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_0593 N515DRAFT_0593 glucokinase

Query= curated2:Q2W5F9
         (321 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0593
          Length = 353

 Score =  208 bits (530), Expect = 1e-58
 Identities = 123/323 (38%), Positives = 175/323 (54%), Gaps = 8/323 (2%)

Query: 6   LVADIGGTHARFALMGPDGEAVNPVVL------RCADYDGPAPAIKAYLAEHAGGVAPKG 59
           L AD+GGTHAR  L+    +   PV +       CA++      +K ++++  G V    
Sbjct: 21  LAADVGGTHARIGLVSQRPDGARPVTVLQYHRYACAEWPSLTAVLKDFVSQLGGAVQVDQ 80

Query: 60  GAFAVASVIDGDRIELTNSPWRFSIAETRQAVGLQRLEVVNDFTAVALSVRHLKPEHLMS 119
            A A A  + GD I   N PW  SI + R ++G++RL VVNDF AVA + + L       
Sbjct: 81  CAVASAGYVLGDAIVNDNLPWPVSIRDIRDSLGIERLAVVNDFEAVAYATQFLVHADTTP 140

Query: 120 VGGGMPEAGL-PIAVLGPGTGLGVSALIPSASGEWTALATEGGHVTMAAATEREARILDR 178
           V       G+ P+ V+GPGTGLG + L+P      T LATE G + ++   ERE  IL  
Sbjct: 141 VIEAQTPGGVGPVLVMGPGTGLGSAVLLPGKPHA-TVLATEAGQIALSPGNEREIEILRV 199

Query: 179 LRTQFDHVSAERVLSGQGLVNLYQAVAALSGHQAVFSTPDVITKRGLDGSCPVSREAVEV 238
           L  +  +VS E  LSG GL+NLY+A+  L G   V + P  IT+  LD S   + EA+EV
Sbjct: 200 LAGERPYVSFEHALSGPGLLNLYRALCVLRGQSPVLAKPSEITRAALDASDAAAVEALEV 259

Query: 239 FFAMMGTVAGNLALSLGAKGGVFIAGGILPRMAEAFRLSSFRTRFEAHGRFQPYLAAIPT 298
           F  ++G+  G+L L  GA+GGVF+AGGILP++ +    SSFR RF   G  + +L  +P 
Sbjct: 260 FCGLLGSFVGDLTLLYGARGGVFLAGGILPQIRDVLLTSSFRERFFNKGVMRAFLQQVPV 319

Query: 299 WLITHPLPAFVGLAGLVTDPKNA 321
            L+ H     +G AG+  +   A
Sbjct: 320 RLMEHGQLGVIGAAGMYLEGHTA 342


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: 379
Number of extensions: 22
Number of successful extensions: 4
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: 353
Length adjustment: 28
Effective length of query: 293
Effective length of database: 325
Effective search space:    95225
Effective search space used:    95225
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: 49 (23.5 bits)

Align candidate N515DRAFT_0593 N515DRAFT_0593 (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.9774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    9.2e-72  227.9   0.0    1.1e-71  227.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0593  N515DRAFT_0593 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0593  N515DRAFT_0593 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.7   0.0   1.1e-71   1.1e-71       1     315 []      21     333 ..      21     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 1.1e-71
                                    TIGR00749   1 lvgdiGGtnarlalvevapgeieqv.....ktyssedfpsleavvrvyleeakvelkdpikgcfai 61 
                                                  l++d+GGt+ar++lv   p  +++v     + y + ++psl+av++ + ++    ++   + ++a 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0593  21 LAADVGGTHARIGLVSQRPDGARPVtvlqyHRYACAEWPSLTAVLKDFVSQLGGAVQV-DQCAVAS 85 
                                                  79*************999999999988877889*****************98777765.46889** PP

                                    TIGR00749  62 atPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedli.qlggakveesa 126
                                                  a+ ++gd +   nl W +si +++ +l++++l ++ndf avaya + l + d + ++++  +   +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0593  86 AGYVLGDAIVNDNLPWPVSIRDIRDSLGIERLAVVNDFEAVAYATQFLVHADTTpVIEAQTPGGVG 151
                                                  ***********************************************999888747888899999* PP

                                    TIGR00749 127 aiailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGs 192
                                                  ++ ++G+GtGlG a l++ ++ +  vla+e g + ++P +e ei +l++l  +   vs e  lsG+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 152 PVLVMGPGTGLGSAVLLP-GKPHATVLATEAGQIALSPGNEREIEILRVLAGERPYVSFEHALSGP 216
                                                  ******************.9999******************************************* PP

                                    TIGR00749 193 GlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklg 258
                                                  Gl ++y+al   +g+  v        k+ +i++aal+ sd+ a +ale+f+++lG++ g+l+l  g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 217 GLLNLYRALCVLRGQSPV------LAKPSEITRAALDASDAAAVEALEVFCGLLGSFVGDLTLLYG 276
                                                  *********998865443......35999************************************* PP

                                    TIGR00749 259 arGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                                  arGGv++aGGi+P++ + l +ssfr++f +kG ++++l+++Pv+++ + + G++Ga+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 277 ARGGVFLAGGILPQIRDVLLTSSFRERFFNKGVMRAFLQQVPVRLMEHGQLGVIGAA 333
                                                  *******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (353 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.27
//
[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