Alignments for a candidate for deoC in Sinorhizobium meliloti 1021

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.23405.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.48
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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