Alignments for a candidate for hutG' in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Sinorhizobium meliloti 1021

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate SM_b21164 SM_b21164 formiminoglutamase

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



>FitnessBrowser__Smeli:SM_b21164
          Length = 271

 Score =  555 bits (1429), Expect = e-163
 Identities = 271/271 (100%), Positives = 271/271 (100%)

Query: 1   MAVFEVRQGSSPVILGFPHTGTDVPASIRERLNDNGRILADTDWHIHDLYQGLLPDATAV 60
           MAVFEVRQGSSPVILGFPHTGTDVPASIRERLNDNGRILADTDWHIHDLYQGLLPDATAV
Sbjct: 1   MAVFEVRQGSSPVILGFPHTGTDVPASIRERLNDNGRILADTDWHIHDLYQGLLPDATAV 60

Query: 61  RATFHRYVIDANRDPAGVSLYPGQNTTGLVPETDFDGLPIWKEGEGPTEVDITERLRDFH 120
           RATFHRYVIDANRDPAGVSLYPGQNTTGLVPETDFDGLPIWKEGEGPTEVDITERLRDFH
Sbjct: 61  RATFHRYVIDANRDPAGVSLYPGQNTTGLVPETDFDGLPIWKEGEGPTEVDITERLRDFH 120

Query: 121 APYHAALSAEIARVKAIHGVVVLYDCHSIRSHIPFLFEGRLPDFNIGTDMGKTCATEIER 180
           APYHAALSAEIARVKAIHGVVVLYDCHSIRSHIPFLFEGRLPDFNIGTDMGKTCATEIER
Sbjct: 121 APYHAALSAEIARVKAIHGVVVLYDCHSIRSHIPFLFEGRLPDFNIGTDMGKTCATEIER 180

Query: 181 AAAEIAAGAECYSHILNGRFKGGWTTRHYGRPEQGVHAIQMELAQSTHLATEAPPFALDR 240
           AAAEIAAGAECYSHILNGRFKGGWTTRHYGRPEQGVHAIQMELAQSTHLATEAPPFALDR
Sbjct: 181 AAAEIAAGAECYSHILNGRFKGGWTTRHYGRPEQGVHAIQMELAQSTHLATEAPPFALDR 240

Query: 241 AKADRLRRPLKAILERIETVAKELKRTGSEA 271
           AKADRLRRPLKAILERIETVAKELKRTGSEA
Sbjct: 241 AKADRLRRPLKAILERIETVAKELKRTGSEA 271


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: 396
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: 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 SM_b21164 SM_b21164 (formiminoglutamase)
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.14115.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.3e-118  381.1   0.0   1.5e-118  381.0   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21164  SM_b21164 formiminoglutamase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21164  SM_b21164 formiminoglutamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.0   0.0  1.5e-118  1.5e-118       2     262 ..       3     262 ..       2     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 381.0 bits;  conditional E-value: 1.5e-118
                            TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidvnrdp 75 
                                          ++ev++G++P+++++PhtGtd++ ++++rl+++ ++l+dtdWhi+ ly+++    at vra+++r+vid+nrdp
  lcl|FitnessBrowser__Smeli:SM_b21164   3 VFEVRQGSSPVILGFPHTGTDVPASIRERLNDNGRILADTDWHIHDLYQGLLPD-ATAVRATFHRYVIDANRDP 75 
                                          5789**********************************************9987.9****************** PP

                            TIGR02017  76 sgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgkivlydahsi 149
                                          +g+slypgq+ttgl+Pet+fdg p++k+Ge P+e +i++rl  ++ Pyhaal aei+r++a+hg++vlyd+hsi
  lcl|FitnessBrowser__Smeli:SM_b21164  76 AGVSLYPGQNTTGLVPETDFDGLPIWKEGEGPTEVDITERLRDFHAPYHAALSAEIARVKAIHGVVVLYDCHSI 149
                                          ************************************************************************** PP

                            TIGR02017 150 rsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhygqPqngvhavqlel 223
                                          rs+iP+lfeG+lPdfn+Gt++gk+c+  ++ a+++++a a+ +s++lnGrfkGG++trhyg+P++gvha+q+el
  lcl|FitnessBrowser__Smeli:SM_b21164 150 RSHIPFLFEGRLPDFNIGTDMGKTCATEIERAAAEIAAGAECYSHILNGRFKGGWTTRHYGRPEQGVHAIQMEL 223
                                          ************************************************************************** PP

                            TIGR02017 224 aqrgyleeetePvaydeakaealravlkellealldfae 262
                                          aq+++l+ e+ P+a d aka+ lr  lk +le+++++a+
  lcl|FitnessBrowser__Smeli:SM_b21164 224 AQSTHLATEAPPFALDRAKADRLRRPLKAILERIETVAK 262
                                          ***********************************9997 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 10.57
//
[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