Alignments for a candidate for glk in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Desulfitobacterium hafniense DCB-2

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_049769578.1 DHAF_RS15840 glucokinase

Query= curated2:Q55855
         (355 letters)



>NCBI__GCF_000021925.1:WP_049769578.1
          Length = 363

 Score =  208 bits (530), Expect = 2e-58
 Identities = 133/361 (36%), Positives = 196/361 (54%), Gaps = 37/361 (10%)

Query: 5   GVNFLAGDIGGTKTILALVTINESSPGLARPVTLFEQTYSSPAFPDLVPMVQQFRQEAAF 64
           G  +LAGDIGGTKT+L L ++  +   L R     E+ + S  + DL  ++Q F  E A 
Sbjct: 11  GQLYLAGDIGGTKTLLGLYSLEGTELVLVR-----ERNFPSKDWQDLTALIQGFLDEIAL 65

Query: 65  VLGNPISVAKACFAIAGPVIDNTCRLTNLDWHLSGDRLAQELAIAQ-VDLINDFAAVGYG 123
               P  +   C ++AGP+  + C LTNL+  +    L   L + + + L+ND  A+G G
Sbjct: 66  T---PEDITGGCLSLAGPITQDKCFLTNLNRVIDCPDLRSSLPLRRPLLLVNDLEAMGQG 122

Query: 124 ILGLGSEDLTVLQAAPVDPSGAIA---------------ILGAGTGLGQCYVIPQGQGRY 168
           ++ L  EDL  L  +   PS ++A               ++  GTGLGQ  ++  G    
Sbjct: 123 LMDLRGEDLICLNPSAESPSSSLASSPALSLARPSLNRALIAPGTGLGQAMILADG---- 178

Query: 169 RVFASEGAHGDFAPRSPLEWQLLEYLKKKYSLGRISIERVVSGMGIAMIYEFLRHQYPER 228
           RV A+EGAHGD+APR+  E +L  +L ++Y  G +S ERV+SG G+A +Y FL   Y E 
Sbjct: 179 RVCATEGAHGDYAPRTEQEVRLWRFLAQRY--GHVSYERVLSGPGLADLYRFL---YWEA 233

Query: 229 ESAQFSKLYQTWNREKDQETKTVDLAAAVSQAALEGTDVLADQAMELFLGAYGAEAGNLA 288
            S              D         A +++ AL+G   L  + +ELF+   GAEAGNLA
Sbjct: 234 LSPSLPGPASDSIPAPDSSLTP----AEITKKALDGICTLCTETLELFVKILGAEAGNLA 289

Query: 289 LKLLPRGGLYVAGGIAPKIIPLLEKGSFMQGFSDKGRMQSLMGTIPVQVVLNAKVGLIGA 348
           L+ L  GG+Y+ GGI PKI+P L++  FM+ F  KGR++ L+  IP+ V+LN +  L+GA
Sbjct: 290 LRTLAYGGIYLGGGIPPKILPKLQEDGFMEAFLAKGRLRELLSQIPIYVILNERTPLLGA 349

Query: 349 A 349
           A
Sbjct: 350 A 350


Lambda     K      H
   0.320    0.137    0.399 

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: 19
Number of successful extensions: 6
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: 355
Length of database: 363
Length adjustment: 29
Effective length of query: 326
Effective length of database: 334
Effective search space:   108884
Effective search space used:   108884
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_049769578.1 DHAF_RS15840 (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.3387.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.4e-78  249.5   0.0    1.1e-77  247.4   0.0    1.8  1  lcl|NCBI__GCF_000021925.1:WP_049769578.1  DHAF_RS15840 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_049769578.1  DHAF_RS15840 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.4   0.0   1.1e-77   1.1e-77       1     315 []      15     350 ..      15     350 .. 0.88

  Alignments for each domain:
  == domain 1  score: 247.4 bits;  conditional E-value: 1.1e-77
                                 TIGR00749   1 lvgdiGGtnarlalvevapgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiig 67 
                                               l+gdiGGt++ l+l      e+  v  + + s+d+++l+a+++ +l+e + + +d   gc+++a+Pi++
  lcl|NCBI__GCF_000021925.1:WP_049769578.1  15 LAGDIGGTKTLLGLYSLEGTELVLVreRNFPSKDWQDLTALIQGFLDEIALTPEDITGGCLSLAGPITQ 83 
                                               79************9888888887777899***********************99779*********** PP

                                 TIGR00749  68 dfvrltnldWalsieelkqelalak.lelindfaavayailalkeedliqlggak.............. 121
                                               d + ltnl+  +   +l+ +l l++ l l+nd+ a++ +++ l+ edli l+                 
  lcl|NCBI__GCF_000021925.1:WP_049769578.1  84 DKCFLTNLNRVIDCPDLRSSLPLRRpLLLVNDLEAMGQGLMDLRGEDLICLNPSAespssslasspals 152
                                               ***********************876999*********************9854311111111111111 PP

                                 TIGR00749 122 .veesaaiailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervl 189
                                                + +s   a++ +GtGlG+a+++   dg  +v a+eG+h+d+aPr e+e+ l+++l ++yg+vs ervl
  lcl|NCBI__GCF_000021925.1:WP_049769578.1 153 lARPSLNRALIAPGTGLGQAMILA--DG--RVCATEGAHGDYAPRTEQEVRLWRFLAQRYGHVSYERVL 217
                                               1123445799***********999..66..589************************************ PP

                                 TIGR00749 190 sGsGlvliyealskrkgere.......vsklskeelkekdiseaalegsdvlarralelflsilGalag 251
                                               sG+Gl+ +y++l  +                + + l++ +i+++al+g ++l+ ++lelf+ ilGa+ag
  lcl|NCBI__GCF_000021925.1:WP_049769578.1 218 SGPGLADLYRFLYWEALSPSlpgpasdSIPAPDSSLTPAEITKKALDGICTLCTETLELFVKILGAEAG 286
                                               ***********9877643334455433445567899********************************* PP

                                 TIGR00749 252 nlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                               nlal+ +a+GG+y+ GGi P++++ l++ +f++af  kGrl+ell++iP++v+l++++ llGa+
  lcl|NCBI__GCF_000021925.1:WP_049769578.1 287 NLALRTLAYGGIYLGGGIPPKILPKLQEDGFMEAFLAKGRLRELLSQIPIYVILNERTPLLGAA 350
                                               **************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (363 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 2.63
//
[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