Alignments for a candidate for hutG' in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Dyella japonica UNC79MFTsu3.2

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate N515DRAFT_3725 N515DRAFT_3725 N-formylglutamate deformylase

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



>FitnessBrowser__Dyella79:N515DRAFT_3725
          Length = 266

 Score =  284 bits (726), Expect = 2e-81
 Identities = 141/253 (55%), Positives = 180/253 (71%), Gaps = 3/253 (1%)

Query: 10  FSLHRGSLPLLISIPHLGTQIPADIAATMTPAAQRTDDCDWHLDRLYA-FAKRMGASILA 68
           ++LH+GS PLLIS+PH G+ IP  IAA + P+A+R  D DWH+ RLY   A+ +GAS++ 
Sbjct: 11  YTLHQGSAPLLISLPHDGSFIPESIAARLHPSARRAPDTDWHVGRLYQPLAQALGASVIR 70

Query: 69  PTYARYVIDLNRPPDGANLYPGQDTTGLLPVDTFDKEPLYLDGQLPDEAETTRRRDAYWK 128
           P  +RYV+DLNRP DG  LYPGQ  TGL+    FD  PLYLDGQ PD AE  +R + YW+
Sbjct: 71  PRLSRYVVDLNRPADGHALYPGQRETGLVSTIGFDGVPLYLDGQAPDAAEVQQRVNDYWR 130

Query: 129 PYHEALQGELAALKAKHGKVLLWEAHSIRSHVPRFFEGRLPDFNFGTSNGASAVAGLAEE 188
           PYH+AL  E+A L   HG+V++WE HSIRS VP  FEGRLPD N GT++GAS    L E 
Sbjct: 131 PYHQALAQEIARLLDTHGRVVVWEGHSIRSLVPMLFEGRLPDLNLGTADGASCAPALQER 190

Query: 189 MAATVEQYDGGYTAVANGRFKGGYITREYGQPSQGVHALQLELSQITYMEEHMPYAYDET 248
           +AA +E     Y  V NGRFKGGYITR+Y QP QGV  +QLEL+Q+ YM+E   +AYDE 
Sbjct: 191 LAARLEA-QSDYAFVVNGRFKGGYITRQYAQPEQGVQTVQLELAQLNYMDED-SFAYDEA 248

Query: 249 LAAKVEPLLEALV 261
            AA+++PL+ AL+
Sbjct: 249 KAARLQPLILALL 261


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: 273
Number of extensions: 14
Number of successful extensions: 4
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: 266
Length adjustment: 25
Effective length of query: 246
Effective length of database: 241
Effective search space:    59286
Effective search space used:    59286
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 N515DRAFT_3725 N515DRAFT_3725 (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.20104.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.3e-102  327.9   0.0   2.6e-102  327.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3725  N515DRAFT_3725 N-formylglutamate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3725  N515DRAFT_3725 N-formylglutamate deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.8   0.0  2.6e-102  2.6e-102       2     258 ..      10     265 ..       9     266 .] 0.98

  Alignments for each domain:
  == domain 1  score: 327.8 bits;  conditional E-value: 2.6e-102
                                    TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklyd.fardlGatvvraaisr 66 
                                                  ++++++G+aPllislPh G  +++++++rl  +a+   dtdWh+ +ly+  a+ lGa+v+r ++sr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3725  10 TYTLHQGSAPLLISLPHDGSFIPESIAARLHPSARRAPDTDWHVGRLYQpLAQALGASVIRPRLSR 75 
                                                  6899********************************************846899************ PP

                                    TIGR02017  67 lvidvnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeie 132
                                                  +v+d+nr+ +g++lypgq  tgl+ +  fdg ply dG+aP++ae+++r++ y++Pyh+al++ei+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3725  76 YVVDLNRPADGHALYPGQRETGLVSTIGFDGVPLYLDGQAPDAAEVQQRVNDYWRPYHQALAQEIA 141
                                                  ****************************************************************** PP

                                    TIGR02017 133 rlralhgkivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnG 198
                                                  rl + hg++v+++ hsirs +P lfeG+lPd+nlGt dg+sc+pal+++++a ++ ++ ++ v+nG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3725 142 RLLDTHGRVVVWEGHSIRSLVPMLFEGRLPDLNLGTADGASCAPALQERLAARLEAQSDYAFVVNG 207
                                                  ****************************************************************** PP

                                    TIGR02017 199 rfkGGyitrhygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkelleall 258
                                                  rfkGGyitr+y+qP++gv +vqlelaq +y++e+   +aydeaka+ l+ ++  ll+ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3725 208 RFKGGYITRQYAQPEQGVQTVQLELAQLNYMDED--SFAYDEAKAARLQPLILALLRECV 265
                                                  *******************************965..69************9999999886 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.67
//
[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, or view the source code.

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