Alignments for a candidate for galU in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Desulfovibrio vulgaris Hildenborough

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 206724 DVU1283 UTP-glucose-1-phosphate uridylyltransferase

Query= SwissProt::Q05852
         (292 letters)



>MicrobesOnline__882:206724
          Length = 292

 Score =  276 bits (705), Expect = 5e-79
 Identities = 137/284 (48%), Positives = 194/284 (68%)

Query: 4   VRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSKRA 63
           +RK +IP AG GTR LPATK +PKEMLP+ +KP +QY++EEA ++GI D++ VT + K+ 
Sbjct: 5   IRKVVIPVAGWGTRSLPATKNIPKEMLPVYNKPVVQYVVEEAQKSGIGDVVFVTNRDKKI 64

Query: 64  IEDHFDYSPELERNLEEKGKTELLEKVKKASNLADIHYIRQKEPKGLGHAVWCARNFIGD 123
           IEDHFDY+ +LE  LE  GKTE+L +V++ + + +I  +RQK+  GLGHAV CAR  + D
Sbjct: 65  IEDHFDYNLQLESVLERAGKTEMLRQVREVAEMVNIISVRQKKQLGLGHAVLCAREIVRD 124

Query: 124 EPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTSEGRRY 183
           EPFAV++GDD++   TPG++QL+D        +IGV +VP ++  RYGII    +    Y
Sbjct: 125 EPFAVMVGDDLMFGMTPGIQQLIDVAVAEHLPVIGVMEVPADKVSRYGIIAGEETAPGIY 184

Query: 184 QVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKLNEIQRV 243
           +V   VEKP    APS LAI+GRYV TP+IF  LE+ + G GGEIQLTDA+Q L + + +
Sbjct: 185 KVSRLVEKPSIAEAPSRLAIVGRYVLTPDIFDSLEKVKPGHGGEIQLTDALQNLADDRGL 244

Query: 244 FAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFMEGLL 287
            A    G R+D G+   ++T  + FA+Q++ LRD L+  +  LL
Sbjct: 245 LAVKIRGMRFDAGDWAEYLTANIYFALQEEGLRDDLISQLRPLL 288


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: 254
Number of extensions: 7
Number of successful extensions: 1
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: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
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 206724 DVU1283 (UTP-glucose-1-phosphate uridylyltransferase)
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.20295.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.2e-107  344.0   0.2   3.6e-107  343.8   0.2    1.0  1  lcl|MicrobesOnline__882:206724  DVU1283 UTP-glucose-1-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206724  DVU1283 UTP-glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.8   0.2  3.6e-107  3.6e-107       1     261 []       5     265 ..       5     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 343.8 bits;  conditional E-value: 3.6e-107
                       TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklekkn 79 
                                     irk+viP+aG+Gtr LPatk iPkemlp+ +kP++qyvveea ++Gi ++v+vt+r+k+ iedhfD++++le+ le+++
  lcl|MicrobesOnline__882:206724   5 IRKVVIPVAGWGTRSLPATKNIPKEMLPVYNKPVVQYVVEEAQKSGIGDVVFVTNRDKKIIEDHFDYNLQLESVLERAG 83 
                                     89***************************************************************************** PP

                       TIGR01099  80 keellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeealkqlielyektgasiiavee 158
                                     k+e+l++vr++ae+++i+ vrqk++ GLGhavl+a+e+v depfav++gDdl+   ++ ++qli++    +  +i+v+e
  lcl|MicrobesOnline__882:206724  84 KTEMLRQVREVAEMVNIISVRQKKQLGLGHAVLCAREIVRDEPFAVMVGDDLMFGMTPGIQQLIDVAVAEHLPVIGVME 162
                                     ******************************************************************************* PP

                       TIGR01099 159 vpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiqltDalrlllek 237
                                     vp+++vs+YG+i+gee+   +y+v+ lvekP+  eaps laivGrYvltp+if+ le++k+G+ggeiqltDal+ l+++
  lcl|MicrobesOnline__882:206724 163 VPADKVSRYGIIAGEETAPGIYKVSRLVEKPSIAEAPSRLAIVGRYVLTPDIFDSLEKVKPGHGGEIQLTDALQNLADD 241
                                     ******************************************************************************* PP

                       TIGR01099 238 eevlavklkgkryDvGdklgylka 261
                                       +lavk++g r+D Gd  +yl+a
  lcl|MicrobesOnline__882:206724 242 RGLLAVKIRGMRFDAGDWAEYLTA 265
                                     *********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (292 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: 00:00:00.01
# Mc/sec: 7.24
//
[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:

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 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