Alignments for a candidate for glk in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Phyllobacterium brassicacearum STM 196

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_106712464.1 CU102_RS17890 glucokinase

Query= curated2:Q11CB2
         (342 letters)



>NCBI__GCF_003010955.1:WP_106712464.1
          Length = 342

 Score =  477 bits (1227), Expect = e-139
 Identities = 229/340 (67%), Positives = 274/340 (80%)

Query: 1   MAYSTDHDVVLDFPILIGDIGGTNARFAIVVDSYAEPREFPVVQTADFATIEDAIQTAIL 60
           M    D D ++ FPIL+GDIGGTNARFAI+VD+YAEP+EFP++QTAD+ TI++AIQ AIL
Sbjct: 1   MVTQADTDHIMKFPILVGDIGGTNARFAILVDAYAEPKEFPIIQTADYPTIDEAIQNAIL 60

Query: 61  DQTHLIPRSAVLAVAGPVNGDEIDLTNSNWVVRPREMMAHLGFSDIVVLNDFEAQALAVV 120
           D T + PRSAVLA+AGPV GDEIDLTN  WVV+PR+MM  LG SDI VLNDFEAQALAVV
Sbjct: 61  DHTSIQPRSAVLAIAGPVEGDEIDLTNCAWVVKPRQMMETLGLSDITVLNDFEAQALAVV 120

Query: 121 ALGEEHLEKIGGNVAETVGSRVVLGPGTGLGVAGLVHARRTWIPVPGEGGHMDLGPRTAR 180
           +L  +HLEK+GG   +  GSR VLGPGTGLGVAG+V +R +W+PVPGEGGH+D+GPRTAR
Sbjct: 121 SLEPKHLEKLGGGPGDPHGSRAVLGPGTGLGVAGMVRSRNSWVPVPGEGGHVDMGPRTAR 180

Query: 181 DEQIFPHLERIEGRVSGEQVLCGRGLVNLYRAIAKADAKEAAFSSPAEITTAGLAQADEI 240
           D ++FPH+E IEGR+SGEQ+LCGRGL N+YRAI K +   A+  +PAEIT AGL+     
Sbjct: 181 DLELFPHIEHIEGRISGEQLLCGRGLQNIYRAICKVNGTPASLQTPAEITAAGLSGESAE 240

Query: 241 AVETLNLFVTYLGRVAGDLGLVFMSRGGVFLTGGIAQKIVPALKNSLFRAAFEDKAPHNE 300
           A ETL LFV YLGR+AGD  L FM+RGGV+L GGI QKIV  LK+  FR AFEDKAPH E
Sbjct: 241 AKETLALFVVYLGRLAGDFALTFMARGGVYLAGGIVQKIVAPLKDPSFRQAFEDKAPHGE 300

Query: 301 LMASMPVYVITHPLAALHGLAAYARTPARFGVETAGRRWR 340
           ++   PVY+ITHPLAAL GL+A++RTP RFGV T GRRWR
Sbjct: 301 ILRETPVYIITHPLAALSGLSAFSRTPTRFGVSTEGRRWR 340


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: 466
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: 342
Length adjustment: 29
Effective length of query: 313
Effective length of database: 313
Effective search space:    97969
Effective search space used:    97969
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_106712464.1 CU102_RS17890 (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.736860.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-76  243.7   0.0    1.7e-76  243.5   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106712464.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106712464.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.5   0.0   1.7e-76   1.7e-76       1     313 [.      16     319 ..      16     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.5 bits;  conditional E-value: 1.7e-76
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 
                                           lvgdiGGtnar+a++  a  e +   + ++ d+p + ++++    ++     +p  + +aia+P+ gd + lt
  NCBI__GCF_003010955.1:WP_106712464.1  16 LVGDIGGTNARFAILVDAYAEPKEFPIIQTADYPTIDEAIQNAILDHTSI--QPRSAVLAIAGPVEGDEIDLT 86 
                                           89***********998888899999999*************988777654..4679***************** PP

                             TIGR00749  74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146
                                           n  W +   ++ ++l+l+ + ++ndf a+a+a+ +l+ ++l +lgg + ++ ++ a+lG+GtGlGva +++ s
  NCBI__GCF_003010955.1:WP_106712464.1  87 NCAWVVKPRQMMETLGLSDITVLNDFEAQALAVVSLEPKHLEKLGGGPGDPHGSRAVLGPGTGLGVAGMVR-S 158
                                           **********************************************************************9.9 PP

                             TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219
                                            ++++ ++geGghvd+ Pr   ++ l+  + +  gr+s e++l G Gl +iy+a+ k +g       + + ++
  NCBI__GCF_003010955.1:WP_106712464.1 159 RNSWVPVPGEGGHVDMGPRTARDLELFPHIEHIEGRISGEQLLCGRGLQNIYRAICKVNGT------PASLQT 225
                                           9*****************************9999**********************98854......444559 PP

                             TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292
                                           + +i+ a l g+ + a+++l lf++ lG+lag+ al++ arGGvy+aGGiv +++  lk  sfr+afedk   
  NCBI__GCF_003010955.1:WP_106712464.1 226 PAEITAAGLSGESAEAKETLALFVVYLGRLAGDFALTFMARGGVYLAGGIVQKIVAPLKDPSFRQAFEDKAPH 298
                                           ************************************************************************* PP

                             TIGR00749 293 kellasiPvqvvlkkkvGllG 313
                                           +e+l + Pv+++ +  + l G
  NCBI__GCF_003010955.1:WP_106712464.1 299 GEILRETPVYIITHPLAALSG 319
                                           ************998777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (342 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: 13.29
//
[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