Alignments for a candidate for galU in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Dinoroseobacter shibae DFL-12

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 3610196 Dshi_3577 UTP-glucose-1-phosphate uridylyltransferase (RefSeq)

Query= SwissProt::Q05852
         (292 letters)



>FitnessBrowser__Dino:3610196
          Length = 298

 Score =  285 bits (730), Expect = 7e-82
 Identities = 136/287 (47%), Positives = 201/287 (70%), Gaps = 2/287 (0%)

Query: 2   KKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSK 61
           + V+ A+ P AG+GTRFLPATK++PKE++ +VD+P +QY I+EA  AGIE+ I VT + K
Sbjct: 4   RSVKTAVFPVAGMGTRFLPATKSVPKEIMTLVDRPLVQYAIDEARAAGIEEFIFVTSRGK 63

Query: 62  RAIEDHFDYSPELERNLEEKGKTELLEKVKKAS-NLADIHYIRQKEPKGLGHAVWCARNF 120
            A+ED+FD +P+LE+ LE+KGKT+LLE ++  + +   I Y+RQ    GLGHAVWCAR  
Sbjct: 64  SALEDYFDAAPQLEQTLEDKGKTKLLEILRNTNMDSGAIAYVRQTRALGLGHAVWCARRL 123

Query: 121 IGDEPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTSEG 180
           +G+EPFAV+L DD++ AE P L Q+++ Y++   +++   +VP ++   YGI+D     G
Sbjct: 124 LGNEPFAVILPDDVIAAEKPCLAQMVEAYQELGGNMVATMEVPMDKASAYGIVDVEEDMG 183

Query: 181 RRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAI-QKLNE 239
              +VK  +EKP    APSNLA++GRY+ +PE+   L++ Q+GAGGEIQLTDAI Q++  
Sbjct: 184 SVVRVKGMIEKPKAEDAPSNLAVIGRYILSPEVLDNLDKGQIGAGGEIQLTDAIAQEITS 243

Query: 240 IQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFMEGL 286
              V+ + F G+RYD G K GF+  T+ FA+   +LRD+L  F++ L
Sbjct: 244 KNNVYGFRFSGQRYDCGSKAGFLQATVSFALARPDLRDELSDFLQEL 290


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: 241
Number of extensions: 8
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: 292
Length of database: 298
Length adjustment: 26
Effective length of query: 266
Effective length of database: 272
Effective search space:    72352
Effective search space used:    72352
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 3610196 Dshi_3577 (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.1974.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-105  338.0   0.0   2.4e-105  337.8   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610196  Dshi_3577 UTP-glucose-1-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610196  Dshi_3577 UTP-glucose-1-phosphate uridylyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.8   0.0  2.4e-105  2.4e-105       1     261 []       6     268 ..       6     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 337.8 bits;  conditional E-value: 2.4e-105
                         TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklek 77 
                                       +++av+P+aG+Gtr+LPatk++Pke++++vd+Pl+qy+++ea +aGiee ++vt+r+k a+ed+fD + +le++le+
  lcl|FitnessBrowser__Dino:3610196   6 VKTAVFPVAGMGTRFLPATKSVPKEIMTLVDRPLVQYAIDEARAAGIEEFIFVTSRGKSALEDYFDAAPQLEQTLED 82 
                                       689************************************************************************** PP

                         TIGR01099  78 knkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeealkqlielyektgasi 153
                                       k+k++ll+ +r+       i yvrq +a GLGhav++a++l+g+epfav+l+Dd++++e+++l+q++e+y++ g ++
  lcl|FitnessBrowser__Dino:3610196  83 KGKTKLLEILRNTNMDsGAIAYVRQTRALGLGHAVWCARRLLGNEPFAVILPDDVIAAEKPCLAQMVEAYQELGGNM 159
                                       ***********9865449*********************************************************** PP

                         TIGR01099 154 iaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiqltDa 230
                                       +a +evp ++ s+YG++d+ee   ++++vk ++ekPk+e+apsnla++GrY+l+pe+ + l++ ++G+ggeiqltDa
  lcl|FitnessBrowser__Dino:3610196 160 VATMEVPMDKASAYGIVDVEEDMGSVVRVKGMIEKPKAEDAPSNLAVIGRYILSPEVLDNLDKGQIGAGGEIQLTDA 236
                                       ***************************************************************************** PP

                         TIGR01099 231 lrl.llekeevlavklkgkryDvGdklgylka 261
                                       +++ +++k++v++++++g+ryD+G+k g+l+a
  lcl|FitnessBrowser__Dino:3610196 237 IAQeITSKNNVYGFRFSGQRYDCGSKAGFLQA 268
                                       *861557889********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (298 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 8.54
//
[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