GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Marinobacter adhaerens HP15

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate GFF2219 HP15_2173 glucokinase

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



>FitnessBrowser__Marino:GFF2219
          Length = 321

 Score =  254 bits (649), Expect = 2e-72
 Identities = 136/313 (43%), Positives = 185/313 (59%), Gaps = 1/313 (0%)

Query: 2   TKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDG-C 60
           T Y+LVGD+GGTNAR AL +  + +    K     +Y +L+  +R YL    V   DG C
Sbjct: 4   THYSLVGDIGGTNARFALVEQGTVQPRAIKILPCGEYANLDDAVRDYLARVGVSEVDGAC 63

Query: 61  IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120
           +A+A P+ G  V MTN+ W F   E++   G+S  ++INDFTA+++ +P +  +HL+   
Sbjct: 64  LAVASPVRGTQVRMTNNHWLFDTEEVRAQFGWSRFKVINDFTAMALGVPHVANDHLVHVC 123

Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180
           G      +P  V G GTGLGV+ LV ++  WV L  EGGHVDFAP  + E  +L IL+A 
Sbjct: 124 GGPGDSRRPRLVMGPGTGLGVSGLVPIEHGWVPLMTEGGHVDFAPTDDAEMAVLRILKAR 183

Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240
            G VS ER+L G GL+NLY+A  +          P+ IT  A+ ++    R  LS FC I
Sbjct: 184 FGRVSVERILCGQGLLNLYQAHAEIQGVAAPLDAPEKITAAAVENTDRLARHTLSHFCEI 243

Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300
           +GR  GN  L LG+ GGVF+ GGI+PRFLEFF  S FR  FEDKGR +  +   PVY++ 
Sbjct: 244 LGRVAGNGVLTLGSTGGVFLCGGILPRFLEFFLESPFRNGFEDKGRMRPLLEFTPVYVVT 303

Query: 301 HDNPGLLGSGAHL 313
               GLLG+   L
Sbjct: 304 EPYTGLLGAAEAL 316


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: 320
Number of extensions: 13
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: 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 GFF2219 HP15_2173 (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.9486.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    1.8e-98  315.7   0.0    2.1e-98  315.5   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2219  HP15_2173 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2219  HP15_2173 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.5   0.0   2.1e-98   2.1e-98       1     315 []       8     313 ..       8     313 .. 0.96

  Alignments for each domain:
  == domain 1  score: 315.5 bits;  conditional E-value: 2.1e-98
                           TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltnl 75 
                                         lvgdiGGtnar+alve  + + +++k++ + ++ +l ++vr yl +  v+  d   +c+a+a+P+ g  vr+tn+
  lcl|FitnessBrowser__Marino:GFF2219   8 LVGDIGGTNARFALVEQGTVQPRAIKILPCGEYANLDDAVRDYLARVGVSEVD--GACLAVASPVRGTQVRMTNN 80 
                                         89******************************************998887666..7******************* PP

                           TIGR00749  76 dWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgry 150
                                         +W +  ee++ +++ ++ ++indf+a+a++++ + +++l+ + g + +   +  ++G+GtGlGv+ l++  +  +
  lcl|FitnessBrowser__Marino:GFF2219  81 HWLFDTEEVRAQFGWSRFKVINDFTAMALGVPHVANDHLVHVCGGPGDSRRPRLVMGPGTGLGVSGLVP-IEHGW 154
                                         *********************************************************************.9999* PP

                           TIGR00749 151 kvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdise 225
                                         + l +eGghvdfaP+++ e+ +l++l++++grvs+er+l G+Gl ++y+a  + +g      +      +++i+ 
  lcl|FitnessBrowser__Marino:GFF2219 155 VPLMTEGGHVDFAPTDDAEMAVLRILKARFGRVSVERILCGQGLLNLYQAHAEIQG------VAAPLDAPEKITA 223
                                         ************************************************99666553......3334458999*** PP

                           TIGR00749 226 aalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiP 300
                                         aa+e++d lar++l+ f+ ilG++agn  l+lg+ GGv+++GGi+Prf+e++ +s+fr++fedkGr++ ll+  P
  lcl|FitnessBrowser__Marino:GFF2219 224 AAVENTDRLARHTLSHFCEILGRVAGNGVLTLGSTGGVFLCGGILPRFLEFFLESPFRNGFEDKGRMRPLLEFTP 298
                                         *************************************************************************** PP

                           TIGR00749 301 vqvvlkkkvGllGag 315
                                         v+vv +  +GllGa+
  lcl|FitnessBrowser__Marino:GFF2219 299 VYVVTEPYTGLLGAA 313
                                         *************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.08
//
[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