Alignments for a candidate for hutG' in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Paraburkholderia bryophila 376MFSha3.1

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate H281DRAFT_04867 H281DRAFT_04867 N-formylglutamate deformylase

Query= reanno::BFirm:BPHYT_RS07585
         (271 letters)



>FitnessBrowser__Burk376:H281DRAFT_04867
          Length = 270

 Score =  483 bits (1243), Expect = e-141
 Identities = 235/269 (87%), Positives = 248/269 (92%), Gaps = 1/269 (0%)

Query: 1   MTASNTPPVFSLHRGSLPLLISIPHLGTQIPADIAATMTPAAQRTDDCDWHLDRLYAFAK 60
           MTASNTPPVF+LHRGSLPLLISIPH+GT+IP DIA TMTP A RTDDCDWHLDRLYAFAK
Sbjct: 1   MTASNTPPVFTLHRGSLPLLISIPHVGTEIPVDIAGTMTPVAFRTDDCDWHLDRLYAFAK 60

Query: 61  RMGASILAPTYARYVIDLNRPPDGANLYPGQDTTGLLPVDTFDKEPLYLDGQLPDEAETT 120
           RMGASIL PTYARYVIDLNRPPDGANLYPGQDTTGLLPVDTFDKEPLYL+G LPDEAE  
Sbjct: 61  RMGASILMPTYARYVIDLNRPPDGANLYPGQDTTGLLPVDTFDKEPLYLEGHLPDEAEVA 120

Query: 121 RRRDAYWKPYHEALQGELAALKAKHGKVLLWEAHSIRSHVPRFFEGRLPDFNFGTSNGAS 180
           RRRDAYW PYH+AL GELAALKA+HGKVLLWEAHSIRSHVPRFFEGRLPDFNFGTSNGAS
Sbjct: 121 RRRDAYWVPYHDALAGELAALKARHGKVLLWEAHSIRSHVPRFFEGRLPDFNFGTSNGAS 180

Query: 181 AVAGLAEEMAATVEQYDGGYTAVANGRFKGGYITREYGQPSQGVHALQLELSQITYMEEH 240
           AVAGL EE+AA VE++ GGY+AVANGRFKGG+ITR YGQPSQGVHA+QLELSQITYM+E 
Sbjct: 181 AVAGLGEELAAVVERH-GGYSAVANGRFKGGFITRHYGQPSQGVHAVQLELSQITYMQEQ 239

Query: 241 MPYAYDETLAAKVEPLLEALVVKALERVK 269
            PYAYDE LAAKVEPLLE LV  A ERVK
Sbjct: 240 PPYAYDEALAAKVEPLLEQLVATASERVK 268


Lambda     K      H
   0.317    0.134    0.403 

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: 368
Number of extensions: 12
Number of successful extensions: 2
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: 271
Length of database: 270
Length adjustment: 25
Effective length of query: 246
Effective length of database: 245
Effective search space:    60270
Effective search space used:    60270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate H281DRAFT_04867 H281DRAFT_04867 (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.14919.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.3e-109  349.0   0.0   9.8e-109  348.8   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04867  H281DRAFT_04867 N-formylglutamat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04867  H281DRAFT_04867 N-formylglutamate deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.8   0.0  9.8e-109  9.8e-109       3     257 ..      10     263 ..       8     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 348.8 bits;  conditional E-value: 9.8e-109
                                    TIGR02017   3 levqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlv 68 
                                                  ++++rG++Pllis+Ph Gt+++ +++  ++  a  + d+dWh+++ly+fa+ +Ga+++  ++ r+v
  lcl|FitnessBrowser__Burk376:H281DRAFT_04867  10 FTLHRGSLPLLISIPHVGTEIPVDIAGTMTPVAFRTDDCDWHLDRLYAFAKRMGASILMPTYARYV 75 
                                                  6899************************************************************** PP

                                    TIGR02017  69 idvnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierl 134
                                                  id+nr+p+ga lypgq ttgl+P +tfd eply +G+ P+eae+++r++ y+ Pyh+al+ e++ l
  lcl|FitnessBrowser__Burk376:H281DRAFT_04867  76 IDLNRPPDGANLYPGQDTTGLLPVDTFDKEPLYLEGHLPDEAEVARRRDAYWVPYHDALAGELAAL 141
                                                  ****************************************************************** PP

                                    TIGR02017 135 ralhgkivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrf 200
                                                  +a hgk++l++ahsirs++Pr+feG+lPdfn Gt +g+s+  +l ++++av+++  g+s v nGrf
  lcl|FitnessBrowser__Burk376:H281DRAFT_04867 142 KARHGKVLLWEAHSIRSHVPRFFEGRLPDFNFGTSNGASAVAGLGEELAAVVERHGGYSAVANGRF 207
                                                  ****************************************************************** PP

                                    TIGR02017 201 kGGyitrhygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkelleal 257
                                                  kGG+itrhygqP++gvhavqlel+q +y++ e+ P+aydea a+++  +l++l+ ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04867 208 KGGFITRHYGQPSQGVHAVQLELSQITYMQ-EQPPYAYDEALAAKVEPLLEQLVATA 263
                                                  ******************************.99********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (270 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: 10.66
//
[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