Alignments for a candidate for hutG' in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Sphingomonas koreensis DSMZ 15582

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate Ga0059261_3962 Ga0059261_3962 N-formylglutamate amidohydrolase

Query= reanno::Korea:Ga0059261_3962
         (264 letters)



>FitnessBrowser__Korea:Ga0059261_3962
          Length = 264

 Score =  545 bits (1403), Expect = e-160
 Identities = 264/264 (100%), Positives = 264/264 (100%)

Query: 1   MIHVEQGSAPLIVSVPHAGTVIPADIQGLVSPELARYDADLYVDHLYAFARGLDATIVRT 60
           MIHVEQGSAPLIVSVPHAGTVIPADIQGLVSPELARYDADLYVDHLYAFARGLDATIVRT
Sbjct: 1   MIHVEQGSAPLIVSVPHAGTVIPADIQGLVSPELARYDADLYVDHLYAFARGLDATIVRT 60

Query: 61  TVSRTVIDVNRDPSGQTLYPGQFTTGLCPIQTFDGTPLYEPGALPDAHEIERRRAEWFDP 120
           TVSRTVIDVNRDPSGQTLYPGQFTTGLCPIQTFDGTPLYEPGALPDAHEIERRRAEWFDP
Sbjct: 61  TVSRTVIDVNRDPSGQTLYPGQFTTGLCPIQTFDGTPLYEPGALPDAHEIERRRAEWFDP 120

Query: 121 YHTALAIQIERLRAIHPAIVVYDAHSIRSVVPKLFDGELPNFNIGTNDGTSCAPALTQAV 180
           YHTALAIQIERLRAIHPAIVVYDAHSIRSVVPKLFDGELPNFNIGTNDGTSCAPALTQAV
Sbjct: 121 YHTALAIQIERLRAIHPAIVVYDAHSIRSVVPKLFDGELPNFNIGTNDGTSCAPALTQAV 180

Query: 181 EAICDASPYSRVTNGRFKGGWITRHYARPAGGVHSIQMELAMRTYLVETPAHWPPPWHEE 240
           EAICDASPYSRVTNGRFKGGWITRHYARPAGGVHSIQMELAMRTYLVETPAHWPPPWHEE
Sbjct: 181 EAICDASPYSRVTNGRFKGGWITRHYARPAGGVHSIQMELAMRTYLVETPAHWPPPWHEE 240

Query: 241 TAQACQSVLRPILSAAIDFAKAPK 264
           TAQACQSVLRPILSAAIDFAKAPK
Sbjct: 241 TAQACQSVLRPILSAAIDFAKAPK 264


Lambda     K      H
   0.321    0.136    0.426 

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: 382
Number of extensions: 8
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: 264
Length of database: 264
Length adjustment: 25
Effective length of query: 239
Effective length of database: 239
Effective search space:    57121
Effective search space used:    57121
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 Ga0059261_3962 Ga0059261_3962 (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.1019.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-116  374.1   0.0   2.1e-116  373.9   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3962  Ga0059261_3962 N-formylglutamate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3962  Ga0059261_3962 N-formylglutamate amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.9   0.0  2.1e-116  2.1e-116       3     262 ..       2     261 ..       1     262 [. 0.99

  Alignments for each domain:
  == domain 1  score: 373.9 bits;  conditional E-value: 2.1e-116
                                 TIGR02017   3 levqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidv 71 
                                               ++v++G+aPl++s+Ph+Gt ++ +++ +lvs+ +a+ d+d ++++ly+far l at+vr+++sr+vidv
  lcl|FitnessBrowser__Korea:Ga0059261_3962   2 IHVEQGSAPLIVSVPHAGTVIPADIQ-GLVSPELARYDADLYVDHLYAFARGLDATIVRTTVSRTVIDV 69 
                                               789********************995.8***************************************** PP

                                 TIGR02017  72 nrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgk 140
                                               nrdpsg++lypgq ttgl+P +tfdg+ply+ G  P+++ei++r++++f+Pyh+al+ +ierlra+h+ 
  lcl|FitnessBrowser__Korea:Ga0059261_3962  70 NRDPSGQTLYPGQFTTGLCPIQTFDGTPLYEPGALPDAHEIERRRAEWFDPYHTALAIQIERLRAIHPA 138
                                               ********************************************************************* PP

                                 TIGR02017 141 ivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhy 209
                                               iv+ydahsirsv+P+lf+G+lP+fn+Gtndg sc+pal++avea+c+ a+ +s+v+nGrfkGG+itrhy
  lcl|FitnessBrowser__Korea:Ga0059261_3962 139 IVVYDAHSIRSVVPKLFDGELPNFNIGTNDGTSCAPALTQAVEAICD-ASPYSRVTNGRFKGGWITRHY 206
                                               ***********************************************.********************* PP

                                 TIGR02017 210 gqPqngvhavqlelaqrgylee..etePvaydeakaealravlkellealldfae 262
                                               ++P+ gvh++q+ela r+yl e    +P +++e++a+a + vl+ +l+a++dfa+
  lcl|FitnessBrowser__Korea:Ga0059261_3962 207 ARPAGGVHSIQMELAMRTYLVEtpAHWPPPWHEETAQACQSVLRPILSAAIDFAK 261
                                               ********************998889***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (264 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: 00:00:00.03
# Mc/sec: 1.98
//
[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