GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Desulfovibrio vulgaris Miyazaki F

Align UTP--glucose-1-phosphate uridylyltransferase; Alpha-D-glucosyl-1-phosphate uridylyltransferase; General stress protein 33; GSP33; UDP-glucose pyrophosphorylase; UDPGP; Uridine diphosphoglucose pyrophosphorylase; EC 2.7.7.9 (characterized)
to candidate 8499282 DvMF_0060 UTP-glucose-1-phosphate uridylyltransferase (RefSeq)

Query= SwissProt::Q05852
         (292 letters)



>FitnessBrowser__Miya:8499282
          Length = 291

 Score =  284 bits (726), Expect = 2e-81
 Identities = 140/284 (49%), Positives = 198/284 (69%)

Query: 4   VRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSKRA 63
           +RK +IP AG GTR LPATK +PKEMLP+ +KP +QY++EEA+ +GI D++ VT + K+ 
Sbjct: 3   IRKVVIPVAGWGTRSLPATKNIPKEMLPVYNKPVVQYVVEEAMRSGIGDVVFVTNRDKKI 62

Query: 64  IEDHFDYSPELERNLEEKGKTELLEKVKKASNLADIHYIRQKEPKGLGHAVWCARNFIGD 123
           IEDHFDY+ +LE  LE  GKTE+L +V++ + + +I  IRQK+  GLGHAV CAR+ + D
Sbjct: 63  IEDHFDYNLQLEGVLERAGKTEMLRQVREVAEMVNIISIRQKQQLGLGHAVLCARDVVRD 122

Query: 124 EPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTSEGRRY 183
           E FAV++GDD++   TPG++QL+D        +IGV +VP ++ +RYGII         +
Sbjct: 123 ESFAVMVGDDLMFGMTPGIKQLIDVAASERLPVIGVMEVPADKVNRYGIISGEEFAPGIF 182

Query: 184 QVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKLNEIQRV 243
           +V   VEKP  G APS LAI+GRYV TP+IF  LE+ + G GGEIQLTDA+Q L + + +
Sbjct: 183 KVNKLVEKPKLGEAPSRLAIVGRYVLTPDIFRCLEQMKPGHGGEIQLTDALQMLADDRGL 242

Query: 244 FAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFMEGLL 287
            A    G R+D G+   ++T  + FA+QD+ELRD+LV  ++ LL
Sbjct: 243 LAVKIRGMRFDAGDWAEYLTANIYFALQDEELRDELVRQLKPLL 286


Lambda     K      H
   0.317    0.138    0.389 

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: 258
Number of extensions: 12
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: 292
Length of database: 291
Length adjustment: 26
Effective length of query: 266
Effective length of database: 265
Effective search space:    70490
Effective search space used:    70490
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: 48 (23.1 bits)

Align candidate 8499282 DvMF_0060 (UTP-glucose-1-phosphate uridylyltransferase (RefSeq))
to HMM TIGR01099 (galU: UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9))

# 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/TIGR01099.hmm
# target sequence database:        /tmp/gapView.540819.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01099  [M=261]
Accession:   TIGR01099
Description: galU: UTP--glucose-1-phosphate uridylyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.2e-108  346.5   0.1   5.9e-108  346.4   0.1    1.0  1  lcl|FitnessBrowser__Miya:8499282  DvMF_0060 UTP-glucose-1-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499282  DvMF_0060 UTP-glucose-1-phosphate uridylyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.4   0.1  5.9e-108  5.9e-108       1     261 []       3     263 ..       3     263 .. 1.00

  Alignments for each domain:
  == domain 1  score: 346.4 bits;  conditional E-value: 5.9e-108
                         TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklek 77 
                                       irk+viP+aG+Gtr LPatk iPkemlp+ +kP++qyvveea+++Gi ++v+vt+r+k+ iedhfD++++le  le+
  lcl|FitnessBrowser__Miya:8499282   3 IRKVVIPVAGWGTRSLPATKNIPKEMLPVYNKPVVQYVVEEAMRSGIGDVVFVTNRDKKIIEDHFDYNLQLEGVLER 79 
                                       89*************************************************************************** PP

                         TIGR01099  78 knkeellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeealkqlielyektgasii 154
                                       ++k+e+l++vr++ae+++i+ +rqk++ GLGhavl+a+++v de+fav++gDdl+   ++ +kqli++    +  +i
  lcl|FitnessBrowser__Miya:8499282  80 AGKTEMLRQVREVAEMVNIISIRQKQQLGLGHAVLCARDVVRDESFAVMVGDDLMFGMTPGIKQLIDVAASERLPVI 156
                                       ***************************************************************************** PP

                         TIGR01099 155 aveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiqltDal 231
                                       +v+evp+++v++YG+i+gee    +++v++lvekPk  eaps laivGrYvltp+if+ le++k+G+ggeiqltDal
  lcl|FitnessBrowser__Miya:8499282 157 GVMEVPADKVNRYGIISGEEFAPGIFKVNKLVEKPKLGEAPSRLAIVGRYVLTPDIFRCLEQMKPGHGGEIQLTDAL 233
                                       ***************************************************************************** PP

                         TIGR01099 232 rlllekeevlavklkgkryDvGdklgylka 261
                                       ++l+++  +lavk++g r+D Gd  +yl+a
  lcl|FitnessBrowser__Miya:8499282 234 QMLADDRGLLAVKIRGMRFDAGDWAEYLTA 263
                                       ***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (291 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: 22.91
//
[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