Alignments for a candidate for hutG' in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Cupriavidus basilensis 4G11

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate RR42_RS16895 RR42_RS16895 N-formylglutamate amidohydrolase

Query= reanno::Cup4G11:RR42_RS16895
         (271 letters)



>FitnessBrowser__Cup4G11:RR42_RS16895
          Length = 271

 Score =  551 bits (1421), Expect = e-162
 Identities = 271/271 (100%), Positives = 271/271 (100%)

Query: 1   MAFSTDTPAFTLHRGTRPMLVSMPHVGTHLPACVSDRLTAEARTVPDTDWHLERLYDFAR 60
           MAFSTDTPAFTLHRGTRPMLVSMPHVGTHLPACVSDRLTAEARTVPDTDWHLERLYDFAR
Sbjct: 1   MAFSTDTPAFTLHRGTRPMLVSMPHVGTHLPACVSDRLTAEARTVPDTDWHLERLYDFAR 60

Query: 61  ELGASILVATHSRYVVDLNRPPDNANLYPGQDTTGLCPVDTFDKTPIYADASGLPADDEI 120
           ELGASILVATHSRYVVDLNRPPDNANLYPGQDTTGLCPVDTFDKTPIYADASGLPADDEI
Sbjct: 61  ELGASILVATHSRYVVDLNRPPDNANLYPGQDTTGLCPVDTFDKTPIYADASGLPADDEI 120

Query: 121 AARRDAIWRPYHGALAEELARLRAEHGTVALWDAHSIRSVLPRFFEGKLTDFNLGTANGA 180
           AARRDAIWRPYHGALAEELARLRAEHGTVALWDAHSIRSVLPRFFEGKLTDFNLGTANGA
Sbjct: 121 AARRDAIWRPYHGALAEELARLRAEHGTVALWDAHSIRSVLPRFFEGKLTDFNLGTANGA 180

Query: 181 SCDAALANQLLDIAGALPGYTSVLNGRFKGGYITRQYGAPAQGVQAVQLELTQSAYMSET 240
           SCDAALANQLLDIAGALPGYTSVLNGRFKGGYITRQYGAPAQGVQAVQLELTQSAYMSET
Sbjct: 181 SCDAALANQLLDIAGALPGYTSVLNGRFKGGYITRQYGAPAQGVQAVQLELTQSAYMSET 240

Query: 241 YPFAYDEARATRIQPTLKTMLETVLGYVEAR 271
           YPFAYDEARATRIQPTLKTMLETVLGYVEAR
Sbjct: 241 YPFAYDEARATRIQPTLKTMLETVLGYVEAR 271


Lambda     K      H
   0.320    0.134    0.408 

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: 373
Number of extensions: 6
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: 271
Length adjustment: 25
Effective length of query: 246
Effective length of database: 246
Effective search space:    60516
Effective search space used:    60516
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 RR42_RS16895 RR42_RS16895 (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.9893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-111  357.9   0.0   1.9e-111  357.7   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS16895  RR42_RS16895 N-formylglutamate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS16895  RR42_RS16895 N-formylglutamate amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.7   0.0  1.9e-111  1.9e-111       3     261 ..      10     268 ..       8     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 357.7 bits;  conditional E-value: 1.9e-111
                                 TIGR02017   3 levqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidv 71 
                                               ++++rG+ P+l+s+Ph Gt+l+  v++rl+++a+++ dtdWh+e+lydfar+lGa+++ a+ sr+v+d+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16895  10 FTLHRGTRPMLVSMPHVGTHLPACVSDRLTAEARTVPDTDWHLERLYDFARELGASILVATHSRYVVDL 78 
                                               6789***************************************************************** PP

                                 TIGR02017  72 nrdpsgaslypgqattgliPettfdgeplykdGea.PseaeikkrltkyfkPyhaalraeierlralhg 139
                                               nr+p++a lypgq ttgl+P +tfd +p+y d    P ++ei+ r++ +++Pyh al++e++rlra hg
  lcl|FitnessBrowser__Cup4G11:RR42_RS16895  79 NRPPDNANLYPGQDTTGLCPVDTFDKTPIYADASGlPADDEIAARRDAIWRPYHGALAEELARLRAEHG 147
                                               ******************************997644********************************* PP

                                 TIGR02017 140 kivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrh 208
                                               ++ l+dahsirsv+Pr+feGkl dfnlGt +g+scd ala+++ +++    g++svlnGrfkGGyitr+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16895 148 TVALWDAHSIRSVLPRFFEGKLTDFNLGTANGASCDAALANQLLDIAGALPGYTSVLNGRFKGGYITRQ 216
                                               ************************************************9******************** PP

                                 TIGR02017 209 ygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkellealldfa 261
                                               yg P++gv avqlel+q++y++ et P+aydea+a+ ++ +lk++le++l + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS16895 217 YGAPAQGVQAVQLELTQSAYMS-ETYPFAYDEARATRIQPTLKTMLETVLGYV 268
                                               **********************.*************************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (271 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: 9.78
//
[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