GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmB in Weissella oryzae SG25

Align beta-Phosphoglucomutase (EC 5.4.2.6) (characterized)
to candidate WP_027698533.1 TT13_RS02545 beta-phosphoglucomutase

Query= BRENDA::P71447
         (221 letters)



>NCBI__GCF_000691805.2:WP_027698533.1
          Length = 223

 Score =  164 bits (416), Expect = 9e-46
 Identities = 88/192 (45%), Positives = 122/192 (63%), Gaps = 9/192 (4%)

Query: 3   KAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADK 62
           K   FD+DGV+ DTA +H  AW+ +A+E+G    + +  E LKG+ R  SL  IL   D 
Sbjct: 8   KGFAFDMDGVLADTARFHAIAWRQIADEVGTTWTE-ELAEALKGIDRMGSLDLILQAGDV 66

Query: 63  KVSAEEF-----KELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASK 117
              AE++     + LA +KNDNY  +I  ++ AD  PGI   L +L +   K+++ASASK
Sbjct: 67  ---AEQYDLPAREALANKKNDNYRALISKLTSADALPGIFPFLDELLAAGYKMSIASASK 123

Query: 118 NGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQA 177
           N PF++E++ +  YFDAI DPA V A KP P IF AAA A+ +AP   +GLEDS AGI++
Sbjct: 124 NAPFIVERLGMEKYFDAIVDPASVKAGKPDPAIFAAAAAAIDLAPEVVVGLEDSAAGIKS 183

Query: 178 IKDSGALPIGVG 189
           I D+G L IG+G
Sbjct: 184 INDAGELSIGIG 195


Lambda     K      H
   0.316    0.135    0.377 

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: 159
Number of extensions: 6
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: 221
Length of database: 223
Length adjustment: 22
Effective length of query: 199
Effective length of database: 201
Effective search space:    39999
Effective search space used:    39999
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)

Align candidate WP_027698533.1 TT13_RS02545 (beta-phosphoglucomutase)
to HMM TIGR01990 (pgmB: beta-phosphoglucomutase (EC 5.4.2.6))

# 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/TIGR01990.hmm
# target sequence database:        /tmp/gapView.2751933.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01990  [M=187]
Accession:   TIGR01990
Description: bPGM: beta-phosphoglucomutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-71  226.5   0.0    1.5e-71  226.3   0.0    1.0  1  NCBI__GCF_000691805.2:WP_027698533.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691805.2:WP_027698533.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   0.0   1.5e-71   1.5e-71       1     187 []       7     195 ..       7     195 .. 0.99

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 1.5e-71
                             TIGR01990   1 lkaviFDlDGvitdtaeyhylawkkladelgiefdeelnesLkGvsReesleailkkakk..kyseeekeela 71 
                                           +k++ FD+DGv++dta++h  aw+++ade+g +++eel+e+LkG+ R+ sl+ il+ ++   +y    +e+la
  NCBI__GCF_000691805.2:WP_027698533.1   7 IKGFAFDMDGVLADTARFHAIAWRQIADEVGTTWTEELAEALKGIDRMGSLDLILQAGDVaeQYDLPAREALA 79 
                                           79******************************************************9987779999******* PP

                             TIGR01990  72 erknekYvellkeltpedvlpgikelleelkkkkikialasasknaklvleklelkdkfdaivdaaevkkgkP 144
                                           ++kn++Y+ l+++lt++d lpgi  +l+el ++++k+++asaskna++++e+l+++++fdaivd+a+vk gkP
  NCBI__GCF_000691805.2:WP_027698533.1  80 NKKNDNYRALISKLTSADALPGIFPFLDELLAAGYKMSIASASKNAPFIVERLGMEKYFDAIVDPASVKAGKP 152
                                           ************************************************************************* PP

                             TIGR01990 145 dPeiFlaaaeklgvspeecigieDaeaGieaikaagilavgvg 187
                                           dP iF aaa++++++pe ++g+eD++aGi++i++ag l++g+g
  NCBI__GCF_000691805.2:WP_027698533.1 153 DPAIFAAAAAAIDLAPEVVVGLEDSAAGIKSINDAGELSIGIG 195
                                           *****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (187 nodes)
Target sequences:                          1  (223 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: 13.12
//
[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:

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