GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Paraburkholderia bryophila 376MFSha3.1

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate H281DRAFT_00163 H281DRAFT_00163 glucokinase /transcriptional regulator, RpiR family

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__Burk376:H281DRAFT_00163
          Length = 638

 Score =  262 bits (670), Expect = 1e-74
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 4/316 (1%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKV-EVKDGCIAIA 64
           L+ D+GGTNAR AL +   GEI     Y   DYP +  VI+ YL++ K+  V    IAIA
Sbjct: 22  LLADIGGTNARFAL-ETGPGEIGSVHVYPCADYPGVAEVIKKYLKDTKIGRVNHAAIAIA 80

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            P+ GD V+MTNH W+FSI   ++ LGF  L ++NDFTA++MA+P L     +Q GG   
Sbjct: 81  NPVDGDQVSMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGGGTR 140

Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184
                I + G GTG+GV+ L+  D RW++L  EGGH  FAP  E E I+L+  R +  HV
Sbjct: 141 RPNSVIGLLGPGTGMGVSGLIPADDRWIALGSEGGHATFAPADEREDIVLQYARKKWSHV 200

Query: 185 SAERVLSGPGLVNLYRAIVKAD-NRLPENLKPKDITERALADSCTDCRRALSLFCVIMGR 243
           S ERV +GPG+  +YRA+   D  R+  N+   +I +RAL         ++ +FC I+G 
Sbjct: 201 SFERVAAGPGIEVIYRALAGRDKKRVAANVDTVEIVKRALEGEPL-AAESVDVFCGILGT 259

Query: 244 FGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDN 303
           F GN+A+ LG  GG++I GG+VPR  EFF  S FR  FE KGRF+ Y+ ++P Y+I  + 
Sbjct: 260 FAGNIAVTLGALGGIYIGGGVVPRLGEFFARSSFRKRFEAKGRFEAYLQNVPTYVITAEY 319

Query: 304 PGLLGSGAHLRQTLGH 319
           P  LG  A L + L +
Sbjct: 320 PAFLGVSAILAEQLSN 335


Lambda     K      H
   0.322    0.141    0.426 

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: 578
Number of extensions: 25
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: 638
Length adjustment: 33
Effective length of query: 288
Effective length of database: 605
Effective search space:   174240
Effective search space used:   174240
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate H281DRAFT_00163 H281DRAFT_00163 (glucokinase /transcriptional regulator, RpiR family)
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.11064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.6e-101  324.5   0.0   5.6e-101  323.9   0.0    1.3  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00163  H281DRAFT_00163 glucokinase /tra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00163  H281DRAFT_00163 glucokinase /transcriptional regulator, RpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.9   0.0  5.6e-101  5.6e-101       1     313 [.      22     324 ..      22     326 .. 0.96

  Alignments for each domain:
  == domain 1  score: 323.9 bits;  conditional E-value: 5.6e-101
                                    TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPii 66 
                                                  l++diGGtnar+al e  pgei +v++y + d+p + +v++ yl+++k+   +  ++++aia P+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00163  22 LLADIGGTNARFAL-ETGPGEIGSVHVYPCADYPGVAEVIKKYLKDTKIGRVN--HAAIAIANPVD 84 
                                                  79************.*******************************9987777..8********** PP

                                    TIGR00749  67 gdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailG 132
                                                  gd v +tn+dW++sie +++ l++  l ++ndf+a a+a+++l + + +q+gg    +++ i +lG
  lcl|FitnessBrowser__Burk376:H281DRAFT_00163  85 GDQVSMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGGGTRRPNSVIGLLG 150
                                                  ****************************************************************** PP

                                    TIGR00749 133 aGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliy 198
                                                  +GtG+Gv+ li+ +d+r+ +l +eGgh+ faP +e e ++l+y+rkk+++vs erv +G+G+ +iy
  lcl|FitnessBrowser__Burk376:H281DRAFT_00163 151 PGTGMGVSGLIP-ADDRWIALGSEGGHATFAPADEREDIVLQYARKKWSHVSFERVAAGPGIEVIY 215
                                                  ************.9**************************************************** PP

                                    TIGR00749 199 ealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvy 264
                                                  +al  r+     +k   ++    +i ++aleg+ +la +++++f++ilG++agn+a++lga GG+y
  lcl|FitnessBrowser__Burk376:H281DRAFT_00163 216 RALAGRD-----KKRVAANVDTVEIVKRALEGE-PLAAESVDVFCGILGTFAGNIAVTLGALGGIY 275
                                                  *****99.....33334677788999*****97.788899************************** PP

                                    TIGR00749 265 vaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313
                                                  + GG+vPr+ e++ +ssfr++fe kGr++++l+++P +v+  + + +lG
  lcl|FitnessBrowser__Burk376:H281DRAFT_00163 276 IGGGVVPRLGEFFARSSFRKRFEAKGRFEAYLQNVPTYVITAEYPAFLG 324
                                                  *****************************************99998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (638 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: 17.59
//
[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