Alignments for a candidate for glk in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Collimonas pratensis Ter91

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_061942024.1 CPter91_RS16295 glucokinase

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



>NCBI__GCF_001584185.1:WP_061942024.1
          Length = 661

 Score =  253 bits (645), Expect = 1e-71
 Identities = 133/319 (41%), Positives = 185/319 (57%), Gaps = 7/319 (2%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYL-----EEHKVEVKDGC 60
           L+ DVGGTNAR AL + A G+I   +T    DY      +  YL     +    +V+   
Sbjct: 23  LLADVGGTNARFAL-ERAPGQIDTIQTLRCADYAEFAQAVETYLAYSATQGAHAQVRHAA 81

Query: 61  IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120
           IAIA P+ GD + MTNH WAFSI   ++ L    L ++NDFTA+SM++P L++ H +Q G
Sbjct: 82  IAIANPVQGDDIKMTNHNWAFSIENTRRRLNLDTLLVVNDFTALSMSLPHLEQAHCVQIG 141

Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180
           G   + G  + + GAGTGLGV  L+  + RW++L  EGGHV FAP    EA +L      
Sbjct: 142 GGRALSGGVVGLVGAGTGLGVGGLIPTEGRWIALGSEGGHVTFAPGDAREAAVLAYCWRT 201

Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADN-RLPENLKPKDITERALADSCTDCRRALSLFCV 239
             HVSAER++SGPG+  +Y+A+ +      PE L+   I ERAL      C   +  FC 
Sbjct: 202 YSHVSAERLVSGPGIEMIYQALAELQGIAKPEPLQTAQIVERALQGQDGLCMEVVECFCA 261

Query: 240 IMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLI 299
           ++G    ++A+ LGT GG++I GG+VPR  E+F  S FRA FE+KGRF  Y+  IP ++I
Sbjct: 262 MLGTVAADVAVTLGTLGGLYIGGGVVPRLGEYFARSPFRARFENKGRFSSYLAKIPTFVI 321

Query: 300 VHDNPGLLGSGAHLRQTLG 318
               P  +G  A L + LG
Sbjct: 322 TAPYPAFVGVAAILSEHLG 340


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: 558
Number of extensions: 34
Number of successful extensions: 3
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: 661
Length adjustment: 33
Effective length of query: 288
Effective length of database: 628
Effective search space:   180864
Effective search space used:   180864
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: 51 (24.3 bits)

Align candidate WP_061942024.1 CPter91_RS16295 (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.3690814.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-100  321.4   0.1   5.2e-100  320.7   0.1    1.3  1  NCBI__GCF_001584185.1:WP_061942024.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584185.1:WP_061942024.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.7   0.1  5.2e-100  5.2e-100       1     313 [.      23     330 ..      23     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 320.7 bits;  conditional E-value: 5.2e-100
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkd.pi.kgcfaiatPiigdfvr 71 
                                           l++d+GGtnar+al e apg+i++++t+++ d+ ++ ++v  yl  ++++  +  + ++++aia P+ gd ++
  NCBI__GCF_001584185.1:WP_061942024.1  23 LLADVGGTNARFAL-ERAPGQIDTIQTLRCADYAEFAQAVETYLAYSATQGAHaQVrHAAIAIANPVQGDDIK 94 
                                           79************.*****************************99888766635579*************** PP

                             TIGR00749  72 ltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliq 144
                                           +tn++Wa+sie++++ l l  l ++ndf+a +++++ l++ + +q+gg ++  ++ + ++GaGtGlGv  li+
  NCBI__GCF_001584185.1:WP_061942024.1  95 MTNHNWAFSIENTRRRLNLDTLLVVNDFTALSMSLPHLEQAHCVQIGGGRALSGGVVGLVGAGTGLGVGGLIP 167
                                           ************************************************************************* PP

                             TIGR00749 145 qsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskee 217
                                            ++gr+ +l +eGghv faP +  e+ +l y  + y++vsaer++sG+G+ +iy+al + +g  + +      
  NCBI__GCF_001584185.1:WP_061942024.1 168 -TEGRWIALGSEGGHVTFAPGDAREAAVLAYCWRTYSHVSAERLVSGPGIEMIYQALAELQGIAKPE-----P 234
                                           .9********************************************************999766554.....4 PP

                             TIGR00749 218 lkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkG 290
                                           l+  +i e+al+g+d l+ + +e f+++lG++a+++a++lg+ GG+y+ GG+vPr+ e++ +s+fra+fe+kG
  NCBI__GCF_001584185.1:WP_061942024.1 235 LQTAQIVERALQGQDGLCMEVVECFCAMLGTVAADVAVTLGTLGGLYIGGGVVPRLGEYFARSPFRARFENKG 307
                                           5577899****************************************************************** PP

                             TIGR00749 291 rlkellasiPvqvvlkkkvGllG 313
                                           r+ ++la+iP  v+    + ++G
  NCBI__GCF_001584185.1:WP_061942024.1 308 RFSSYLAKIPTFVITAPYPAFVG 330
                                           **************988888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (661 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: 47.66
//
[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:

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 2024 update 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