GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutG' in Pseudomonas fluorescens FW300-N2C3

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate AO356_09590 AO356_09590 N-formylglutamate deformylase

Query= reanno::pseudo5_N2C3_1:AO356_09590
         (267 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09590
          Length = 267

 Score =  551 bits (1419), Expect = e-162
 Identities = 267/267 (100%), Positives = 267/267 (100%)

Query: 1   VEKVLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGAS 60
           VEKVLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGAS
Sbjct: 1   VEKVLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGAS 60

Query: 61  TLAAEYSRFVVDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERATYLQQV 120
           TLAAEYSRFVVDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERATYLQQV
Sbjct: 61  TLAAEYSRFVVDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERATYLQQV 120

Query: 121 WMPYHQALRQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLA 180
           WMPYHQALRQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLA
Sbjct: 121 WMPYHQALRQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLA 180

Query: 181 SQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEFEPFNYRP 240
           SQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEFEPFNYRP
Sbjct: 181 SQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEFEPFNYRP 240

Query: 241 DLAAPTQVVLRELLEGFLAWGQKTYKH 267
           DLAAPTQVVLRELLEGFLAWGQKTYKH
Sbjct: 241 DLAAPTQVVLRELLEGFLAWGQKTYKH 267


Lambda     K      H
   0.321    0.138    0.425 

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 AO356_09590 AO356_09590 (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.14064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.1e-122  394.5   0.0   1.3e-122  394.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09590  AO356_09590 N-formylglutamate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09590  AO356_09590 N-formylglutamate deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.3   0.0  1.3e-122  1.3e-122       2     262 ..       4     262 ..       3     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 394.3 bits;  conditional E-value: 1.3e-122
                                       TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraai 64 
                                                     +l++++G++Pll+s+Ph+G++lt+av+++l  +a++l dtdWhi +ly+fa++lGa++++a++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09590   4 VLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGASTLAAEY 66 
                                                     799************************************************************ PP

                                       TIGR02017  65 srlvidvnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaal 127
                                                     sr+v+d+nr+ +++++y+g attgl+P+t+fdg pl+++G +Ps++e++++l++++ Pyh+al
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09590  67 SRFVVDLNRPSDDKPMYVG-ATTGLYPATLFDGVPLFREGLEPSAEERATYLQQVWMPYHQAL 128
                                                     *******************.******************************************* PP

                                       TIGR02017 128 raeierlralhgkivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakak 190
                                                     r+e++rl+a +g+++l+dahsirsviP+lf+GklPdfnlGt++g+scdp+la+++ea+ca+  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09590 129 RQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLASQLEAICARHG 191
                                                     *************************************************************** PP

                                       TIGR02017 191 glssvlnGrfkGGyitrhygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkel 253
                                                      +++vlnGrfkGG+itrhyg+P++++havqlel+q++y+e e eP+ y+++ a+++++vl+el
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09590 192 QFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYME-EFEPFNYRPDLAAPTQVVLREL 253
                                                     ***************************************9.********************** PP

                                       TIGR02017 254 lealldfae 262
                                                     le  l++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09590 254 LEGFLAWGQ 262
                                                     *******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: 00:00:00.01
# Mc/sec: 6.78
//
[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