Alignments for a candidate for hutG' in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Pseudomonas fluorescens GW456-L13

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate PfGW456L13_316 N-formylglutamate deformylase (EC 3.5.1.68)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_316
         (267 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316
          Length = 267

 Score =  552 bits (1422), Expect = e-162
 Identities = 267/267 (100%), Positives = 267/267 (100%)

Query: 1   VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPDAKSLPDTDWHIPQLYDFAAELGAS 60
           VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPDAKSLPDTDWHIPQLYDFAAELGAS
Sbjct: 1   VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPDAKSLPDTDWHIPQLYDFAAELGAS 60

Query: 61  TLAAEYSRFVIDLNRPSDDKPLYVGATTGLYPATLFDGIPLFREGLEPSKEERATYLEQI 120
           TLAAEYSRFVIDLNRPSDDKPLYVGATTGLYPATLFDGIPLFREGLEPSKEERATYLEQI
Sbjct: 61  TLAAEYSRFVIDLNRPSDDKPLYVGATTGLYPATLFDGIPLFREGLEPSKEERATYLEQI 120

Query: 121 WTPYHSTLQQELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTFNGASCDPQLA 180
           WTPYHSTLQQELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTFNGASCDPQLA
Sbjct: 121 WTPYHSTLQQELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTFNGASCDPQLA 180

Query: 181 TRLEAICALHDNYTHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEFEPFRYRP 240
           TRLEAICALHDNYTHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEFEPFRYRP
Sbjct: 181 TRLEAICALHDNYTHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEFEPFRYRP 240

Query: 241 DLAEPTRLVLKELLQGLLAWGEKHYKR 267
           DLAEPTRLVLKELLQGLLAWGEKHYKR
Sbjct: 241 DLAEPTRLVLKELLQGLLAWGEKHYKR 267


Lambda     K      H
   0.321    0.140    0.431 

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: 439
Number of extensions: 9
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 PfGW456L13_316 (N-formylglutamate deformylase (EC 3.5.1.68))
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.31392.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   5.3e-123  395.6   0.0   6.1e-123  395.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316  N-formylglutamate deformylase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316  N-formylglutamate deformylase (EC 3.5.1.68)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.4   0.0  6.1e-123  6.1e-123       2     262 ..       4     262 ..       3     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 395.4 bits;  conditional E-value: 6.1e-123
                                              TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGa 57 
                                                            +l++++G++Pllis+Ph+G++lt+ave++l  +ak+l dtdWhi +lydfa +lGa
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316   4 VLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPDAKSLPDTDWHIPQLYDFAAELGA 59 
                                                            799***************************************************** PP

                                              TIGR02017  58 tvvraaisrlvidvnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeik 113
                                                            ++++a++sr+vid+nr+ ++++ly+g attgl+P+t+fdg pl+++G +Ps++e++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316  60 STLAAEYSRFVIDLNRPSDDKPLYVG-ATTGLYPATLFDGIPLFREGLEPSKEERA 114
                                                            **************************.***************************** PP

                                              TIGR02017 114 krltkyfkPyhaalraeierlralhgkivlydahsirsviPrlfeGklPdfnlGtn 169
                                                            ++l++++ Pyh++l++e++rl+a +g+++l+dahsirs iP+lf+GklPdfnlGt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316 115 TYLEQIWTPYHSTLQQELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTF 170
                                                            ******************************************************** PP

                                              TIGR02017 170 dgkscdpaladaveavcakakglssvlnGrfkGGyitrhygqPqngvhavqlelaq 225
                                                            +g+scdp la ++ea+ca    +++vlnGrfkGG+itrhyg+P++++havqlel q
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316 171 NGASCDPQLATRLEAICALHDNYTHVLNGRFKGGHITRHYGNPAENIHAVQLELGQ 226
                                                            ******************************************************** PP

                                              TIGR02017 226 rgyleeetePvaydeakaealravlkellealldfae 262
                                                             +y+e e eP+ y+++ ae++r vlkell+ ll+++e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_316 227 CTYME-EFEPFRYRPDLAEPTRLVLKELLQGLLAWGE 262
                                                            ****9.*****************************97 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.44
//
[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