Alignments for a candidate for araD in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for araD in Escherichia coli BW25113

Align L-ribulose-5-phosphate 4-epimerase; EC 5.1.3.4 (characterized)
to candidate 14207 b0061 L-ribulose-5-phosphate 4-epimerase (NCBI)

Query= CharProtDB::CH_001292
         (231 letters)



>FitnessBrowser__Keio:14207
          Length = 231

 Score =  476 bits (1224), Expect = e-139
 Identities = 231/231 (100%), Positives = 231/231 (100%)

Query: 1   MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPSGVDYSVMTADDMVVVS 60
           MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPSGVDYSVMTADDMVVVS
Sbjct: 1   MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPSGVDYSVMTADDMVVVS 60

Query: 61  IETGEVVEGTKKPSSDTPTHRLLYQAFPSIGGIVHTHSRHATIWAQAGQSIPATGTTHAD 120
           IETGEVVEGTKKPSSDTPTHRLLYQAFPSIGGIVHTHSRHATIWAQAGQSIPATGTTHAD
Sbjct: 61  IETGEVVEGTKKPSSDTPTHRLLYQAFPSIGGIVHTHSRHATIWAQAGQSIPATGTTHAD 120

Query: 121 YFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQGIDAAQMPGVLVHSHGPFAWGKNA 180
           YFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQGIDAAQMPGVLVHSHGPFAWGKNA
Sbjct: 121 YFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQGIDAAQMPGVLVHSHGPFAWGKNA 180

Query: 181 EDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLDKHYLRKHGAKAYYGQ 231
           EDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLDKHYLRKHGAKAYYGQ
Sbjct: 181 EDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLDKHYLRKHGAKAYYGQ 231


Lambda     K      H
   0.318    0.133    0.404 

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: 361
Number of extensions: 3
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: 231
Length of database: 231
Length adjustment: 23
Effective length of query: 208
Effective length of database: 208
Effective search space:    43264
Effective search space used:    43264
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 14207 b0061 (L-ribulose-5-phosphate 4-epimerase (NCBI))
to HMM TIGR00760 (araD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4))

# 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/TIGR00760.hmm
# target sequence database:        /tmp/gapView.30680.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00760  [M=228]
Accession:   TIGR00760
Description: araD: L-ribulose-5-phosphate 4-epimerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-139  449.0   0.3   1.3e-139  448.9   0.3    1.0  1  lcl|FitnessBrowser__Keio:14207  b0061 L-ribulose-5-phosphate 4-e


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14207  b0061 L-ribulose-5-phosphate 4-epimerase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.9   0.3  1.3e-139  1.3e-139       1     228 []       1     231 []       1     231 [] 1.00

  Alignments for each domain:
  == domain 1  score: 448.9 bits;  conditional E-value: 1.3e-139
                       TIGR00760   1 mleelkkevleanlalpkhklvtftwgnvsaidrekelvvikpsgveydeltaddlvvvdle.gevvegdkkpssdtpt 78 
                                     mle+lk++vleanlalpkh+lvt+twgnvsa+dre++++vikpsgv+y+++tadd+vvv++e gevveg+kkpssdtpt
  lcl|FitnessBrowser__Keio:14207   1 MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPSGVDYSVMTADDMVVVSIEtGEVVEGTKKPSSDTPT 79 
                                     9*************************************************************9**************** PP

                       TIGR00760  79 hlalykafpeiggivhthsrhatiwaqagkdipalgtthadyfygaipctremteeeikgeyeletgkvivetfeek.. 155
                                     h++ly+afp+iggivhthsrhatiwaqag++ipa+gtthadyfyg+ipctr+mt++ei+geye+etg+vivetfe++  
  lcl|FitnessBrowser__Keio:14207  80 HRLLYQAFPSIGGIVHTHSRHATIWAQAGQSIPATGTTHADYFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQgi 158
                                     *****************************************************************************99 PP

                       TIGR00760 156 dpaqipgvlvhshgpfawgkdaadavhnavvleevakmalkslqlakelkplqkelldkhylrkhganayygq 228
                                     d+aq+pgvlvhshgpfawgk+a+davhna+vleeva+m+++++qla++l+++q++lldkhylrkhga+ayygq
  lcl|FitnessBrowser__Keio:14207 159 DAAQMPGVLVHSHGPFAWGKNAEDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLDKHYLRKHGAKAYYGQ 231
                                     ************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (231 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: 8.56
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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 (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