GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Phyllobacterium leguminum ORS 1419

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_110752346.1 C7477_RS11865 deoxyribose-phosphate aldolase

Query= BRENDA::P0A6L0
         (259 letters)



>NCBI__GCF_003217235.1:WP_110752346.1
          Length = 256

 Score =  238 bits (608), Expect = 7e-68
 Identities = 130/256 (50%), Positives = 168/256 (65%), Gaps = 6/256 (2%)

Query: 3   DLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKE 62
           D ++ +LR L L+DLT L+D+ T + V  L  +A TP G+TAAICI+PRFI  A+  L  
Sbjct: 5   DRRSLALRVLSLIDLTDLDDNSTAQGVAELSARAITPHGHTAAICIWPRFIETAKALLHG 64

Query: 63  QGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLV 122
            G   +R+ATV NFPHG  DID  LAETR AI+ GADE+D+V PYR   A    +   ++
Sbjct: 65  TG---VRVATVVNFPHGGTDIDGVLAETRRAISDGADEIDLVLPYRDFAANGAALSRQMI 121

Query: 123 KACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESA 182
            + K+ C    V LKVI+ETG+L DEA I  ASE++++ GADFIKTSTGKV +NATP + 
Sbjct: 122 GSVKKLCGR-KVKLKVILETGKLADEAAIESASEVALEEGADFIKTSTGKVEINATPAAL 180

Query: 183 RIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLA 242
           RIM+E IR+ G     G KPAGG+RT +DA +YL  AD + G  W     +RFGAS LL 
Sbjct: 181 RIMLEAIRESG--SAAGVKPAGGIRTLDDAAQYLDFADAIMGEGWVKPETFRFGASKLLD 238

Query: 243 SLLKALGHGDGKSASS 258
            +L  LG G   +ASS
Sbjct: 239 DVLGQLGSGASSTASS 254


Lambda     K      H
   0.317    0.133    0.373 

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: 211
Number of extensions: 8
Number of successful extensions: 4
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: 259
Length of database: 256
Length adjustment: 24
Effective length of query: 235
Effective length of database: 232
Effective search space:    54520
Effective search space used:    54520
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: 47 (22.7 bits)

Align candidate WP_110752346.1 C7477_RS11865 (deoxyribose-phosphate aldolase)
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.3437139.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    5.4e-66  208.1   0.2    6.8e-66  207.7   0.2    1.0  1  NCBI__GCF_003217235.1:WP_110752346.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217235.1:WP_110752346.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.7   0.2   6.8e-66   6.8e-66       2     204 ..      13     222 ..      12     226 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.7 bits;  conditional E-value: 6.8e-66
                             TIGR00126   2 lakliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevk 72 
                                           +++liD+t l++++t + +++l a A+++  ++aa+c+ p++++ Ak lL+gt v+++tvv+FP+G ++++  
  NCBI__GCF_003217235.1:WP_110752346.1  13 VLSLIDLTDLDDNSTAQGVAELSARAITPhgHTAAICIWPRFIETAKALLHGTGVRVATVVNFPHGGTDIDGV 85 
                                           5789************************9889***************************************** PP

                             TIGR00126  73 llEakeaieeGAdEvDvviniaalkdkneevviedikavveaca.kvllKvilEtalLtdeekk.kAseisie 143
                                           l+E++ ai+ GAdE+D+v++++ + ++  ++  + i +v++ c+ kv+lKvilEt++L de+ + +Ase+++e
  NCBI__GCF_003217235.1:WP_110752346.1  86 LAETRRAISDGADEIDLVLPYRDFAANGAALSRQMIGSVKKLCGrKVKLKVILETGKLADEAAIeSASEVALE 158
                                           ********************************************9***************987769******* PP

                             TIGR00126 144 agadfvKtstgfsakgAtvedvrlmkkvvgd...evgvKasGGvrtaedalalieagaerigas 204
                                            gadf+Ktstg++  +At++  r+m +++++     gvK++GG+rt +da ++++ ++  +g  
  NCBI__GCF_003217235.1:WP_110752346.1 159 EGADFIKTSTGKVEINATPAALRIMLEAIREsgsAAGVKPAGGIRTLDDAAQYLDFADAIMGEG 222
                                           *****************************998889***********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (256 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: 15.33
//
[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:

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