Alignments for a candidate for glk in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Derxia gummosa DSM 723

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_028312615.1 H566_RS0118565 glucokinase

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



>NCBI__GCF_000482785.1:WP_028312615.1
          Length = 322

 Score =  261 bits (667), Expect = 2e-74
 Identities = 145/310 (46%), Positives = 187/310 (60%), Gaps = 2/310 (0%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKV-EVKDGCIAIA 64
           LVGD+GGTNAR AL       I+ A+T     +      I  YL E  +   +   I IA
Sbjct: 11  LVGDIGGTNARFALIAAPGAPITDARTLPCASHAGPREAIDAYLAEGGLPRPRAAAIGIA 70

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            PITGD V MTN+ W FSI ++++ LG   L  INDFTA+++A+P L  + L+Q GG   
Sbjct: 71  NPITGDAVRMTNNPWRFSIEQVRRELGLDRLLFINDFTALALALPTLAADELVQIGGKAA 130

Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIG-H 183
           V GK +A+ GAGTGLG++ LV   +RWV L GEGGHV  A     EA ++E LR   G H
Sbjct: 131 VPGKALALLGAGTGLGISGLVPHGERWVPLEGEGGHVTLAAFDAREARVVEALRRRHGGH 190

Query: 184 VSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGR 243
           VSAERVLSGPGL  L+ A+ + D    + L    IT RALA  C  C   + +FC ++G 
Sbjct: 191 VSAERVLSGPGLEALHAALAEVDELPADGLDAAAITGRALAGGCDRCAATVDMFCAMLGT 250

Query: 244 FGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDN 303
              +LAL LG  GGV+I GG+VPR  E F +S FRA FE+KGRF +Y+  IPV++I  D 
Sbjct: 251 VAADLALTLGARGGVYIGGGVVPRLGERFASSPFRARFEEKGRFGDYLAGIPVFVIHADY 310

Query: 304 PGLLGSGAHL 313
           P L G+   L
Sbjct: 311 PALRGAARAL 320


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: 354
Number of extensions: 20
Number of successful extensions: 3
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: 322
Length adjustment: 28
Effective length of query: 293
Effective length of database: 294
Effective search space:    86142
Effective search space used:    86142
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 WP_028312615.1 H566_RS0118565 (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.14374.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.6e-96  307.0   0.0    8.6e-96  306.9   0.0    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028312615.1  H566_RS0118565 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028312615.1  H566_RS0118565 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.9   0.0   8.6e-96   8.6e-96       1     315 []      11     317 ..      11     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 306.9 bits;  conditional E-value: 8.6e-96
                                 TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdf 69 
                                               lvgdiGGtnar+al+      i  ++t+ +  +    +++  yl e    l  p  +++ ia Pi+gd 
  lcl|NCBI__GCF_000482785.1:WP_028312615.1  11 LVGDIGGTNARFALIAAPGAPITDARTLPCASHAGPREAIDAYLAEG--GLPRPRAAAIGIANPITGDA 77 
                                               89************8887888***********************987..578899************** PP

                                 TIGR00749  70 vrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlG 138
                                               vr+tn+ W +sie++++el+l +l  indf+a a+a+++l  ++l+q+gg  +++++a a+lGaGtGlG
  lcl|NCBI__GCF_000482785.1:WP_028312615.1  78 VRMTNNPWRFSIEQVRRELGLDRLLFINDFTALALALPTLAADELVQIGGKAAVPGKALALLGAGTGLG 146
                                               ********************************************************************* PP

                                 TIGR00749 139 vatliqqsdgrykvlageGghvdfaPrseleillleylrkky.grvsaervlsGsGlvliyealskrkg 206
                                               ++ l++   +r++ l geGghv +a ++  e+ ++e lr++  g+vsaervlsG+Gl  ++ al + + 
  lcl|NCBI__GCF_000482785.1:WP_028312615.1 147 ISGLVP-HGERWVPLEGEGGHVTLAAFDAREARVVEALRRRHgGHVSAERVLSGPGLEALHAALAEVD- 213
                                               ******.5679*****************************9999*************99999987665. PP

                                 TIGR00749 207 erevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfie 275
                                                     l+ + l    i+ +al+g +  +  ++++f+++lG++a++lal+lgarGGvy+ GG+vPr+ e
  lcl|NCBI__GCF_000482785.1:WP_028312615.1 214 -----ELPADGLDAAAITGRALAGGCDRCAATVDMFCAMLGTVAADLALTLGARGGVYIGGGVVPRLGE 277
                                               .....99*99*********************************************************** PP

                                 TIGR00749 276 llkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                                + +s+fra+fe+kGr++++la iPv v+  + + l Ga+
  lcl|NCBI__GCF_000482785.1:WP_028312615.1 278 RFASSPFRARFEEKGRFGDYLAGIPVFVIHADYPALRGAA 317
                                               **************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (322 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.70
//
[ok]

This GapMind analysis is from Sep 24 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