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_4210 N515DRAFT_4210 glucokinase

Query= curated2:B4SRZ6
         (335 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4210
          Length = 339

 Score =  326 bits (835), Expect = 6e-94
 Identities = 170/326 (52%), Positives = 219/326 (67%), Gaps = 6/326 (1%)

Query: 2   SASSQPVLVADIGGTNARFALADTSLDAPLQQDSIREYAVAEFPSLGDAARHHLEQIGAT 61
           S SS   L+AD+GGTN RFALAD +L  PL  DS+R Y V +FPS+ D  R +    G +
Sbjct: 3   STSSAKTLLADLGGTNVRFALADPALPQPLLLDSVRRYRVKDFPSMADTIRQYFADSGLS 62

Query: 62  ASRGVFAVAGR-VDGDEARITNHPWVISRSRTAAMLGFDELHLINDFAAQAMAISLLQSD 120
           A R V A AGR VDG+  ++TN+PW +S    AA L FD + LINDFAAQ MA+ LL  +
Sbjct: 63  AGRAVIAAAGRIVDGETVKVTNNPWQVSAHGLAADLKFDSVRLINDFAAQGMAVPLLACN 122

Query: 121 DVVQVGGAAWVPGKPG--QPRNYAVIGPGTGLGVGGLILRHGRCYPLETEGGHVSFPPGT 178
           ++  VG     P K G    + + V+GPGTGLGV GL+LR GR   LETEGGH  F   T
Sbjct: 123 ELQPVGAPQ--PPKIGAHHSQTFVVVGPGTGLGVAGLLLRDGRWTVLETEGGHAGFAAHT 180

Query: 179 PEEIRILEILSEQFGRVSNERLICGPGLVNIHRAVCEMAGIDPGQLQPVDVTARALHG-D 237
            E++ IL  L+ +FGRVSNER+ICG GLVN++ A+ ++ G+   +  P D+T RA  G D
Sbjct: 181 AEDVEILHRLNARFGRVSNERMICGNGLVNLYLALADIEGLKAEEYTPEDITTRANAGTD 240

Query: 238 PQAMRTVDVFCAVFGAIAGDLVLTQGAWDGVFLTGGLTPKMLDSLQHSGFRQRFEHKGRF 297
           P  +RTV+    +FG++AGDLVL+ G WDGVFLTGG+ P +L  LQH GFR+RFE KGRF
Sbjct: 241 PLCVRTVETLAGIFGSVAGDLVLSLGGWDGVFLTGGVLPILLPWLQHGGFRERFESKGRF 300

Query: 298 SSIMARVPSLAVMHPHAGLLGAAAYA 323
              M +VP++A+MH   GLLGAAA+A
Sbjct: 301 KETMEQVPTVAMMHAETGLLGAAAFA 326


Lambda     K      H
   0.321    0.137    0.414 

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: 323
Number of extensions: 15
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: 335
Length of database: 339
Length adjustment: 28
Effective length of query: 307
Effective length of database: 311
Effective search space:    95477
Effective search space used:    95477
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_4210 N515DRAFT_4210 (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.25764.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    8.8e-82  260.8   0.0      1e-81  260.6   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_4210  N515DRAFT_4210 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4210  N515DRAFT_4210 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.6   0.0     1e-81     1e-81       1     315 []      10     323 ..      10     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: 260.6 bits;  conditional E-value: 1e-81
                                    TIGR00749   1 lvgdiGGtnarlalveva...pgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiat 63 
                                                  l++d+GGtn r+al + a   p ++++v+ y+ +dfps+ + +r+y  ++  + +    + +a a+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4210  10 LLADLGGTNVRFALADPAlpqPLLLDSVRRYRVKDFPSMADTIRQYFADSGLSAGR---AVIAAAG 72 
                                                  79*************8764346789999*************************999...99***** PP

                                    TIGR00749  64 Piig.dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakv.....e 123
                                                   i++ ++v++tn+ W++s + l+ +l +  + lindfaa+++a++ l  ++l  +g+ ++     +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4210  73 RIVDgETVKVTNNPWQVSAHGLAADLKFDSVRLINDFAAQGMAVPLLACNELQPVGAPQPpkigaH 138
                                                  999548*************************************************99654211215 PP

                                    TIGR00749 124 esaaiailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervl 189
                                                  +s++  ++G+GtGlGva l+   dgr+ vl +eGgh+ fa +  +++ +l+ l +++grvs er++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 139 HSQTFVVVGPGTGLGVAGLLL-RDGRWTVLETEGGHAGFAAHTAEDVEILHRLNARFGRVSNERMI 203
                                                  678889*************99.8******************************************* PP

                                    TIGR00749 190 sGsGlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlal 255
                                                   G Glv++y al   +       l+ ee +++di+ +a +g+d+l+ r++e++ +i+G++ag+l l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 204 CGNGLVNLYLALADIE------GLKAEEYTPEDITTRANAGTDPLCVRTVETLAGIFGSVAGDLVL 263
                                                  ***********98777......68889*************************************** PP

                                    TIGR00749 256 klgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                                   lg   Gv+++GG++P ++++l++++fr++fe kGr+ke ++++P   ++++++GllGa+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 264 SLGGWDGVFLTGGVLPILLPWLQHGGFRERFESKGRFKETMEQVPTVAMMHAETGLLGAA 323
                                                  **********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (339 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: 00:00:00.00
# Mc/sec: 10.73
//
[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