Alignments for a candidate for glk in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Sphingomonas koreensis DSMZ 15582

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate Ga0059261_0355 Ga0059261_0355 glucokinase, proteobacterial type

Query= curated2:P21908
         (324 letters)



>FitnessBrowser__Korea:Ga0059261_0355
          Length = 323

 Score =  407 bits (1045), Expect = e-118
 Identities = 199/323 (61%), Positives = 248/323 (76%), Gaps = 1/323 (0%)

Query: 1   MEIVAIDIGGTHARFSIAEVSNGRVLSLGEETTFKTAEHASLQLAWERFGEKLGRPLPRA 60
           +E+VA+DIGGTHARF+IAEV  GRV+S+GE  T KTAEH S QLAW+     LGR +PRA
Sbjct: 1   VEVVAVDIGGTHARFAIAEVEGGRVVSIGEPVTQKTAEHGSFQLAWQASARALGREMPRA 60

Query: 61  AAIAWAGPVHGEVLKLTNNPWVLRPATLNEKLDIDTHVLINDFGAVAHAVAHMDSSYLDH 120
           AAIA A P++ E++KLTNNPW++RP  + E+L++D++ LINDFGAV HAVA + S +  H
Sbjct: 61  AAIAIASPINDELIKLTNNPWIIRPPLIKERLEVDSYSLINDFGAVGHAVAQLPSEHFLH 120

Query: 121 ICGPDEALPSDGVITILGPGTGLGVAHLLRTEG-RYFVIETEGGHIDFAPLDRLEDKILA 179
           ICGPD      G IT+ GPGTGLGVA + RT    Y VI TEGGH+DFAPLD +ED I+ 
Sbjct: 121 ICGPDAPFAEKGAITVCGPGTGLGVAQVFRTGPLSYHVISTEGGHMDFAPLDGIEDSIVK 180

Query: 180 RLRERFRRVSIERIISGPGLGNIYEALAAIEGVPFSLLDDIKLWQMALEGKDNLAEAALD 239
           RLR  + RVS ERI++GPG+  IYE LA IEG     L+D ++W +A EGKD+LA AALD
Sbjct: 181 RLRSTYTRVSAERIVAGPGIVPIYETLAEIEGKRTHRLNDKEIWTLAFEGKDSLAMAALD 240

Query: 240 RFCLSLGAIAGDLALAQGATSVVIGGGVGLRIASHLPESGFRQRFVSKGRFERVMSKIPV 299
           RFCLSLGA+AGDLALA G T VVI GG+GL++  HL  SGF QRF++KGRF+ +MS IPV
Sbjct: 241 RFCLSLGAVAGDLALAHGPTGVVIAGGLGLKLKDHLVNSGFGQRFIAKGRFQALMSSIPV 300

Query: 300 KLITYPQPGLLGAAAAYANKYSE 322
           KLIT+PQPGL GAAAAYA ++++
Sbjct: 301 KLITHPQPGLYGAAAAYAQEHTQ 323


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: 431
Number of extensions: 17
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: 323
Length adjustment: 28
Effective length of query: 296
Effective length of database: 295
Effective search space:    87320
Effective search space used:    87320
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 Ga0059261_0355 Ga0059261_0355 (glucokinase, proteobacterial type)
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.19272.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-75  240.2   0.0      2e-75  240.0   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0355  Ga0059261_0355 glucokinase, prot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0355  Ga0059261_0355 glucokinase, proteobacterial type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.0   0.0     2e-75     2e-75       2     315 .]       5     314 ..       4     314 .. 0.91

  Alignments for each domain:
  == domain 1  score: 240.0 bits;  conditional E-value: 2e-75
                                 TIGR00749   2 vgdiGGtnarlalvevapgeieqv...ktyssedfpsleavvrvyleeakvelkd..pikgcfaiatPi 65 
                                               + diGGt+ar+a+ ev  g++ ++    t ++ ++ s++ + +     ++  l+   p  +++aia+Pi
  lcl|FitnessBrowser__Korea:Ga0059261_0355   5 AVDIGGTHARFAIAEVEGGRVVSIgepVTQKTAEHGSFQLAWQ----ASARALGRemPRAAAIAIASPI 69 
                                               57*******************9997555566666666655444....444444442477********** PP

                                 TIGR00749  66 igdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlgg..akveesaaiailG 132
                                                +++++ltn+ W +    +k+ l +    lindf av+ a++ l +e++  + g  a+  e++ai++ G
  lcl|FitnessBrowser__Korea:Ga0059261_0355  70 NDELIKLTNNPWIIRPPLIKERLEVDSYSLINDFGAVGHAVAQLPSEHFLHICGpdAPFAEKGAITVCG 138
                                               **************************************************99885578899******** PP

                                 TIGR00749 133 aGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyeal 201
                                               +GtGlGva++ + +  +y+v+++eGgh dfaP +  e  +++ lr+ y rvsaer+++G+G+v iye l
  lcl|FitnessBrowser__Korea:Ga0059261_0355 139 PGTGLGVAQVFRTGPLSYHVISTEGGHMDFAPLDGIEDSIVKRLRSTYTRVSAERIVAGPGIVPIYETL 207
                                               ********************************************************************* PP

                                 TIGR00749 202 skrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGiv 270
                                                + +g+r   +     l++k+i   a+eg+d+la  al+ f+  lGa+ag+lal  g+  Gv +aGG+ 
  lcl|FitnessBrowser__Korea:Ga0059261_0355 208 AEIEGKR-THR-----LNDKEIWTLAFEGKDSLAMAALDRFCLSLGAVAGDLALAHGPT-GVVIAGGLG 269
                                               *999655.345.....5599*************************************97.588****** PP

                                 TIGR00749 271 PrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                                ++ ++l +s+f ++f  kGr+++l++siPv+++ + ++Gl Ga+
  lcl|FitnessBrowser__Korea:Ga0059261_0355 270 LKLKDHLVNSGFGQRFIAKGRFQALMSSIPVKLITHPQPGLYGAA 314
                                               *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (323 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.82
//
[ok]

This GapMind analysis is from Sep 17 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, or view the source code.

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