Alignments for a candidate for hutG' in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Pseudomonas simiae WCS417

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate GFF346 PS417_01765 N-formylglutamate amidohydrolase

Query= reanno::pseudo3_N2E3:AO353_12285
         (266 letters)



>FitnessBrowser__WCS417:GFF346
          Length = 266

 Score =  486 bits (1250), Expect = e-142
 Identities = 233/265 (87%), Positives = 249/265 (93%)

Query: 1   VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPEAKSLPDTDWHIPTLYEFAAELGAS 60
           +DKVLNFKQGRVPLLISMPHAG+RLTPAVEAGLIPEA+SLPDTDWHIPTLY+FA ELGAS
Sbjct: 1   MDKVLNFKQGRVPLLISMPHAGLRLTPAVEAGLIPEAQSLPDTDWHIPTLYDFAEELGAS 60

Query: 61  TLAAEYSRFVIDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERASYLEKV 120
           TLAAEYSRFVIDLNRPSDDKP+Y GATTGLYPATLFDGVPLFREGLEPS  ERASYL+KV
Sbjct: 61  TLAAEYSRFVIDLNRPSDDKPLYAGATTGLYPATLFDGVPLFREGLEPSEAERASYLQKV 120

Query: 121 WTPYHSTLQQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPQLA 180
           W PYH TLQ+ELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGA+CDP+LA
Sbjct: 121 WGPYHRTLQEELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGAACDPELA 180

Query: 181 SQLEAICARHTDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEVEPFRYRP 240
           +QLEAICA H  Y+HVLNGRFKGGHITRHYG+PA++IHAVQLEL Q  YMEE EPFRYRP
Sbjct: 181 NQLEAICAAHPQYTHVLNGRFKGGHITRHYGDPAQDIHAVQLELCQSAYMEEFEPFRYRP 240

Query: 241 DLAAPTQVVLKELLQGLLAWGQKHY 265
           DLA PT+VVLK+LLQ LLAWGQK Y
Sbjct: 241 DLAEPTRVVLKQLLQELLAWGQKRY 265


Lambda     K      H
   0.320    0.137    0.420 

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: 395
Number of extensions: 8
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate GFF346 PS417_01765 (N-formylglutamate amidohydrolase)
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.21221.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.8e-123  394.8   0.0     1e-122  394.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF346  PS417_01765 N-formylglutamate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF346  PS417_01765 N-formylglutamate amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.7   0.0    1e-122    1e-122       2     262 ..       4     262 ..       3     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 394.7 bits;  conditional E-value: 1e-122
                          TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidvnrdpsg 77 
                                        +l++++G++Pllis+Ph+G++lt+ave++l  +a++l dtdWhi  lydfa++lGa++++a++sr+vid+nr+ ++
  lcl|FitnessBrowser__WCS417:GFF346   4 VLNFKQGRVPLLISMPHAGLRLTPAVEAGLIPEAQSLPDTDWHIPTLYDFAEELGASTLAAEYSRFVIDLNRPSDD 79 
                                        799************************************************************************* PP

                          TIGR02017  78 aslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgkivlydahsirsvi 153
                                        ++ly+g attgl+P+t+fdg pl+++G +Pseae++++l+k++ Pyh +l++e++rl+a +g+++l+dahsirsvi
  lcl|FitnessBrowser__WCS417:GFF346  80 KPLYAG-ATTGLYPATLFDGVPLFREGLEPSEAERASYLQKVWGPYHRTLQEELARLKAEFGYALLFDAHSIRSVI 154
                                        ******.********************************************************************* PP

                          TIGR02017 154 PrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhygqPqngvhavqlelaqrgyl 229
                                        P+lf+GklPdfnlGt++g++cdp la+++ea+ca    +++vlnGrfkGG+itrhyg+P++++havqlel+q++y+
  lcl|FitnessBrowser__WCS417:GFF346 155 PHLFDGKLPDFNLGTFNGAACDPELANQLEAICAAHPQYTHVLNGRFKGGHITRHYGDPAQDIHAVQLELCQSAYM 230
                                        **************************************************************************** PP

                          TIGR02017 230 eeetePvaydeakaealravlkellealldfae 262
                                        e e eP+ y+++ ae++r+vlk+ll+ ll++++
  lcl|FitnessBrowser__WCS417:GFF346 231 E-EFEPFRYRPDLAEPTRVVLKQLLQELLAWGQ 262
                                        9.*****************************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: 9.37
//
[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