Alignments for a candidate for hutG' in Pseudomonas putida KT2440

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.10798.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: 8.55
//
[ok]

This GapMind analysis is from Sep 17 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:

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