GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Magnetospirillum magneticum AMB-1

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_011384511.1 AMB_RS10655 glucokinase

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



>NCBI__GCF_000009985.1:WP_011384511.1
          Length = 321

 Score =  259 bits (663), Expect = 5e-74
 Identities = 146/311 (46%), Positives = 183/311 (58%), Gaps = 4/311 (1%)

Query: 1   MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHK--VEVKD 58
           M++  LV D+GGT+AR AL     GE          DY      I+ YL EH   V  K 
Sbjct: 1   MSQMVLVADIGGTHARFALMG-PDGEAVNPVVLRCADYDGPAPAIKAYLAEHAGGVAPKG 59

Query: 59  GCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQ 118
           G  A+A  I GD + +TN  W FSIAE ++ +G   LE++NDFTAV++++  LK EHL+ 
Sbjct: 60  GAFAVASVIDGDRIELTNSPWRFSIAETRQAVGLQRLEVVNDFTAVALSVRHLKPEHLMS 119

Query: 119 FGGAEPVEGKPIAVYGAGTGLGVAHLV-HVDKRWVSLPGEGGHVDFAPNSEEEAIILEIL 177
            GG  P  G PIAV G GTGLGV+ L+      W +L  EGGHV  A  +E EA IL+ L
Sbjct: 120 VGGGMPEAGLPIAVLGPGTGLGVSALIPSASGEWTALATEGGHVTMAAATEREARILDRL 179

Query: 178 RAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLF 237
           R +  HVSAERVLSG GLVNLY+A+            P  IT+R L  SC   R A+ +F
Sbjct: 180 RTQFDHVSAERVLSGQGLVNLYQAVAALSGHQAVFSTPDVITKRGLDGSCPVSREAVEVF 239

Query: 238 CVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVY 297
             +MG   GNLAL+LG  GGVFIAGGI+PR  E F+ S FR  FE  GRF+ Y+  IP +
Sbjct: 240 FAMMGTVAGNLALSLGAKGGVFIAGGILPRMAEAFRLSSFRTRFEAHGRFQPYLAAIPTW 299

Query: 298 LIVHDNPGLLG 308
           LI H  P  +G
Sbjct: 300 LITHPLPAFVG 310


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: 324
Number of extensions: 20
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: 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 WP_011384511.1 AMB_RS10655 (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.508960.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.3e-97  311.1   0.0    5.2e-97  310.8   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384511.1  AMB_RS10655 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384511.1  AMB_RS10655 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.8   0.0   5.2e-97   5.2e-97       1     313 [.       6     310 ..       6     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 310.8 bits;  conditional E-value: 5.2e-97
                                 TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdf 69 
                                               lv+diGGt+ar+al+      +++  ++++ d++   ++++ yl e++  +  p  g+fa+a+ i gd 
  lcl|NCBI__GCF_000009985.1:WP_011384511.1   6 LVADIGGTHARFALMGPDGEAVNP-VVLRCADYDGPAPAIKAYLAEHAGGVA-PKGGAFAVASVIDGDR 72 
                                               89************6655555555.59*********************9986.689************* PP

                                 TIGR00749  70 vrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlG 138
                                               ++ltn  W +si+e++q ++l++le++ndf+ava+++  lk e+l+ +gg  +e + +ia+lG+GtGlG
  lcl|NCBI__GCF_000009985.1:WP_011384511.1  73 IELTNSPWRFSIAETRQAVGLQRLEVVNDFTAVALSVRHLKPEHLMSVGGGMPEAGLPIAVLGPGTGLG 141
                                               ********************************************************************* PP

                                 TIGR00749 139 vatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkge 207
                                               v+ li+ + g + +la+eGghv +a   e e+ +l+ lr+++++vsaervlsG+Glv++y+a+    g+
  lcl|NCBI__GCF_000009985.1:WP_011384511.1 142 VSALIPSASGEWTALATEGGHVTMAAATEREARILDRLRTQFDHVSAERVLSGQGLVNLYQAVAALSGH 210
                                               ***************************************************************999976 PP

                                 TIGR00749 208 revsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiel 276
                                               + v        ++  i+++ l+gs++++r+a+e+f +++G++agnlal lga+GGv++aGGi+Pr+ e 
  lcl|NCBI__GCF_000009985.1:WP_011384511.1 211 QAV------FSTPDVITKRGLDGSCPVSREAVEVFFAMMGTVAGNLALSLGAKGGVFIAGGILPRMAEA 273
                                               654......45899******************************************************* PP

                                 TIGR00749 277 lkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313
                                               ++ ssfr +fe  Gr++ +la iP  ++ +  + ++G
  lcl|NCBI__GCF_000009985.1:WP_011384511.1 274 FRLSSFRTRFEAHGRFQPYLAAIPTWLITHPLPAFVG 310
                                               ****************************998777666 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.91
//
[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:

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:

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:

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:

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