Alignments for a candidate for glk in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Pseudovibrio axinellae Ad2

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_068000403.1 PsAD2_RS00270 glucokinase

Query= curated2:Q11CB2
         (342 letters)



>NCBI__GCF_001623255.1:WP_068000403.1
          Length = 349

 Score =  317 bits (813), Expect = 2e-91
 Identities = 156/329 (47%), Positives = 218/329 (66%), Gaps = 1/329 (0%)

Query: 11  LDFPILIGDIGGTNARFAIVVDSYAEPREFPVVQTADFATIEDAIQTAILDQTHLIPRSA 70
           L +P+L+ DIGGTNARFA++ D  +         T   ATI+DAI+TA+L+  H  PRSA
Sbjct: 11  LSYPVLVADIGGTNARFALIEDPNSATILCGQESTKAHATIQDAIRTAVLNAGHATPRSA 70

Query: 71  VLAVAGPVNGDEIDLTNSNWVVRPREMMAHLGFSDIVVLNDFEAQALAVVALGEEHLEKI 130
           +LA+A PV+GD+I LTN+NWV+ P  ++  LG   + ++NDFEAQ LA+ +L    L++I
Sbjct: 71  LLAIAAPVSGDQIPLTNANWVIEPPALIEELGLEQVAIVNDFEAQGLALPSLTSGDLDQI 130

Query: 131 GGNVAETVGSRVVLGPGTGLGVAGLVHARRTWIPVPGEGGHMDLGPRTARDEQIFPHLER 190
           GG  A+   ++ VLGPGTGLG   L+HA   WIPVPGEGGH++LGP +  + +I+P +ER
Sbjct: 131 GGGDAKANTTKFVLGPGTGLGAGALIHACGKWIPVPGEGGHVELGPLSDEEYRIWPFIER 190

Query: 191 IEGRVSGEQVLCGRGLVNLYRAIAKADAKEAAFSSPAEITTAGLAQADEIAVETLNLFVT 250
           + GR+  EQ++CG GLV L RA+ +AD  + +F +P+++  A   + DE+A + + LF  
Sbjct: 191 LGGRIGAEQIICGAGLVRLARAVLRADNLDRSFENPSDVPGAA-DEGDEVAQKVMRLFCA 249

Query: 251 YLGRVAGDLGLVFMSRGGVFLTGGIAQKIVPALKNSLFRAAFEDKAPHNELMASMPVYVI 310
            LGRVAGD  +  ++ GGV+L GGIA KI   L    FRAAFE KAPH  +M S+P Y++
Sbjct: 250 ALGRVAGDFAITNLAGGGVYLAGGIAPKISHWLHGGEFRAAFEAKAPHEAIMRSIPTYIV 309

Query: 311 THPLAALHGLAAYARTPARFGVETAGRRW 339
            H   AL GLAAY   P  + V+  GR W
Sbjct: 310 KHSSPALAGLAAYTHAPESYLVDQTGRSW 338


Lambda     K      H
   0.321    0.138    0.404 

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: 405
Number of extensions: 25
Number of successful extensions: 3
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: 342
Length of database: 349
Length adjustment: 29
Effective length of query: 313
Effective length of database: 320
Effective search space:   100160
Effective search space used:   100160
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_068000403.1 PsAD2_RS00270 (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.515340.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.6e-75  238.2   0.0      8e-75  238.0   0.0    1.0  1  NCBI__GCF_001623255.1:WP_068000403.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001623255.1:WP_068000403.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.0   0.0     8e-75     8e-75       1     313 [.      16     318 ..      16     320 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.0 bits;  conditional E-value: 8e-75
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 
                                           lv+diGGtnar+al+e            s++++  +++++r    +a      p  + +aia+P+ gd + lt
  NCBI__GCF_001623255.1:WP_068000403.1  16 LVADIGGTNARFALIEDPNSATILCGQESTKAHATIQDAIRTAVLNAGHA--TPRSALLAIAAPVSGDQIPLT 86 
                                           89*************65444444445679999*********988777665..4669***************** PP

                             TIGR00749  74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146
                                           n +W +    l +el+l+++ ++ndf a+++a+++l + dl q+gg +++ ++++ +lG+GtGlG   li+ +
  NCBI__GCF_001623255.1:WP_068000403.1  87 NANWVIEPPALIEELGLEQVAIVNDFEAQGLALPSLTSGDLDQIGGGDAKANTTKFVLGPGTGLGAGALIH-A 158
                                           ***********************************************************************.8 PP

                             TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219
                                            g++  ++geGghv++ P s++e+ ++ ++ +  gr+ ae+++ G+Glv + +a+ +++       l ++  +
  NCBI__GCF_001623255.1:WP_068000403.1 159 CGKWIPVPGEGGHVELGPLSDEEYRIWPFIERLGGRIGAEQIICGAGLVRLARAVLRAD------NLDRSFEN 225
                                           9*******************************99***********************99......78889999 PP

                             TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292
                                           + d+  aa eg++ +a++ + lf+++lG++ag+ a++ +a GGvy+aGGi+P++ ++l+ + fraafe k   
  NCBI__GCF_001623255.1:WP_068000403.1 226 PSDVPGAADEGDE-VAQKVMRLFCAALGRVAGDFAITNLAGGGVYLAGGIAPKISHWLHGGEFRAAFEAKAPH 297
                                           ******9999986.5899******************************************************* PP

                             TIGR00749 293 kellasiPvqvvlkkkvGllG 313
                                           ++++ siP ++v ++ + l G
  NCBI__GCF_001623255.1:WP_068000403.1 298 EAIMRSIPTYIVKHSSPALAG 318
                                           ******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (349 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.18
//
[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 2024 update 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