Alignments for a candidate for hutG' in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Phaeobacter inhibens BS107

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate GFF3578 PGA1_c36330 N-formylglutamate deformylase HutG

Query= reanno::Phaeo:GFF3578
         (261 letters)



>FitnessBrowser__Phaeo:GFF3578
          Length = 261

 Score =  553 bits (1425), Expect = e-162
 Identities = 261/261 (100%), Positives = 261/261 (100%)

Query: 1   MIEVTQGASPLVLGLPHTGTDVPPEVWACLNETGRALADTDWHIHDLYAGLAEGITTVRT 60
           MIEVTQGASPLVLGLPHTGTDVPPEVWACLNETGRALADTDWHIHDLYAGLAEGITTVRT
Sbjct: 1   MIEVTQGASPLVLGLPHTGTDVPPEVWACLNETGRALADTDWHIHDLYAGLAEGITTVRT 60

Query: 61  PVHRYVIDVNRDPGGISLYPGQNTTTLVPLTDFDGLPIWQEGKEPNEAEITRRRDAYHAP 120
           PVHRYVIDVNRDPGGISLYPGQNTTTLVPLTDFDGLPIWQEGKEPNEAEITRRRDAYHAP
Sbjct: 61  PVHRYVIDVNRDPGGISLYPGQNTTTLVPLTDFDGLPIWQEGKEPNEAEITRRRDAYHAP 120

Query: 121 YHAALMAELERVKAIHGFAILYDCHSIRGDIPFLFEGRLPDFNTGTNMGTTCDPEIEALT 180
           YHAALMAELERVKAIHGFAILYDCHSIRGDIPFLFEGRLPDFNTGTNMGTTCDPEIEALT
Sbjct: 121 YHAALMAELERVKAIHGFAILYDCHSIRGDIPFLFEGRLPDFNTGTNMGTTCDPEIEALT 180

Query: 181 VAHCEAAEGYTSTLNGRFKGGWTTRHYGRPADGLHAIQMELAQATYCQESPPWTYLPERA 240
           VAHCEAAEGYTSTLNGRFKGGWTTRHYGRPADGLHAIQMELAQATYCQESPPWTYLPERA
Sbjct: 181 VAHCEAAEGYTSTLNGRFKGGWTTRHYGRPADGLHAIQMELAQATYCQESPPWTYLPERA 240

Query: 241 EQLRAPLTNILTDLKNWRPSA 261
           EQLRAPLTNILTDLKNWRPSA
Sbjct: 241 EQLRAPLTNILTDLKNWRPSA 261


Lambda     K      H
   0.319    0.137    0.439 

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: 437
Number of extensions: 5
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: 261
Length of database: 261
Length adjustment: 25
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate GFF3578 PGA1_c36330 (N-formylglutamate deformylase HutG)
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.8758.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.5e-113  362.7   0.0   6.1e-113  362.6   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3578  PGA1_c36330 N-formylglutamate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3578  PGA1_c36330 N-formylglutamate deformylase HutG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.6   0.0  6.1e-113  6.1e-113       3     260 ..       2     257 ..       1     260 [. 0.98

  Alignments for each domain:
  == domain 1  score: 362.6 bits;  conditional E-value: 6.1e-113
                          TIGR02017   3 levqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidvnrdpsga 78 
                                        +ev++G +Pl+++lPhtGtd++++v++ l+++ +al+dtdWhi+ ly+++ + G t+vr+ ++r+vidvnrdp g 
  lcl|FitnessBrowser__Phaeo:GFF3578   2 IEVTQGASPLVLGLPHTGTDVPPEVWACLNETGRALADTDWHIHDLYAGLAE-GITTVRTPVHRYVIDVNRDPGGI 76 
                                        6899*********************************************998.59********************* PP

                          TIGR02017  79 slypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgkivlydahsirsviP 154
                                        slypgq+tt+l+P t+fdg p++++G++P+eaei++r++ y+ Pyhaal ae+er++a+hg ++lyd+hsir  iP
  lcl|FitnessBrowser__Phaeo:GFF3578  77 SLYPGQNTTTLVPLTDFDGLPIWQEGKEPNEAEITRRRDAYHAPYHAALMAELERVKAIHGFAILYDCHSIRGDIP 152
                                        **************************************************************************** PP

                          TIGR02017 155 rlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhygqPqngvhavqlelaqrgyle 230
                                        +lfeG+lPdfn Gtn+g +cdp +++  +a c+ a+g++s lnGrfkGG++trhyg+P++g+ha+q+elaq +y +
  lcl|FitnessBrowser__Phaeo:GFF3578 153 FLFEGRLPDFNTGTNMGTTCDPEIEALTVAHCEAAEGYTSTLNGRFKGGWTTRHYGRPADGLHAIQMELAQATYCQ 228
                                        **************************************************************************** PP

                          TIGR02017 231 eetePvaydeakaealravlkellealldf 260
                                         e+ P +y +++ae+lra l ++l+ l ++
  lcl|FitnessBrowser__Phaeo:GFF3578 229 -ESPPWTYLPERAEQLRAPLTNILTDLKNW 257
                                        .9***********************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (261 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: 6.85
//
[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