GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutG' in Pseudomonas putida KT2440

Align N-formylglutamate amidohydrolase (EC 3.5.1.68) (characterized)
to candidate PP_5029 PP_5029 N-formylglutamate deformylase

Query= metacyc::MONOMER-11615
         (267 letters)



>FitnessBrowser__Putida:PP_5029
          Length = 267

 Score =  509 bits (1311), Expect = e-149
 Identities = 242/267 (90%), Positives = 255/267 (95%)

Query: 1   MDKVLSFHQGRLPLLISMPHAGLRLSDAVRDGLVEEARSLPDTDWHIPQLYDFARDLGAS 60
           MDKVLSFHQGRLPLLISMPHAGLRL+DAVRDGLV++A+SLPDTDWHIPQLYDFARD+GAS
Sbjct: 1   MDKVLSFHQGRLPLLISMPHAGLRLTDAVRDGLVDQAQSLPDTDWHIPQLYDFARDMGAS 60

Query: 61  VVAAEYSRFVIDLNRPDDDKPLYAGATTGLYPATLFEGEPLFKEGLAPSGEERKRYLEQI 120
           VVAAEYSRFVIDLNRP+DDKPLY GATTGLYPATLF GEPLFK+GLAPSGEERKRYLEQI
Sbjct: 61  VVAAEYSRFVIDLNRPEDDKPLYVGATTGLYPATLFGGEPLFKDGLAPSGEERKRYLEQI 120

Query: 121 WRPYHGTLRRELDRLREQFGYALLWDAHSIRSHIPHLFDGKLPDFNLGTFNGASCDPVLA 180
           WRPYH T+RRELDRLREQFGYALLWDAHSIRS IPHLFDGKLPDFNLGTFNGASCDP LA
Sbjct: 121 WRPYHTTIRRELDRLREQFGYALLWDAHSIRSLIPHLFDGKLPDFNLGTFNGASCDPALA 180

Query: 181 ERLQGVCAEATGYSHVLNGRFKGGHITRHYGDPAKHIHAVQLELAQSTYMEETEPFTYRE 240
           +RLQGVCA+  GY+HVLNGRFKGGHITRHYGDPA HIHAVQLELAQSTYMEE EPF YRE
Sbjct: 181 DRLQGVCAKVQGYNHVLNGRFKGGHITRHYGDPANHIHAVQLELAQSTYMEEVEPFAYRE 240

Query: 241 DLAQPTQVVLKQLLQALLAWGAERYQR 267
           DLAQPTQ VL+QLLQALLAWG ERY+R
Sbjct: 241 DLAQPTQAVLRQLLQALLAWGDERYKR 267


Lambda     K      H
   0.321    0.139    0.430 

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: 384
Number of extensions: 12
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: 267
Length of database: 267
Length adjustment: 25
Effective length of query: 242
Effective length of database: 242
Effective search space:    58564
Effective search space used:    58564
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate PP_5029 PP_5029 (N-formylglutamate deformylase)
to HMM TIGR02017 (hutG: N-formylglutamate deformylase (EC 3.5.1.68))

# 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/TIGR02017.hmm
# target sequence database:        /tmp/gapView.7099.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02017  [M=263]
Accession:   TIGR02017
Description: hutG_amidohyd: N-formylglutamate deformylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.3e-136  437.7   0.0   8.3e-136  437.5   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5029  PP_5029 N-formylglutamate deform


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5029  PP_5029 N-formylglutamate deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.5   0.0  8.3e-136  8.3e-136       2     263 .]       4     263 ..       3     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 437.5 bits;  conditional E-value: 8.3e-136
                           TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidvnrdps 76 
                                         +l++++G++Pllis+Ph+G++ltdav+++lv++a++l dtdWhi +lydfard+Ga+vv+a++sr+vid+nr+++
  lcl|FitnessBrowser__Putida:PP_5029   4 VLSFHQGRLPLLISMPHAGLRLTDAVRDGLVDQAQSLPDTDWHIPQLYDFARDMGASVVAAEYSRFVIDLNRPED 78 
                                         799************************************************************************ PP

                           TIGR02017  77 gaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgkivlydahsirs 151
                                         +++ly+g attgl+P+t+f+gepl+kdG aPs +e+k++l+++++Pyh+++r+e++rlr+++g+++l+dahsirs
  lcl|FitnessBrowser__Putida:PP_5029  79 DKPLYVG-ATTGLYPATLFGGEPLFKDGLAPSGEERKRYLEQIWRPYHTTIRRELDRLREQFGYALLWDAHSIRS 152
                                         *******.******************************************************************* PP

                           TIGR02017 152 viPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhygqPqngvhavqlelaqr 226
                                          iP+lf+GklPdfnlGt++g+scdpalad+++ vcak++g+++vlnGrfkGG+itrhyg+P+n++havqlelaq+
  lcl|FitnessBrowser__Putida:PP_5029 153 LIPHLFDGKLPDFNLGTFNGASCDPALADRLQGVCAKVQGYNHVLNGRFKGGHITRHYGDPANHIHAVQLELAQS 227
                                         *************************************************************************** PP

                           TIGR02017 227 gyleeetePvaydeakaealravlkellealldfaee 263
                                         +y+e e+eP+ay+e+ a++++avl++ll+all++++e
  lcl|FitnessBrowser__Putida:PP_5029 228 TYME-EVEPFAYREDLAQPTQAVLRQLLQALLAWGDE 263
                                         ***9.*****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (267 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: 9.28
//
[ok]

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

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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