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.3975.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.22
//
[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:

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:

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:

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:

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