDM 242
           ITASIL+KKLA GL +LV+DVK+G+G+FM     +E LA ++V VANGAGVRT+AL+TDM
Sbjct: 182 ITASILSKKLAAGLRSLVLDVKLGNGSFMTDPAETEVLARSLVEVANGAGVRTSALITDM 241

Query: 243 NQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKLQA 302
           N+ LA +AGNA+E+   + +L GE    RL  V MAL  EML++  +A  +AEA A  + 
Sbjct: 242 NEPLADAAGNALEIENCLAYLRGEKAGTRLDQVVMALAAEMLVAAGIAAHEAEAEAMARR 301

Query: 303 VLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALGMA 362
           VL +G+A E FG MV    GP DFV+    YL  A    AV A   G+++   TR LGMA
Sbjct: 302 VLGSGEAMERFGLMVHRLGGPADFVDRPGAYLAKAPAILAVPAGRHGYLTSCKTRELGMA 361

Query: 363 VVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAAIK 422
           V+ +GGGR +  D ID+ VG T +  LG +V+   P+A +HA D++  +  AK V     
Sbjct: 362 VIELGGGRIRPDDRIDHRVGLTGLRPLGTKVEKGEPIAFVHAADQSQAEAIAKRVVTLYA 421

Query: 423 LADKAPESTPTVYRRI 438
           +AD+ P   P +  ++
Sbjct: 422 IADEEPARRPVIVSKL 437


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: 505
Number of extensions: 22
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: 440
Length adjustment: 32
Effective length of query: 408
Effective length of database: 408
Effective search space:   166464
Effective search space used:   166464
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 SMc04122 SMc04122 (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.4067.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.1e-234  763.6   6.9   3.5e-234  763.4   6.9    1.0  1  lcl|FitnessBrowser__Smeli:SMc04122  SMc04122 thymidine phosphorylase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04122  SMc04122 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  763.4   6.9  3.5e-234  3.5e-234       1     436 [.       3     436 ..       3     437 .. 1.00

  Alignments for each domain:
  == domain 1  score: 763.4 bits;  conditional E-value: 3.5e-234
                           TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldwkdld 75 
                                         +lpqeiirkkrdg++l+++eia f++gvtd+svsegq+aa+amav+f+g+++de+valtlamrdsG++ldw+  d
  lcl|FitnessBrowser__Smeli:SMc04122   3 MLPQEIIRKKRDGDRLDPAEIAGFIAGVTDGSVSEGQAAAFAMAVWFSGMNRDECVALTLAMRDSGETLDWS--D 75 
                                         89**********************************************************************..* PP

                           TIGR02643  76 lngPvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfrkvvkdvGv 150
                                         l++P+vdkhstGGvGd+vslmlaPivaacG++vPmisGrGlGhtGGtldkle+iPGyd++P++elfr+v+++vG+
  lcl|FitnessBrowser__Smeli:SMc04122  76 LARPIVDKHSTGGVGDNVSLMLAPIVAACGAAVPMISGRGLGHTGGTLDKLESIPGYDIQPSPELFRRVADEVGC 150
                                         *************************************************************************** PP

                           TIGR02643 151 aiiGqtadlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesleeseelarslve 225
                                         aiiGqtadlaPadkrlyairdvtatv+s+plitasilskklaaGl++lvldvk+GnG+fm++ +e+e+larslve
  lcl|FitnessBrowser__Smeli:SMc04122 151 AIIGQTADLAPADKRLYAIRDVTATVDSVPLITASILSKKLAAGLRSLVLDVKLGNGSFMTDPAETEVLARSLVE 225
                                         *************************************************************************** PP

                           TIGR02643 226 vangaGvrttalitdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellvsgklaadeaeaeakle 300
                                         vangaGvrt+alitdmn++la+aaGna+e+++++++l+Gek+++rl++v++alaae+lv++++aa+eaeaea+++
  lcl|FitnessBrowser__Smeli:SMc04122 226 VANGAGVRTSALITDMNEPLADAAGNALEIENCLAYLRGEKAGTRLDQVVMALAAEMLVAAGIAAHEAEAEAMAR 300
                                         *************************************************************************** PP

                           TIGR02643 301 avlesGraaerfarmvaalgGPadfvekpekylakaaiakavkaaregylseidtrelGlavvalGGGrrkaddk 375
                                         +vl+sG+a+erf+ mv++lgGPadfv++p +ylaka++++av+a r+gyl++++trelG+av++lGGGr+++dd+
  lcl|FitnessBrowser__Smeli:SMc04122 301 RVLGSGEAMERFGLMVHRLGGPADFVDRPGAYLAKAPAILAVPAGRHGYLTSCKTRELGMAVIELGGGRIRPDDR 375
                                         *************************************************************************** PP

                           TIGR02643 376 ldlsvGltdllelGekvekeeplavvhaadeedaeeaakavkkalkiadeaPeeakvvler 436
                                         +d++vGlt l++lG+kvek+ep+a+vhaad+++ae++ak+v+++++iade+P++++v++++
  lcl|FitnessBrowser__Smeli:SMc04122 376 IDHRVGLTGLRPLGTKVEKGEPIAFVHAADQSQAEAIAKRVVTLYAIADEEPARRPVIVSK 436
                                         **********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (437 nodes)
Target sequences:                          1  (440 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: 10.01
//
[ok]

This GapMind analysis is from Sep 17 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)
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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