GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Rhizobium freirei PRF 81

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_037155368.1 RHSP_RS30180 glucokinase

Query= curated2:B9JYQ5
         (340 letters)



>NCBI__GCF_000359745.1:WP_037155368.1
          Length = 340

 Score =  464 bits (1195), Expect = e-135
 Identities = 223/336 (66%), Positives = 269/336 (80%), Gaps = 1/336 (0%)

Query: 5   HDNDHMPFPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKSGF 64
           H +   PFP+L+GDIGGTNARF IL DA++    F  + TA+F TID AI+   L+KS  
Sbjct: 6   HSDAPQPFPILIGDIGGTNARFSILADANSEQVHFPVVQTANFETIDDAIK-LTLEKSKL 64

Query: 65  QPRSAILAVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASLGRN 124
           QPRSAILA+AGP++ DEIPLTNC WVIRPK MIA+LG +DVL++NDFEAQALA A +  +
Sbjct: 65  QPRSAILAMAGPVQGDEIPLTNCDWVIRPKTMIANLGIEDVLIINDFEAQALAIAEVADD 124

Query: 125 DREPIGPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQIF 184
            RE IG  +E    SR +LGPGTGLGV GL++T H W PVPGEGGH+D+GPRS+RD QI+
Sbjct: 125 HRESIGETSENETASRAVLGPGTGLGVAGLIHTQHQWIPVPGEGGHIDLGPRSERDLQIW 184

Query: 185 PHIERIEGRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVETM 244
           PH+E IEGRIS EQ++CGRG+ +LY+AIC ADGIEP   +PAD+T HAL G D    ET+
Sbjct: 185 PHLETIEGRISAEQVICGRGLQNLYHAICKADGIEPSLKEPADITTHALAGTDKQAEETL 244

Query: 245 TLFVTYLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMKTI 304
           TLFVTYLGR+AGD+AL+FMARGGV+LSGGISQKI+P L+ P FR AFEDKAPHTEMMKTI
Sbjct: 245 TLFVTYLGRVAGDIALIFMARGGVYLSGGISQKILPALQKPEFRDAFEDKAPHTEMMKTI 304

Query: 305 PTFVAIHPQAALSGLAAYARTPSSYGVKHEGRRWQR 340
           PT V  HP AALSGLA+YAR P+S+G+  EGRRW+R
Sbjct: 305 PTHVVTHPLAALSGLASYARKPASFGLATEGRRWRR 340


Lambda     K      H
   0.322    0.140    0.445 

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: 433
Number of extensions: 12
Number of successful extensions: 2
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: 340
Length of database: 340
Length adjustment: 28
Effective length of query: 312
Effective length of database: 312
Effective search space:    97344
Effective search space used:    97344
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: 49 (23.5 bits)

Align candidate WP_037155368.1 RHSP_RS30180 (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.1712326.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.9e-81  259.7   0.0    2.2e-81  259.5   0.0    1.0  1  NCBI__GCF_000359745.1:WP_037155368.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359745.1:WP_037155368.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.5   0.0   2.2e-81   2.2e-81       1     313 [.      16     318 ..      16     320 .. 0.95

  Alignments for each domain:
  == domain 1  score: 259.5 bits;  conditional E-value: 2.2e-81
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 
                                           l+gdiGGtnar++++  a  e     + ++ +f+ + +++++ le++k + +    + +a+a+P+ gd + lt
  NCBI__GCF_000359745.1:WP_037155368.1  16 LIGDIGGTNARFSILADANSEQVHFPVVQTANFETIDDAIKLTLEKSKLQPRS---AILAMAGPVQGDEIPLT 85 
                                           79***********975555555566899*******************997666...99*************** PP

                             TIGR00749  74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146
                                           n dW +  +++  +l+++ + +indf a+a+ai+ + +++   +g    +e+a+ a+lG+GtGlGva li+ +
  NCBI__GCF_000359745.1:WP_037155368.1  86 NCDWVIRPKTMIANLGIEDVLIINDFEAQALAIAEVADDHRESIGETSENETASRAVLGPGTGLGVAGLIH-T 157
                                           ***********************************************************************.9 PP

                             TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219
                                           + ++  ++geGgh+d+ Prse +++++  l +  gr+sae+v+ G Gl ++y+a+ k++g +       + ++
  NCBI__GCF_000359745.1:WP_037155368.1 158 QHQWIPVPGEGGHIDLGPRSERDLQIWPHLETIEGRISAEQVICGRGLQNLYHAICKADGIEP------SLKE 224
                                           ********************************99*************************7764......3457 PP

                             TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292
                                           + di+  al+g+d  a+++l lf++ lG++ag++al + arGGvy++GGi  ++++ l+k  fr afedk   
  NCBI__GCF_000359745.1:WP_037155368.1 225 PADITTHALAGTDKQAEETLTLFVTYLGRVAGDIALIFMARGGVYLSGGISQKILPALQKPEFRDAFEDKAPH 297
                                           99*********************************************************************** PP

                             TIGR00749 293 kellasiPvqvvlkkkvGllG 313
                                            e++++iP +vv +  + l G
  NCBI__GCF_000359745.1:WP_037155368.1 298 TEMMKTIPTHVVTHPLAALSG 318
                                           ************998887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (340 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 16.35
//
[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:

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