Alignments for a candidate for glk in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Pseudomonas stutzeri A1501

Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_011914522.1 PST_RS17435 glucokinase

Query= reanno::WCS417:GFF4431
         (318 letters)



>NCBI__GCF_000013785.1:WP_011914522.1
          Length = 322

 Score =  412 bits (1059), Expect = e-120
 Identities = 201/318 (63%), Positives = 237/318 (74%)

Query: 1   MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60
           M+LALVGDIGGTNARFALWR+  L ++RV ATAD ++PE A++ YL   GL  G +GA C
Sbjct: 1   MRLALVGDIGGTNARFALWRNARLEAVRVLATADFATPELAVEYYLASLGLAPGSVGAAC 60

Query: 61  LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120
           L+ AGPV G++F FTNNHWRL +  FC  LQ+DELLL+NDF+AMALGMTR+   + R++C
Sbjct: 61  LACAGPVKGEQFVFTNNHWRLGRRDFCGALQLDELLLINDFAAMALGMTRVAEAQRRIIC 120

Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180
            G  E   PA+VIGPGTGLGV TLL L  G + ALPGEGGHVDLPL+   E  LWQ ++ 
Sbjct: 121 NGVAETGAPALVIGPGTGLGVATLLPLAGGGWQALPGEGGHVDLPLADAYEAALWQQLFA 180

Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240
            +GHV AE  LSGGGL  LYRA+C +    P L +P  +TAA LAGD +A   L+QF +W
Sbjct: 181 GLGHVRAEDVLSGGGLLLLYRALCLLHDQAPRLASPAEVTAAALAGDTLAAATLEQFCVW 240

Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300
           LGRVAGNNVLT G R GVYIVGGV+PRFADFF  SGFA+ FA KGCMS Y   +PVWLVT
Sbjct: 241 LGRVAGNNVLTLGARAGVYIVGGVVPRFADFFAASGFARGFASKGCMSAYLADVPVWLVT 300

Query: 301 APYSGLTGAGVALEQAFA 318
           A Y GL GAGVALEQA A
Sbjct: 301 AEYPGLEGAGVALEQALA 318


Lambda     K      H
   0.320    0.139    0.429 

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: 353
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: 318
Length of database: 322
Length adjustment: 28
Effective length of query: 290
Effective length of database: 294
Effective search space:    85260
Effective search space used:    85260
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_011914522.1 PST_RS17435 (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.2662.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.3e-79  252.9   0.1    2.6e-79  252.7   0.1    1.0  1  lcl|NCBI__GCF_000013785.1:WP_011914522.1  PST_RS17435 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011914522.1  PST_RS17435 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.7   0.1   2.6e-79   2.6e-79       1     315 []       5     310 ..       5     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 252.7 bits;  conditional E-value: 2.6e-79
                                 TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdf 69 
                                               lvgdiGGtnar+al      ++e+v+++ + df   e +v +yl       +    +c+a a+P+ g+ 
  lcl|NCBI__GCF_000013785.1:WP_011914522.1   5 LVGDIGGTNARFAL--WRNARLEAVRVLATADFATPELAVEYYLASLGLAPGSVGAACLACAGPVKGEQ 71 
                                               89************..67778999*********************99999988679************* PP

                                 TIGR00749  70 vrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlG 138
                                                 +tn++W l   +    l l +l lindfaa+a++++ + e +   +    +e++a+  ++G+GtGlG
  lcl|NCBI__GCF_000013785.1:WP_011914522.1  72 FVFTNNHWRLGRRDFCGALQLDELLLINDFAAMALGMTRVAEAQRRIICNGVAETGAPALVIGPGTGLG 140
                                               ******************************************99999999999**************** PP

                                 TIGR00749 139 vatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkge 207
                                               vatl++ + g +++l+geGghvd+   +  e+ l++ l + +g+v ae vlsG Gl l+y+al   +  
  lcl|NCBI__GCF_000013785.1:WP_011914522.1 141 VATLLPLAGGGWQALPGEGGHVDLPLADAYEAALWQQLFAGLGHVRAEDVLSGGGLLLLYRALCLLH-- 207
                                               ***************************************************************9887.. PP

                                 TIGR00749 208 revsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiel 276
                                               ++  +l      + +++ aal+g+ +la  +le f++ lG++agn  l+lgar Gvy++GG+vPrf ++
  lcl|NCBI__GCF_000013785.1:WP_011914522.1 208 DQAPRLA----SPAEVTAAALAGD-TLAAATLEQFCVWLGRVAGNNVLTLGARAGVYIVGGVVPRFADF 271
                                               5678888....89*********97.67889*************************************** PP

                                 TIGR00749 277 lkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                               + +s+f  +f  kG + ++la++Pv +v  + +Gl Gag
  lcl|NCBI__GCF_000013785.1:WP_011914522.1 272 FAASGFARGFASKGCMSAYLADVPVWLVTAEYPGLEGAG 310
                                               *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (322 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: 00:00:00.01
# Mc/sec: 9.93
//
[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