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

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.4598.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.95
//
[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