Alignments for a candidate for glk in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Burkholderia phytofirmans PsJN

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate BPHYT_RS05010 BPHYT_RS05010 RpiR family transcriptional regulator

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



>FitnessBrowser__BFirm:BPHYT_RS05010
          Length = 638

 Score =  261 bits (668), Expect = 2e-74
 Identities = 138/316 (43%), Positives = 192/316 (60%), Gaps = 4/316 (1%)

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

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            P+ GD V+MTNH W+FSI   ++ LGF  L ++NDFTA++MA+P L     +Q G    
Sbjct: 81  NPVDGDQVSMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGVGAR 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 SFERVAAGPGIEVIYRALAGRDKKRVAANVDTIEIVKRALEGEPL-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 FAGNIAVTLGALGGIYIGGGVVPRLGEFFSRSSFRKRFEAKGRFEAYLQNVPTYVITAEY 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: 562
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 BPHYT_RS05010 BPHYT_RS05010 (RpiR family transcriptional regulator)
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.1603.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.6e-101  325.0   0.0     4e-101  324.4   0.0    1.3  1  lcl|FitnessBrowser__BFirm:BPHYT_RS05010  BPHYT_RS05010 RpiR family transc


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS05010  BPHYT_RS05010 RpiR family transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.4   0.0    4e-101    4e-101       1     313 [.      22     324 ..      22     326 .. 0.96

  Alignments for each domain:
  == domain 1  score: 324.4 bits;  conditional E-value: 4e-101
                                TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfv 70 
                                              l++diGGtnar+al e +pgei +vk+y + d+p + +v++ yl+++k+   +  ++++aia P+ gd v
  lcl|FitnessBrowser__BFirm:BPHYT_RS05010  22 LLADIGGTNARFAL-ETSPGEIGSVKVYPCADYPGVAEVIKKYLKDTKIGRVN--HAAIAIANPVDGDQV 88 
                                              79************.*******************************9987777..8************** PP

                                TIGR00749  71 rltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGva 140
                                               +tn+dW++sie +++ l++  l ++ndf+a a+a+++l + + +q+g     +++ i +lG+GtG+Gv+
  lcl|FitnessBrowser__BFirm:BPHYT_RS05010  89 SMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGVGARRPNSVIGLLGPGTGMGVS 158
                                              ********************************************************************** PP

                                TIGR00749 141 tliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerev 210
                                               li+ +d+r+ +l +eGgh+ faP +e e ++l+y+rkk+++vs erv +G+G+ +iy+al  r+     
  lcl|FitnessBrowser__BFirm:BPHYT_RS05010 159 GLIP-ADDRWIALGSEGGHATFAPADEREDIVLQYARKKWSHVSFERVAAGPGIEVIYRALAGRD----- 222
                                              ****.9*********************************************************99..... PP

                                TIGR00749 211 sklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkks 280
                                              +k   ++    +i ++aleg+ +la +++++f++ilG++agn+a++lga GG+y+ GG+vPr+ e++ +s
  lcl|FitnessBrowser__BFirm:BPHYT_RS05010 223 KKRVAANVDTIEIVKRALEGE-PLAAESVDVFCGILGTFAGNIAVTLGALGGIYIGGGVVPRLGEFFSRS 291
                                              33334677788899*****97.788899****************************************** PP

                                TIGR00749 281 sfraafedkGrlkellasiPvqvvlkkkvGllG 313
                                              sfr++fe kGr++++l+++P +v+  + + +lG
  lcl|FitnessBrowser__BFirm:BPHYT_RS05010 292 SFRKRFEAKGRFEAYLQNVPTYVITAEYPAFLG 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: 17.12
//
[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