GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Oscillibacter ruminantium GH1

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_040660816.1 ON16_RS07550 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_000307265.1:WP_040660816.1
          Length = 329

 Score =  359 bits (922), Expect = e-104
 Identities = 189/331 (57%), Positives = 230/331 (69%), Gaps = 3/331 (0%)

Query: 1   MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60
           M+ILVLGGAGYIGSH    LV  G++ VVV D+L TG R AV   A FY+GD+ D+ F  
Sbjct: 1   MSILVLGGAGYIGSHTALALVNAGRD-VVVADNLETGFRKAVPEMARFYKGDIRDRAFCD 59

Query: 61  KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120
            +F E   +D VIHFAA S VGESM  PLKY+ NN  G   LLE M   GV  IVFSSTA
Sbjct: 60  GLF-EREQIDGVIHFAANSQVGESMTNPLKYYANNMGGTRVLLESMVAHGVGKIVFSSTA 118

Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180
           ATYG PE +PILET    P N YGE+KL ME +MKW   A+G++YV LRYFN  GA    
Sbjct: 119 ATYGEPERVPILETDATVPTNCYGETKLSMEKMMKWISVAHGLRYVALRYFNACGAQPDG 178

Query: 181 RLVRTRS-ETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVE 239
            +    + ETHL+P+ILQV  G REKI IFGDDY TPDGT +RDY+H  DLA AH+LA++
Sbjct: 179 SIGEAHNPETHLIPVILQVPGGQREKISIFGDDYPTPDGTCIRDYIHVCDLAQAHILALD 238

Query: 240 YLRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKART 299
           YL    E+  FNLG+  GFS  +++E ARKVTG  IP E   RR GDP  LIASSEKA+T
Sbjct: 239 YLLSSGENNVFNLGNGVGFSVKEVIEEARKVTGHAIPTEVLPRRAGDPAQLIASSEKAKT 298

Query: 300 VLGWKPQFDNIEKIIASAWAWHSSHPKGYDD 330
           +LGWKP+F+++  II +AW WH +HP+G++D
Sbjct: 299 LLGWKPEFEDLHTIIQTAWDWHKTHPRGFED 329


Lambda     K      H
   0.318    0.136    0.401 

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: 14
Number of successful extensions: 4
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: 332
Length of database: 329
Length adjustment: 28
Effective length of query: 304
Effective length of database: 301
Effective search space:    91504
Effective search space used:    91504
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_040660816.1 ON16_RS07550 (UDP-glucose 4-epimerase GalE)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# 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/TIGR01179.hmm
# target sequence database:        /tmp/gapView.76678.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-138  445.3   0.0   6.2e-138  445.1   0.0    1.0  1  NCBI__GCF_000307265.1:WP_040660816.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000307265.1:WP_040660816.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.1   0.0  6.2e-138  6.2e-138       2     330 ..       3     325 ..       2     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 445.1 bits;  conditional E-value: 6.2e-138
                             TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 
                                           iLv GgaGyiGsh++ +l ++g +vvv Dnl +g+++a++++       +++gd++d++  + ++e+e+id v
  NCBI__GCF_000307265.1:WP_040660816.1   3 ILVLGGAGYIGSHTALALVNAGRDVVVADNLETGFRKAVPEMA-----RFYKGDIRDRAFCDGLFEREQIDGV 70 
                                           9*****************************************9.....5************************ PP

                             TIGR01179  75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147
                                           iHfaa  +vgEs+++PlkYY+nn+ +t +Lle+m+++gv k++Fss+aa+Yge+e+vpi E+ ++ p+n YG+
  NCBI__GCF_000307265.1:WP_040660816.1  71 IHFAANSQVGESMTNPLKYYANNMGGTRVLLESMVAHGVGKIVFSSTAATYGEPERVPILETDATVPTNCYGE 143
                                           ************************************************************************* PP

                             TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptk 220
                                           +kl +E+++k ++ a ++l++v+LRYFn++GA+++g+iGea++++thli+++++v  g+rek++ifG+dypt+
  NCBI__GCF_000307265.1:WP_040660816.1 144 TKLSMEKMMKWISVA-HGLRYVALRYFNACGAQPDGSIGEAHNPETHLIPVILQVPGGQREKISIFGDDYPTP 215
                                           ************999.********************************************************* PP

                             TIGR01179 221 DGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpas 293
                                           DGtc+RDyiHv+Dla+aH+ al++l ++ge +v+nlG+g gfsvkevie+++kv+g+ i++e+ +rRaGDpa+
  NCBI__GCF_000307265.1:WP_040660816.1 216 DGTCIRDYIHVCDLAQAHILALDYLLSSGENNVFNLGNGVGFSVKEVIEEARKVTGHAIPTEVLPRRAGDPAQ 288
                                           ************************************************************************* PP

                             TIGR01179 294 lvadaskikrelgwkpkyddLeeiiksawdWekklke 330
                                           l+a+++k+k+ lgwkp+++dL++ii++awdW+k++++
  NCBI__GCF_000307265.1:WP_040660816.1 289 LIASSEKAKTLLGWKPEFEDLHTIIQTAWDWHKTHPR 325
                                           *********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (329 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: 25.50
//
[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