Alignments for a candidate for glk in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Acidovorax sp. GW101-3H11

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate Ac3H11_2067 Glucokinase (EC 2.7.1.2)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2067
          Length = 325

 Score =  227 bits (579), Expect = 3e-64
 Identities = 127/298 (42%), Positives = 177/298 (59%), Gaps = 4/298 (1%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEV-KDGCIAIA 64
           L+ D+GGTN RLA     +G ++  +      +P+++A +  YL+E  V   ++    IA
Sbjct: 6   LLADIGGTNIRLAWQASPTGPLNDTRVLPCAQFPTVDAALAAYLQEVGVPTPREAAFGIA 65

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            P+TGD + MTNH+W+FS   +++  GF  L +INDFTA+++A+P+L  E L   GG   
Sbjct: 66  NPVTGDAIRMTNHSWSFSQRAVREAFGFERLVVINDFTALALALPLLTPEQLRPVGGGAA 125

Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLP--GEGGHVDFAPNSEEEAIILEILRAEIG 182
           V G  IA+ G GTGLGV+ LV      + +P  GEGGHV  A  ++ E  +L IL+   G
Sbjct: 126 VPGAAIALLGPGTGLGVSGLVFPPGSHLGVPLSGEGGHVTLAAQTQREFDVLAILQERYG 185

Query: 183 HVSAERVLSGPGLVNLYRAIVKADNRLPENL-KPKDITERALADSCTDCRRALSLFCVIM 241
           HVSAER + G GLV+LY A+ +   R  + +     +TE AL  +      AL LFC  +
Sbjct: 186 HVSAERAVCGAGLVDLYHALRRLAQRGGKEISSAAQVTELALQANDPLALEALELFCGFL 245

Query: 242 GRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLI 299
           G   GNLAL LG  GGVFI GG+VPR   +F  S FRA FE KGRF+ Y+  IP ++I
Sbjct: 246 GSVAGNLALTLGARGGVFIGGGMVPRLGAWFDQSPFRARFESKGRFQSYLAGIPCWVI 303


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: 320
Number of extensions: 18
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: 325
Length adjustment: 28
Effective length of query: 293
Effective length of database: 297
Effective search space:    87021
Effective search space used:    87021
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: 48 (23.1 bits)

Align candidate Ac3H11_2067 (Glucokinase (EC 2.7.1.2))
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.16861.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    7.1e-90  287.4   0.0      8e-90  287.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067  Glucokinase (EC 2.7.1.2)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067  Glucokinase (EC 2.7.1.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.3   0.0     8e-90     8e-90       1     314 [.       6     314 ..       6     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 287.3 bits;  conditional E-value: 8e-90
                                        TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaia 62 
                                                      l++diGGtn rla   + +g ++  +++ + +fp + a++  yl+e    +  p +++f ia
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067   6 LLADIGGTNIRLAWQASPTGPLNDTRVLPCAQFPTVDAALAAYLQEVG--VPTPREAAFGIA 65 
                                                      79************888899*************************975..56778******* PP

                                        TIGR00749  63 tPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakvee 124
                                                       P++gd +r+tn++W++s   +++ +++++l +indf+a a+a++ l  e+l  +gg  +++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067  66 NPVTGDAIRMTNHSWSFSQRAVREAFGFERLVVINDFTALALALPLLTPEQLRPVGGGAAVP 127
                                                      ************************************************************** PP

                                        TIGR00749 125 saaiailGaGtGlGvatliqqsdgry.kvlageGghvdfaPrseleillleylrkkygrvsa 185
                                                      +aaia+lG+GtGlGv+ l+     ++ + l+geGghv +a + + e+ +l +l+++yg+vsa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 128 GAAIALLGPGTGLGVSGLVFPPGSHLgVPLSGEGGHVTLAAQTQREFDVLAILQERYGHVSA 189
                                                      ****************99975554442669******************************** PP

                                        TIGR00749 186 ervlsGsGlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilG 247
                                                      er + G+Glv +y+al++       ++  ke     +++e al+ +d+la +alelf++ lG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 190 ERAVCGAGLVDLYHALRRLA-----QRGGKEISSAAQVTELALQANDPLALEALELFCGFLG 246
                                                      ****************9988.....667777778899************************* PP

                                        TIGR00749 248 alagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvl.kkk 308
                                                      ++agnlal+lgarGGv++ GG+vPr+  ++++s+fra+fe kGr++++la iP  v+   ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 247 SVAGNLALTLGARGGVFIGGGMVPRLGAWFDQSPFRARFESKGRFQSYLAGIPCWVIDpGAT 308
                                                      *******************************************************9952477 PP

                                        TIGR00749 309 vGllGa 314
                                                      + l Ga
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 309 PALHGA 314
                                                      888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (325 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.04
//
[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