Alignments for a candidate for glk in Brucella inopinata BO1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Brucella inopinata BO1

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_025200402.1 BIBO1_RS19405 glucokinase

Query= curated2:Q11CB2
         (342 letters)



>NCBI__GCF_000182725.1:WP_025200402.1
          Length = 343

 Score =  452 bits (1162), Expect = e-132
 Identities = 223/337 (66%), Positives = 270/337 (80%)

Query: 6   DHDVVLDFPILIGDIGGTNARFAIVVDSYAEPREFPVVQTADFATIEDAIQTAILDQTHL 65
           D +    FP+L+ DIGGTNARFAI+VDS AEP+EFPV+QTAD+ATI++AIQ AILDQT +
Sbjct: 6   DAEQSFKFPVLVCDIGGTNARFAILVDSNAEPKEFPVLQTADYATIDEAIQRAILDQTAI 65

Query: 66  IPRSAVLAVAGPVNGDEIDLTNSNWVVRPREMMAHLGFSDIVVLNDFEAQALAVVALGEE 125
            PRS +LAVAGPV+GDEIDLTN +WVVRP++M+A LGF D+ VLNDFEAQALAVV+L   
Sbjct: 66  QPRSVILAVAGPVDGDEIDLTNCDWVVRPKKMIADLGFEDVTVLNDFEAQALAVVSLEGH 125

Query: 126 HLEKIGGNVAETVGSRVVLGPGTGLGVAGLVHARRTWIPVPGEGGHMDLGPRTARDEQIF 185
           H+E+IGG   E V +RVVLGPGTGLGVAGLV  R  W+PVPGEGGH+D+GPRT RD QIF
Sbjct: 126 HMEQIGGKPEEAVATRVVLGPGTGLGVAGLVRTRHAWVPVPGEGGHIDIGPRTERDYQIF 185

Query: 186 PHLERIEGRVSGEQVLCGRGLVNLYRAIAKADAKEAAFSSPAEITTAGLAQADEIAVETL 245
           PH+ERIEGRV+GEQ+L GRGL NLY  I  AD       +P +IT+AGL  ++  A ETL
Sbjct: 186 PHIERIEGRVTGEQILSGRGLRNLYLGICAADKITPTLETPVDITSAGLDGSNPQATETL 245

Query: 246 NLFVTYLGRVAGDLGLVFMSRGGVFLTGGIAQKIVPALKNSLFRAAFEDKAPHNELMASM 305
           +LF TYLGR+AGDL L+FM+ GGV+L+GGI  +I+ ALK   FRAAFEDKAPH  +M  +
Sbjct: 246 DLFATYLGRLAGDLALIFMAHGGVYLSGGIPVRILSALKAGSFRAAFEDKAPHKAIMRDI 305

Query: 306 PVYVITHPLAALHGLAAYARTPARFGVETAGRRWRLR 342
           PV VIT+ LAAL GL+A+ARTP+RF V T GRRWR+R
Sbjct: 306 PVRVITYQLAALTGLSAFARTPSRFEVSTEGRRWRMR 342


Lambda     K      H
   0.321    0.138    0.404 

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: 429
Number of extensions: 12
Number of successful extensions: 1
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: 342
Length of database: 343
Length adjustment: 29
Effective length of query: 313
Effective length of database: 314
Effective search space:    98282
Effective search space used:    98282
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_025200402.1 BIBO1_RS19405 (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.2802160.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.2e-74  236.5   0.0    2.7e-74  236.3   0.0    1.0  1  NCBI__GCF_000182725.1:WP_025200402.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000182725.1:WP_025200402.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.3   0.0   2.7e-74   2.7e-74       1     313 [.      16     319 ..      16     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: 236.3 bits;  conditional E-value: 2.7e-74
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrv.yleeakvelkdpikgcfaiatPiigdfvrl 72 
                                           lv diGGtnar+a++  +  e +   ++++ d+  + ++++   l++++++   p    +a+a+P+ gd + l
  NCBI__GCF_000182725.1:WP_025200402.1  16 LVCDIGGTNARFAILVDSNAEPKEFPVLQTADYATIDEAIQRaILDQTAIQ---PRSVILAVAGPVDGDEIDL 85 
                                           799**********987788899999************99975156666665...55689************** PP

                             TIGR00749  73 tnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqq 145
                                           tn dW +  +++  +l+++ + ++ndf a+a+a+ +l+ +++ q+gg + e  a+  +lG+GtGlGva l++ 
  NCBI__GCF_000182725.1:WP_025200402.1  86 TNCDWVVRPKKMIADLGFEDVTVLNDFEAQALAVVSLEGHHMEQIGGKPEEAVATRVVLGPGTGLGVAGLVR- 157
                                           ***********************************************************************9. PP

                             TIGR00749 146 sdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeel 218
                                           +   ++ ++geGgh+d  Pr e +++++  + +  grv+ e++lsG Gl ++y  +  ++      k++ +  
  NCBI__GCF_000182725.1:WP_025200402.1 158 TRHAWVPVPGEGGHIDIGPRTERDYQIFPHIERIEGRVTGEQILSGRGLRNLYLGICAAD------KITPTLE 224
                                           999****************************9999**********************999......8888999 PP

                             TIGR00749 219 kekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGr 291
                                           ++ di+ a l+gs++ a ++l+lf + lG+lag+lal + a+GGvy++GGi  r++  lk++sfraafedk  
  NCBI__GCF_000182725.1:WP_025200402.1 225 TPVDITSAGLDGSNPQATETLDLFATYLGRLAGDLALIFMAHGGVYLSGGIPVRILSALKAGSFRAAFEDKAP 297
                                           ************************************************************************* PP

                             TIGR00749 292 lkellasiPvqvvlkkkvGllG 313
                                            k+++ +iPv+v+  + + l G
  NCBI__GCF_000182725.1:WP_025200402.1 298 HKAIMRDIPVRVITYQLAALTG 319
                                           *************988877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (343 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: 00:00:00.00
# Mc/sec: 13.96
//
[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 2024 update 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