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_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.4931.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.69
//
[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