GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoC in Shewanella loihica PV-4

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 5210372 Shew_2815 deoxyribose-phosphate aldolase (RefSeq)

Query= BRENDA::P0A6L0
         (259 letters)



>lcl|FitnessBrowser__PV4:5210372 Shew_2815 deoxyribose-phosphate
           aldolase (RefSeq)
          Length = 257

 Score =  343 bits (881), Expect = 2e-99
 Identities = 179/248 (72%), Positives = 206/248 (83%), Gaps = 3/248 (1%)

Query: 1   MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60
           M+DLK ++ +A++LMDLTTLNDDDTD+KVI LCH+AKTP GNTAAICIYPRFIPIARKTL
Sbjct: 1   MSDLKKAAQKAIELMDLTTLNDDDTDQKVIELCHKAKTPAGNTAAICIYPRFIPIARKTL 60

Query: 61  KEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFD 120
            E G  EI+IATVTNFPHGNDDI IA+ ETRAA+AYGADEVDVVFPYRALM GNE VG++
Sbjct: 61  NEMGCEEIKIATVTNFPHGNDDIAIAVLETRAAVAYGADEVDVVFPYRALMEGNETVGYE 120

Query: 121 LVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPE 180
           LVKACKEAC   +VLLKVIIE+G L+D ALIRKASE+SI AGADFIKTSTGKV VNAT E
Sbjct: 121 LVKACKEAC-GDDVLLKVIIESGVLQDPALIRKASELSIDAGADFIKTSTGKVEVNATLE 179

Query: 181 SARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSL 240
           +A IMM VI +   +  VGFKPAGGVR A  A+++L +A+ L G  WA  R +RFGASSL
Sbjct: 180 AAEIMMTVIAEKNPK--VGFKPAGGVRDAAAAEEFLGVAERLLGKGWATPRTFRFGASSL 237

Query: 241 LASLLKAL 248
           L +LL  L
Sbjct: 238 LNNLLHTL 245


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: 242
Number of extensions: 5
Number of successful extensions: 3
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: 257
Length adjustment: 24
Effective length of query: 235
Effective length of database: 233
Effective search space:    54755
Effective search space used:    54755
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 5210372 Shew_2815 (deoxyribose-phosphate aldolase (RefSeq))
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.15274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    8.6e-79  249.9   2.8    1.1e-78  249.6   2.8    1.0  1  lcl|FitnessBrowser__PV4:5210372  Shew_2815 deoxyribose-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210372  Shew_2815 deoxyribose-phosphate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.6   2.8   1.1e-78   1.1e-78       3     207 ..      12     226 ..      10     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 1.1e-78
                        TIGR00126   3 akliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLk..gt.eveictvvgFPlGasttevkllE 75 
                                       +l+D+t+l++d+t++++++lc++Ak++  ++aa+c++p+++++A+++L+  g  e++i+tv++FP+G++++ +++lE
  lcl|FitnessBrowser__PV4:5210372  12 IELMDLTTLNDDDTDQKVIELCHKAKTPagNTAAICIYPRFIPIARKTLNemGCeEIKIATVTNFPHGNDDIAIAVLE 89 
                                      689*************************99*******************988556*********************** PP

                        TIGR00126  76 akeaieeGAdEvDvviniaalkdkneevviedikavveaca.kvllKvilEtalLtdeekk.kAseisieagadfvKt 151
                                      +++a+++GAdEvDvv++++al+++ne v++e +ka++eac+ +vllKvi+E + L+d +++ kAse+si+agadf+Kt
  lcl|FitnessBrowser__PV4:5210372  90 TRAAVAYGADEVDVVFPYRALMEGNETVGYELVKACKEACGdDVLLKVIIESGVLQDPALIrKASELSIDAGADFIKT 167
                                      *****************************************99****************988**************** PP

                        TIGR00126 152 stgfsakgAtvedvrlmkkvvgd...evgvKasGGvrtaedalalieagaerigasaav 207
                                      stg++ ++At+e +++m+ v+++   +vg+K++GGvr+a  a +++ +++ ++g  +a 
  lcl|FitnessBrowser__PV4:5210372 168 STGKVEVNATLEAAEIMMTVIAEknpKVGFKPAGGVRDAAAAEEFLGVAERLLGKGWAT 226
                                      *********************998889***************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (257 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: 7.92
//
[ok]

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

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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