Alignments for a candidate for hutG' in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Rhizobium leguminosarum 3841

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate WP_011654955.1 RL_RS30800 N-formylglutamate deformylase

Query= reanno::Smeli:SM_b21164
         (271 letters)



>NCBI__GCF_000009265.1:WP_011654955.1
          Length = 273

 Score =  423 bits (1087), Expect = e-123
 Identities = 201/262 (76%), Positives = 221/262 (84%)

Query: 5   EVRQGSSPVILGFPHTGTDVPASIRERLNDNGRILADTDWHIHDLYQGLLPDATAVRATF 64
           E+R+G+SP+ILGFPHTGT+VP  I +RLNDNGR+LADTDWHIH LY GLL + T VRATF
Sbjct: 12  EIRRGTSPIILGFPHTGTEVPPEIADRLNDNGRMLADTDWHIHQLYDGLLDNVTTVRATF 71

Query: 65  HRYVIDANRDPAGVSLYPGQNTTGLVPETDFDGLPIWKEGEGPTEVDITERLRDFHAPYH 124
           HRYVIDANRDPAGVSLYPGQNTTGLVP+TDFDG  IWKEG  P + DI  RLRDFHAPYH
Sbjct: 72  HRYVIDANRDPAGVSLYPGQNTTGLVPQTDFDGKAIWKEGAAPNDADIAARLRDFHAPYH 131

Query: 125 AALSAEIARVKAIHGVVVLYDCHSIRSHIPFLFEGRLPDFNIGTDMGKTCATEIERAAAE 184
           AAL+AEI RV+AIHGV +LYDCHSIRSHIPFLFEG+LPDFNIGTDMGKTC + IE+A   
Sbjct: 132 AALAAEIERVRAIHGVAILYDCHSIRSHIPFLFEGKLPDFNIGTDMGKTCDSAIEQATLT 191

Query: 185 IAAGAECYSHILNGRFKGGWTTRHYGRPEQGVHAIQMELAQSTHLATEAPPFALDRAKAD 244
           +   A+ Y  +LNGRFKGGWTTRHYGRPE GVHAIQMELAQSTHL TEA PFA D AKAD
Sbjct: 192 VVEAAKGYDGVLNGRFKGGWTTRHYGRPETGVHAIQMELAQSTHLQTEAAPFAYDAAKAD 251

Query: 245 RLRRPLKAILERIETVAKELKR 266
           RLR  LK IL RIE +A  LKR
Sbjct: 252 RLRVHLKNILVRIEQIAPGLKR 273


Lambda     K      H
   0.320    0.137    0.417 

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: 322
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: 271
Length of database: 273
Length adjustment: 25
Effective length of query: 246
Effective length of database: 248
Effective search space:    61008
Effective search space used:    61008
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 WP_011654955.1 RL_RS30800 (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.3364.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-123  396.6   0.0   2.9e-123  396.4   0.0    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011654955.1  RL_RS30800 N-formylglutamate def


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011654955.1  RL_RS30800 N-formylglutamate deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.4   0.0  2.9e-123  2.9e-123       3     261 ..      11     268 ..       9     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.4 bits;  conditional E-value: 2.9e-123
                                 TIGR02017   3 levqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidv 71 
                                                e++rG++P+++++PhtGt++++++++rl+++ ++l+dtdWhi++lyd++ d   t+vra+++r+vid+
  lcl|NCBI__GCF_000009265.1:WP_011654955.1  11 CEIRRGTSPIILGFPHTGTEVPPEIADRLNDNGRMLADTDWHIHQLYDGLLDN-VTTVRATFHRYVIDA 78 
                                               5799************************************************9.99************* PP

                                 TIGR02017  72 nrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgk 140
                                               nrdp+g+slypgq+ttgl+P+t+fdg++++k+G aP++a+i+ rl  ++ Pyhaal+aeier+ra+hg+
  lcl|NCBI__GCF_000009265.1:WP_011654955.1  79 NRDPAGVSLYPGQNTTGLVPQTDFDGKAIWKEGAAPNDADIAARLRDFHAPYHAALAAEIERVRAIHGV 147
                                               ********************************************************************* PP

                                 TIGR02017 141 ivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhy 209
                                               ++lyd+hsirs+iP+lfeGklPdfn+Gt++gk+cd a+++a   v++ akg+  vlnGrfkGG++trhy
  lcl|NCBI__GCF_000009265.1:WP_011654955.1 148 AILYDCHSIRSHIPFLFEGKLPDFNIGTDMGKTCDSAIEQATLTVVEAAKGYDGVLNGRFKGGWTTRHY 216
                                               ********************************************************************* PP

                                 TIGR02017 210 gqPqngvhavqlelaqrgyleeetePvaydeakaealravlkellealldfa 261
                                               g+P++gvha+q+elaq+++l+ e+ P+ayd+aka+ lr++lk++l +++++a
  lcl|NCBI__GCF_000009265.1:WP_011654955.1 217 GRPETGVHAIQMELAQSTHLQTEAAPFAYDAAKADRLRVHLKNILVRIEQIA 268
                                               *********************************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (273 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: 00:00:00.00
# Mc/sec: 7.51
//
[ok]

This GapMind analysis is from Sep 24 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