Alignments for a candidate for hutG' in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Pseudomonas fluorescens FW300-N1B4

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate Pf1N1B4_1578 N-formylglutamate deformylase (EC 3.5.1.68)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1578
         (266 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578
          Length = 266

 Score =  549 bits (1415), Expect = e-161
 Identities = 266/266 (100%), Positives = 266/266 (100%)

Query: 1   VDKVLNFKQGRVPLLISMPHAGLRLTPVVEAGLIPDAKSLPDTDWHIPRLYEFAAELGAS 60
           VDKVLNFKQGRVPLLISMPHAGLRLTPVVEAGLIPDAKSLPDTDWHIPRLYEFAAELGAS
Sbjct: 1   VDKVLNFKQGRVPLLISMPHAGLRLTPVVEAGLIPDAKSLPDTDWHIPRLYEFAAELGAS 60

Query: 61  TLAAEYSRFVIDLNRPSDDKPLYVGATTGLYPATLFDGIPLFREGMEPSATERATYLEQI 120
           TLAAEYSRFVIDLNRPSDDKPLYVGATTGLYPATLFDGIPLFREGMEPSATERATYLEQI
Sbjct: 61  TLAAEYSRFVIDLNRPSDDKPLYVGATTGLYPATLFDGIPLFREGMEPSATERATYLEQI 120

Query: 121 WTPYHRTLQEELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTFNGASCDPQLA 180
           WTPYHRTLQEELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTFNGASCDPQLA
Sbjct: 121 WTPYHRTLQEELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTFNGASCDPQLA 180

Query: 181 SQLEAICARHGDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEFEPFRYRP 240
           SQLEAICARHGDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEFEPFRYRP
Sbjct: 181 SQLEAICARHGDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEFEPFRYRP 240

Query: 241 DLAAPTQVVLRELLQGLLAWGEKHYR 266
           DLAAPTQVVLRELLQGLLAWGEKHYR
Sbjct: 241 DLAAPTQVVLRELLQGLLAWGEKHYR 266


Lambda     K      H
   0.322    0.140    0.433 

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: 428
Number of extensions: 7
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: 266
Length of database: 266
Length adjustment: 25
Effective length of query: 241
Effective length of database: 241
Effective search space:    58081
Effective search space used:    58081
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: 47 (22.7 bits)

Align candidate Pf1N1B4_1578 (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.18068.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     7e-122  391.9   0.0     8e-122  391.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578  N-formylglutamate deformylase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578  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 !  391.7   0.0    8e-122    8e-122       2     262 ..       4     262 ..       3     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 391.7 bits;  conditional E-value: 8e-122
                                      TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraais 65 
                                                    +l++++G++Pllis+Ph+G++lt+ ve++l  +ak+l dtdWhi +ly+fa +lGa++++a++s
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578   4 VLNFKQGRVPLLISMPHAGLRLTPVVEAGLIPDAKSLPDTDWHIPRLYEFAAELGASTLAAEYS 67 
                                                    799************************************************************* PP

                                      TIGR02017  66 rlvidvnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalra 129
                                                    r+vid+nr+ ++++ly+g attgl+P+t+fdg pl+++G +Ps++e++++l++++ Pyh +l++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578  68 RFVIDLNRPSDDKPLYVG-ATTGLYPATLFDGIPLFREGMEPSATERATYLEQIWTPYHRTLQE 130
                                                    ******************.********************************************* PP

                                      TIGR02017 130 eierlralhgkivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakgls 193
                                                    e++rl+a +g+++l+dahsirs iP+lf+GklPdfnlGt++g+scdp la+++ea+ca+   +s
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578 131 ELARLKAEFGYALLFDAHSIRSIIPHLFDGKLPDFNLGTFNGASCDPQLASQLEAICARHGDYS 194
                                                    **************************************************************** PP

                                      TIGR02017 194 svlnGrfkGGyitrhygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkelleal 257
                                                    +vlnGrfkGG+itrhyg+P++++havqlel q +y+e e eP+ y+++ a+++++vl+ell+ l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578 195 HVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYME-EFEPFRYRPDLAAPTQVVLRELLQGL 257
                                                    ************************************9.************************** PP

                                      TIGR02017 258 ldfae 262
                                                    l+++e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1578 258 LAWGE 262
                                                    ***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (266 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: 7.20
//
[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