Alignments for a candidate for prpD in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Escherichia coli BW25113

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate 14472 b0334 2-methylcitrate dehydratase (NCBI)

Query= BRENDA::P77243
         (483 letters)



>FitnessBrowser__Keio:14472
          Length = 483

 Score =  971 bits (2510), Expect = 0.0
 Identities = 483/483 (100%), Positives = 483/483 (100%)

Query: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60
           MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL
Sbjct: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60

Query: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120
           LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI
Sbjct: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120

Query: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180
           LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST
Sbjct: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180

Query: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240
           AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK
Sbjct: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240

Query: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300
           TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA
Sbjct: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300

Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360
           MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR
Sbjct: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360

Query: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420
           LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV
Sbjct: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420

Query: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480
           VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL
Sbjct: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480

Query: 481 YVI 483
           YVI
Sbjct: 481 YVI 483


Lambda     K      H
   0.321    0.136    0.406 

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: 935
Number of extensions: 17
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 14472 b0334 (2-methylcitrate dehydratase (NCBI))
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))

# 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/TIGR02330.hmm
# target sequence database:        /tmp/gapView.2349258.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02330  [M=468]
Accession:   TIGR02330
Description: prpD: 2-methylcitrate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
   2.6e-284  928.9   0.0   2.9e-284  928.8   0.0    1.0  1  FitnessBrowser__Keio:14472  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Keio:14472  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  928.8   0.0  2.9e-284  2.9e-284       1     468 []      13     483 .]      13     483 .] 0.99

  Alignments for each domain:
  == domain 1  score: 928.8 bits;  conditional E-value: 2.9e-284
                   TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldpvkaafnigal 83 
                                 d++++di+dyv++yei+sk+aydta+y+lldtlgcgl+aleyp+c+kllgp+v+gt+vpng+rvpgt++qldpv+aafniga+
  FitnessBrowser__Keio:14472  13 DREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAM 95 
                                 789******************************************************************************** PP

                   TIGR02330  84 vrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvlalensfnrvgldhvllvkva 166
                                 +rwld+ndtwlaaewghpsdnlggila+ad+lsr+++a+gk+pl++k+vl+amikaheiqg++alensfnrvgldhvllvkva
  FitnessBrowser__Keio:14472  96 IRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVA 178
                                 *********************************************************************************** PP

                   TIGR02330 167 stavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsrgvrlalialkgemgypsalsapvwgfedvl 249
                                 stavva++lg+treeilna+s+a+vdgq+lrtyrhapntg+rkswaagdatsr+vrlal+a++gemgypsal+apvwgf+dv+
  FitnessBrowser__Keio:14472 179 STAVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEMGYPSALTAPVWGFYDVS 261
                                 *********************************************************************************** PP

                   TIGR02330 250 fkkeklklareygsyvmenvlfkisfpaefhaqtaveaavklheevker...ldeierivitthesairiidkkgplanpadr 329
                                 fk+e+++++r+ygsyvmenvlfkisfpaefh+qtaveaa++l+e+++++   +++ie+++i+the++iriidkkgpl+npadr
  FitnessBrowser__Keio:14472 262 FKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAAMTLYEQMQAAgktAADIEKVTIRTHEACIRIIDKKGPLNNPADR 344
                                 ***********************************************9877799***************************** PP

                   TIGR02330 330 dhclqylvavpllfgdlvaedyedavaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveyplg 412
                                 dhc+qy+va+pllfg+l+a+dyed+va+d+rid+lrek++++ed++++++y++++kr+iana++++f+dg+++eev+veyp+g
  FitnessBrowser__Keio:14472 345 DHCIQYMVAIPLLFGRLTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEVVVEYPIG 427
                                 *********************************************************************************** PP

                   TIGR02330 413 hrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468
                                 h+rrr++gipklvdkfk+nla++f++++q+rile++ld+a+le++pvne+ldl+vi
  FitnessBrowser__Keio:14472 428 HARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDLYVI 483
                                 ******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (483 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: 00:00:00.01
# Mc/sec: 17.40
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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