GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Dyella japonica UNC79MFTsu3.2

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate N515DRAFT_0393 N515DRAFT_0393 glucokinase

Query= curated2:Q2W5F9
         (321 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0393
          Length = 333

 Score =  211 bits (538), Expect = 2e-59
 Identities = 128/317 (40%), Positives = 180/317 (56%), Gaps = 8/317 (2%)

Query: 3   QMVLVADIGGTHARFALMGPDGEAVNPVVLRC-----ADYDGPAPAIKAYLAEHAGGVAP 57
           ++VL AD+GGTHAR  L+     A    VL       AD+ G A  +  +LA H G    
Sbjct: 14  KLVLAADVGGTHARIGLVDAAAPAGASGVLAYERYAGADWPGLAEILADFLARHPGHAVD 73

Query: 58  KGGAFAVASVIDGDRIELTNSPWRFSIAETRQAVGLQRLEVVNDFTAVALSVRHLKPEHL 117
           +  A AVA  +    +   N  W   +AE R+ + L+RL+VVNDF A+A + ++L  +  
Sbjct: 74  EA-AIAVAGYVRDGELVAENLRWPVRLAELRERLRLRRLQVVNDFEALAFATQYLGADDS 132

Query: 118 MSVGGGMPEAGLPIAVLGPGTGLGVSALIPSASGEWTALATEGGHVTMAAATEREARILD 177
           ++V      AG P+AV+GPGTGLG + L+P  +G  T L +EGGHV +A  +ERE  +L 
Sbjct: 133 LAVIDAPAAAG-PVAVVGPGTGLGCALLVPDGNGV-TVLPSEGGHVALAPGSEREMALLQ 190

Query: 178 RLRTQFDHVSAERVLSGQGLVNLYQAVAALSGHQAVFSTPDVITKRGLDGSCPVSREAVE 237
            L    D+V    VLSG GLVNLY+A+  L G  AV + P+ I+   LDG   ++ + + 
Sbjct: 191 LLSRGRDYVHTGHVLSGPGLVNLYRAIGELDGLSAVHAQPEQISAAALDGGDALALDTLH 250

Query: 238 VFFAMMGTVAGNLALSLGAKGGVFIAGGILPRMAEAFRLSSFRTRFEAHGRFQPYLAAIP 297
            F AM+G   G+LA+   A GGVF+AGGILP++ E    S+FR RF   G  + +LA +P
Sbjct: 251 TFCAMLGGFVGDLAVLFKASGGVFLAGGILPQLREFLPYSAFRERFFNKGVMRDFLAGVP 310

Query: 298 TWLITHPLPAFVGLAGL 314
             LI H     +G AGL
Sbjct: 311 VRLIEHGRLGVLGAAGL 327


Lambda     K      H
   0.320    0.136    0.403 

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: 370
Number of extensions: 18
Number of successful extensions: 5
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: 333
Length adjustment: 28
Effective length of query: 293
Effective length of database: 305
Effective search space:    89365
Effective search space used:    89365
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: 48 (23.1 bits)

Align candidate N515DRAFT_0393 N515DRAFT_0393 (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.6772.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
      2e-74  236.7   0.1    2.3e-74  236.4   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0393  N515DRAFT_0393 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0393  N515DRAFT_0393 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.4   0.1   2.3e-74   2.3e-74       1     315 []      17     325 ..      17     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: 236.4 bits;  conditional E-value: 2.3e-74
                                    TIGR00749   1 lvgdiGGtnarlalvev.apgeieqv...ktyssedfpsleavvrvyleeakvelkdpikgcfaia 62 
                                                  l++d+GGt+ar++lv+  ap  ++ v   + y + d+p l +++  +l ++  +  d  ++++a+a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0393  17 LAADVGGTHARIGLVDAaAPAGASGVlayERYAGADWPGLAEILADFLARHPGHAVD--EAAIAVA 80 
                                                  79*************7516788888888899*******************9887777..7****** PP

                                    TIGR00749  63 tPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeed.liqlggakveesaa 127
                                                  + + +      nl W +  +el++ l l++l+++ndf a a+a + l+ +d l+++++  +  +++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0393  81 GYVRDGELVAENLRWPVRLAELRERLRLRRLQVVNDFEALAFATQYLGADDsLAVIDA--PAAAGP 144
                                                  *******99**************************************98873666665..45789* PP

                                    TIGR00749 128 iailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsG 193
                                                  +a++G+GtGlG a l+++++g   vl++eGghv +aP se e+ ll++l +  + v    vlsG+G
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0393 145 VAVVGPGTGLGCALLVPDGNG-VTVLPSEGGHVALAPGSEREMALLQLLSRGRDYVHTGHVLSGPG 209
                                                  *****************8887.689***************************************** PP

                                    TIGR00749 194 lvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklga 259
                                                  lv++y+a+ + +       ls  + ++++is aal+g d+la  +l++f+++lG + g+la+ + a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0393 210 LVNLYRAIGELD------GLSAVHAQPEQISAAALDGGDALALDTLHTFCAMLGGFVGDLAVLFKA 269
                                                  ********9888......567777999*************************************** PP

                                    TIGR00749 260 rGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                                   GGv++aGGi+P++ e+l  s+fr++f +kG ++++la +Pv+++ + + G+lGa+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0393 270 SGGVFLAGGILPQLREFLPYSAFRERFFNKGVMRDFLAGVPVRLIEHGRLGVLGAA 325
                                                  ******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (333 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: 7.91
//
[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