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.16153.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.71
//
[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:

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