GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Cronobacter condimenti 1330

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_007667267.1 BN137_RS14745 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>NCBI__GCF_000319285.1:WP_007667267.1
          Length = 321

 Score =  583 bits (1503), Expect = e-171
 Identities = 286/321 (89%), Positives = 297/321 (92%)

Query: 1   MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGC 60
           MTKYALVGDVGGTNARLALCD+ SGEI +AKTYSGLDYPSLEAV+RVYL+EH   V DGC
Sbjct: 1   MTKYALVGDVGGTNARLALCDVDSGEILKAKTYSGLDYPSLEAVVRVYLDEHNATVTDGC 60

Query: 61  IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120
           IAIACPITGDWVAMTNH WAFSIAEMKKNLGF+HLEIINDFTAVSMAIPMLK EHLIQFG
Sbjct: 61  IAIACPITGDWVAMTNHVWAFSIAEMKKNLGFAHLEIINDFTAVSMAIPMLKTEHLIQFG 120

Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180
           G E    KPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIIL+ LRAE
Sbjct: 121 GGEAQPNKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILDQLRAE 180

Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240
           +GHVSAERVLSGPGLVNLYRAIVKAD RLPENL+PKDITERAL DSCTDCRRALSLFCVI
Sbjct: 181 VGHVSAERVLSGPGLVNLYRAIVKADGRLPENLRPKDITERALDDSCTDCRRALSLFCVI 240

Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300
           MGRFGGNLAL LGTFGGV+IAGGIVPRFL+FF ASGFR  FEDKGRFK YV DIPVYLIV
Sbjct: 241 MGRFGGNLALTLGTFGGVYIAGGIVPRFLDFFTASGFRGGFEDKGRFKAYVQDIPVYLIV 300

Query: 301 HDNPGLLGSGAHLRQTLGHIL 321
           HD PGLLG+GAHLRQTLG IL
Sbjct: 301 HDQPGLLGAGAHLRQTLGQIL 321


Lambda     K      H
   0.322    0.141    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: 512
Number of extensions: 11
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: 321
Length of database: 321
Length adjustment: 28
Effective length of query: 293
Effective length of database: 293
Effective search space:    85849
Effective search space used:    85849
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_007667267.1 BN137_RS14745 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

# 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/TIGR00749.hmm
# target sequence database:        /tmp/gapView.1278708.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00749  [M=315]
Accession:   TIGR00749
Description: glk: glucokinase
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-151  490.3   0.0   1.4e-151  490.1   0.0    1.0  1  NCBI__GCF_000319285.1:WP_007667267.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000319285.1:WP_007667267.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.1   0.0  1.4e-151  1.4e-151       1     315 []       6     310 ..       6     310 .. 1.00

  Alignments for each domain:
  == domain 1  score: 490.1 bits;  conditional E-value: 1.4e-151
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 
                                           lvgd+GGtnarlal++v +gei ++ktys++d+psleavvrvyl+e++ ++ d   gc+aia+Pi+gd+v++t
  NCBI__GCF_000319285.1:WP_007667267.1   6 LVGDVGGTNARLALCDVDSGEILKAKTYSGLDYPSLEAVVRVYLDEHNATVTD---GCIAIACPITGDWVAMT 75 
                                           89***************************************************...***************** PP

                             TIGR00749  74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146
                                           n+ Wa+si+e+k++l++a+le+indf+av++ai++lk e+liq+gg +++++++ia++GaGtGlGva+l++ +
  NCBI__GCF_000319285.1:WP_007667267.1  76 NHVWAFSIAEMKKNLGFAHLEIINDFTAVSMAIPMLKTEHLIQFGGGEAQPNKPIAVYGAGTGLGVAHLVH-V 147
                                           ***********************************************************************.* PP

                             TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219
                                           d+r+++l+geGghvdfaP+se+e+++l+ lr+++g+vsaervlsG+Glv++y+a++k++      +l+ e+l+
  NCBI__GCF_000319285.1:WP_007667267.1 148 DKRWVSLPGEGGHVDFAPNSEEEAIILDQLRAEVGHVSAERVLSGPGLVNLYRAIVKAD-----GRLP-ENLR 214
                                           ***********************************************************.....89**.9*** PP

                             TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292
                                           +kdi+e+al++s++++rral+lf++i+G+++gnlal+lg++GGvy+aGGivPrf++++ +s+fr +fedkGr+
  NCBI__GCF_000319285.1:WP_007667267.1 215 PKDITERALDDSCTDCRRALSLFCVIMGRFGGNLALTLGTFGGVYIAGGIVPRFLDFFTASGFRGGFEDKGRF 287
                                           ************************************************************************* PP

                             TIGR00749 293 kellasiPvqvvlkkkvGllGag 315
                                           k+++++iPv++++++++GllGag
  NCBI__GCF_000319285.1:WP_007667267.1 288 KAYVQDIPVYLIVHDQPGLLGAG 310
                                           *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (321 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: 17.86
//
[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:

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