Alignments for a candidate for glk in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Beijerinckia indica ATCC 9039

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_012386200.1 BIND_RS16705 glucokinase

Query= curated2:P21908
         (324 letters)



>NCBI__GCF_000019845.1:WP_012386200.1
          Length = 320

 Score =  417 bits (1072), Expect = e-121
 Identities = 210/317 (66%), Positives = 247/317 (77%)

Query: 1   MEIVAIDIGGTHARFSIAEVSNGRVLSLGEETTFKTAEHASLQLAWERFGEKLGRPLPRA 60
           MEIVA+DIGGTHARF++AEV++GRV+ LGE  T + AEH S QLAWE F +  GR LPRA
Sbjct: 1   MEIVAVDIGGTHARFALAEVADGRVVHLGEAVTLQAAEHGSFQLAWETFAQIAGRALPRA 60

Query: 61  AAIAWAGPVHGEVLKLTNNPWVLRPATLNEKLDIDTHVLINDFGAVAHAVAHMDSSYLDH 120
            AIA A PV GEVLKLTNNPW++RPA + EKL +D   L+NDFGA+AH VA +    L  
Sbjct: 61  VAIAIACPVGGEVLKLTNNPWIIRPALIPEKLHVDAWTLVNDFGAIAHTVAQVGEDQLMP 120

Query: 121 ICGPDEALPSDGVITILGPGTGLGVAHLLRTEGRYFVIETEGGHIDFAPLDRLEDKILAR 180
           I GPD ALP DGVI+I+GPGTGLGV H+LR  G Y VIE EGGHIDFAPLD LED+IL  
Sbjct: 121 ITGPDHALPQDGVISIVGPGTGLGVGHVLRRGGHYHVIECEGGHIDFAPLDSLEDQILKY 180

Query: 181 LRERFRRVSIERIISGPGLGNIYEALAAIEGVPFSLLDDIKLWQMALEGKDNLAEAALDR 240
           +R R+ RVS+ER+ISGPGL NIYEALAAIEG     + D +LW  A+ GKD+LA AALDR
Sbjct: 181 MRHRYPRVSVERLISGPGLVNIYEALAAIEGKSLDPIGDKELWAAAMAGKDSLAAAALDR 240

Query: 241 FCLSLGAIAGDLALAQGATSVVIGGGVGLRIASHLPESGFRQRFVSKGRFERVMSKIPVK 300
           FCLSLGA+ GD+ALA GA SVVI GG+GLRIAS LP+SGF  RF +KGRF  +M+ IPV+
Sbjct: 241 FCLSLGAVCGDIALALGAKSVVIAGGLGLRIASLLPQSGFATRFTAKGRFAPMMATIPVR 300

Query: 301 LITYPQPGLLGAAAAYA 317
            I +PQPGL GAAAA+A
Sbjct: 301 CIIHPQPGLYGAAAAFA 317


Lambda     K      H
   0.320    0.139    0.411 

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: 440
Number of extensions: 21
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: 324
Length of database: 320
Length adjustment: 28
Effective length of query: 296
Effective length of database: 292
Effective search space:    86432
Effective search space used:    86432
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: 48 (23.1 bits)

Align candidate WP_012386200.1 BIND_RS16705 (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.31969.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.8e-75  237.8   0.0    1.1e-74  237.5   0.0    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012386200.1  BIND_RS16705 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012386200.1  BIND_RS16705 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.5   0.0   1.1e-74   1.1e-74       2     315 .]       5     313 ..       4     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 237.5 bits;  conditional E-value: 1.1e-74
                                 TIGR00749   2 vgdiGGtnarlalvevapgeieqv...ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiig 67 
                                               + diGGt+ar+al eva g++  +    t+++ ++ s++ +   + + a   l      ++aia+P+ g
  lcl|NCBI__GCF_000019845.1:WP_012386200.1   5 AVDIGGTHARFALAEVADGRVVHLgeaVTLQAAEHGSFQLAWETFAQIAGRALPR--AVAIAIACPVGG 71 
                                               57*****************99887766899*****************99999876..889********* PP

                                 TIGR00749  68 dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakve..esaaiailGaG 134
                                               ++ +ltn+ W +  + + ++l +    l+ndf a+a +++ ++e++l+ + g +    +++ i+i+G+G
  lcl|NCBI__GCF_000019845.1:WP_012386200.1  72 EVLKLTNNPWIIRPALIPEKLHVDAWTLVNDFGAIAHTVAQVGEDQLMPITGPDHAlpQDGVISIVGPG 140
                                               **************************************************997654227899******* PP

                                 TIGR00749 135 tGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealsk 203
                                               tGlGv ++++   g+y+v+  eGgh+dfaP + le ++l+y+r++y rvs+er++sG+Glv+iyeal  
  lcl|NCBI__GCF_000019845.1:WP_012386200.1 141 TGLGVGHVLR-RGGHYHVIECEGGHIDFAPLDSLEDQILKYMRHRYPRVSVERLISGPGLVNIYEALAA 208
                                               *********9.779*****************************************************99 PP

                                 TIGR00749 204 rkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPr 272
                                                +g+     l  +   +k++  aa++g+d+la  al+ f+  lGa++g++al lga+  v +aGG+  r
  lcl|NCBI__GCF_000019845.1:WP_012386200.1 209 IEGK----SL--DPIGDKELWAAAMAGKDSLAAAALDRFCLSLGAVCGDIALALGAKS-VVIAGGLGLR 270
                                               9843....23..3677999************************************985.88******** PP

                                 TIGR00749 273 fiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                               +  ll +s+f  +f  kGr+  ++a+iPv+ +++ ++Gl Ga+
  lcl|NCBI__GCF_000019845.1:WP_012386200.1 271 IASLLPQSGFATRFTAKGRFAPMMATIPVRCIIHPQPGLYGAA 313
                                               *****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (320 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: 00:00:00.01
# Mc/sec: 7.86
//
[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