Alignments for a candidate for glk in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Klebsiella michiganensis M5al

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate BWI76_RS20510 BWI76_RS20510 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__Koxy:BWI76_RS20510
          Length = 321

 Score =  598 bits (1542), Expect = e-176
 Identities = 290/321 (90%), Positives = 306/321 (95%)

Query: 1   MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGC 60
           MTK+ALVGDVGGTNARLALCD+ SGEIS+AKTYSGLDYPSLEAV++VYLEEH V+V+DGC
Sbjct: 1   MTKFALVGDVGGTNARLALCDLTSGEISRAKTYSGLDYPSLEAVVQVYLEEHNVQVEDGC 60

Query: 61  IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120
           IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLK EHLIQFG
Sbjct: 61  IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKAEHLIQFG 120

Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180
           GA+PVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEE IILE LR E
Sbjct: 121 GAKPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEGIILEELRTE 180

Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240
           +GHVSAERVLSGPGLVNLY AIVK+D RLPENL+PKD+TERALAD+C DCRRALSLFCVI
Sbjct: 181 LGHVSAERVLSGPGLVNLYHAIVKSDGRLPENLQPKDVTERALADTCIDCRRALSLFCVI 240

Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300
           MGRFGGNLAL LGTFGGV+IAGGIVPRFLEFFKASGFR  FEDKGRFK +V DIPVYLIV
Sbjct: 241 MGRFGGNLALTLGTFGGVYIAGGIVPRFLEFFKASGFRGGFEDKGRFKAFVQDIPVYLIV 300

Query: 301 HDNPGLLGSGAHLRQTLGHIL 321
           HDNPGLLGSGAHLRQTLG +L
Sbjct: 301 HDNPGLLGSGAHLRQTLGQVL 321


Lambda     K      H
   0.322    0.141    0.426 

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: 503
Number of extensions: 8
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: 321
Length of database: 321
Length adjustment: 28
Effective length of query: 293
Effective length of database: 293
Effective search space:    85849
Effective search space used:    85849
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS20510 BWI76_RS20510 (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.18120.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     9e-153  494.0   0.0     1e-152  493.9   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS20510  BWI76_RS20510 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS20510  BWI76_RS20510 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.9   0.0    1e-152    1e-152       1     315 []       6     310 ..       6     310 .. 1.00

  Alignments for each domain:
  == domain 1  score: 493.9 bits;  conditional E-value: 1e-152
                               TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvr 71 
                                             lvgd+GGtnarlal++ ++gei+ +ktys++d+psleavv+vylee++v+++d   gc+aia+Pi+gd+v+
  lcl|FitnessBrowser__Koxy:BWI76_RS20510   6 LVGDVGGTNARLALCDLTSGEISRAKTYSGLDYPSLEAVVQVYLEEHNVQVED---GCIAIACPITGDWVA 73 
                                             89***************************************************...*************** PP

                               TIGR00749  72 ltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatl 142
                                             +tn++Wa+si+e+k++l++++le+indf+av++ai++lk e+liq+ggak++e+++ia++GaGtGlGva+l
  lcl|FitnessBrowser__Koxy:BWI76_RS20510  74 MTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKAEHLIQFGGAKPVEGKPIAVYGAGTGLGVAHL 144
                                             *********************************************************************** PP

                               TIGR00749 143 iqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevskl 213
                                             ++ +d+r+++l+geGghvdfaP+se+e ++le lr+++g+vsaervlsG+Glv++y+a++k +      +l
  lcl|FitnessBrowser__Koxy:BWI76_RS20510 145 VH-VDKRWVSLPGEGGHVDFAPNSEEEGIILEELRTELGHVSAERVLSGPGLVNLYHAIVKSD-----GRL 209
                                             **.************************************************************.....89* PP

                               TIGR00749 214 skeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfra 284
                                             + e+l++kd++e+al++++ ++rral+lf++i+G+++gnlal+lg++GGvy+aGGivPrf+e++k+s+fr 
  lcl|FitnessBrowser__Koxy:BWI76_RS20510 210 P-ENLQPKDVTERALADTCIDCRRALSLFCVIMGRFGGNLALTLGTFGGVYIAGGIVPRFLEFFKASGFRG 279
                                             *.9******************************************************************** PP

                               TIGR00749 285 afedkGrlkellasiPvqvvlkkkvGllGag 315
                                             +fedkGr+k+++++iPv++++++++GllG+g
  lcl|FitnessBrowser__Koxy:BWI76_RS20510 280 GFEDKGRFKAFVQDIPVYLIVHDNPGLLGSG 310
                                             *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (321 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: 7.41
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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