GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Sinorhizobium meliloti 1021

Align Deoxyribose-phosphate aldolase; DERA; EC 4.1.2.4; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase (uncharacterized)
to candidate SMc02333 SMc02333 hypothetical protein

Query= curated2:Q92MQ3
         (248 letters)



>FitnessBrowser__Smeli:SMc02333
          Length = 248

 Score =  475 bits (1222), Expect = e-139
 Identities = 248/248 (100%), Positives = 248/248 (100%)

Query: 1   MNNISNRRQPPASLAPRDLAALIDISAVQAFHTEADVRELAGIAVAEGFIAAHALPNFVP 60
           MNNISNRRQPPASLAPRDLAALIDISAVQAFHTEADVRELAGIAVAEGFIAAHALPNFVP
Sbjct: 1   MNNISNRRQPPASLAPRDLAALIDISAVQAFHTEADVRELAGIAVAEGFIAAHALPNFVP 60

Query: 61  LLRSLVPSGGLTLVGGPVGFPSGGHSTRTKTAEAVELAENGAQELDMMINVGRIKSGDFG 120
           LLRSLVPSGGLTLVGGPVGFPSGGHSTRTKTAEAVELAENGAQELDMMINVGRIKSGDFG
Sbjct: 61  LLRSLVPSGGLTLVGGPVGFPSGGHSTRTKTAEAVELAENGAQELDMMINVGRIKSGDFG 120

Query: 121 YVRSEIRAIVEAIAPVPLKVILELAHLTDEEIRAASAIVAESGAAFVKTGTGWTPSATTL 180
           YVRSEIRAIVEAIAPVPLKVILELAHLTDEEIRAASAIVAESGAAFVKTGTGWTPSATTL
Sbjct: 121 YVRSEIRAIVEAIAPVPLKVILELAHLTDEEIRAASAIVAESGAAFVKTGTGWTPSATTL 180

Query: 181 EKLKLIVETVGGAVEIKASGGIRSLDAIAGMMRLGVTRFGINTQVAVDLVRQCAALPGGR 240
           EKLKLIVETVGGAVEIKASGGIRSLDAIAGMMRLGVTRFGINTQVAVDLVRQCAALPGGR
Sbjct: 181 EKLKLIVETVGGAVEIKASGGIRSLDAIAGMMRLGVTRFGINTQVAVDLVRQCAALPGGR 240

Query: 241 LDIAGKAG 248
           LDIAGKAG
Sbjct: 241 LDIAGKAG 248


Lambda     K      H
   0.318    0.135    0.376 

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: 377
Number of extensions: 1
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: 248
Length of database: 248
Length adjustment: 24
Effective length of query: 224
Effective length of database: 224
Effective search space:    50176
Effective search space used:    50176
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: 41 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate SMc02333 SMc02333 (hypothetical protein)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

# 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/TIGR00126.hmm
# target sequence database:        /tmp/gapView.23620.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00126  [M=211]
Accession:   TIGR00126
Description: deoC: deoxyribose-phosphate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      7e-55  171.7   0.2    8.6e-55  171.5   0.2    1.0  1  lcl|FitnessBrowser__Smeli:SMc02333  SMc02333 hypothetical protein


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02333  SMc02333 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.5   0.2   8.6e-55   8.6e-55       2     208 ..      19     226 ..      18     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.5 bits;  conditional E-value: 8.6e-55
                           TIGR00126   2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgt.eveictvvgFPlGasttevkllE 75 
                                         la liD +a++a +te+d+ +l   A+  +f+a+   p++v+l + l+       +   vgFP+G + t++k +E
  lcl|FitnessBrowser__Smeli:SMc02333  19 LAALIDISAVQAFHTEADVRELAGIAVAEGFIAAHALPNFVPLLRSLVPSGgLTLVGGPVGFPSGGHSTRTKTAE 93 
                                         799********************************************996615557789**************** PP

                           TIGR00126  76 akeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdeekkkAseisieagadfvK 150
                                         a e +e+GA+E+D++in++ +k+++   v ++i+a+vea+a v+lKvilE a+Ltdee++ As i  e+ga+fvK
  lcl|FitnessBrowser__Smeli:SMc02333  94 AVELAENGAQELDMMINVGRIKSGDFGYVRSEIRAIVEAIAPVPLKVILELAHLTDEEIRAASAIVAESGAAFVK 168
                                         *************************************************************************** PP

                           TIGR00126 151 tstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaava 208
                                         t tg++    t+e  +l+ ++vg+ v +KasGG+r  + +  ++  g +r+g ++ va
  lcl|FitnessBrowser__Smeli:SMc02333 169 TGTGWTPSATTLEKLKLIVETVGGAVEIKASGGIRSLDAIAGMMRLGVTRFGINTQVA 226
                                         ****************************************************888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (248 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: 00:00:00.00
# Mc/sec: 9.84
//
[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:

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