Alignments for a candidate for galU in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Marinobacter adhaerens HP15

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate GFF1978 HP15_1935 UTP-glucose-1-phosphate uridylyltransferase

Query= BRENDA::O25363
         (273 letters)



>FitnessBrowser__Marino:GFF1978
          Length = 278

 Score =  356 bits (914), Expect = e-103
 Identities = 171/271 (63%), Positives = 211/271 (77%), Gaps = 1/271 (0%)

Query: 1   MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKR 60
           MIKKCLFP AGYGTRFLP TK +PKE+LP+V+KPL+QY VEEA EAG      VTGR KR
Sbjct: 1   MIKKCLFPVAGYGTRFLPATKAMPKEILPVVNKPLVQYGVEEAAEAGIHEFGFVTGRGKR 60

Query: 61  SLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIG 120
           ++ED+FD SYE+E QI G+ KE  L SIR +I+   F++ RQ +MKGLGHAILTG  L+G
Sbjct: 61  AIEDHFDISYELEQQIAGSGKEELLTSIRELIDHNSFAFTRQNEMKGLGHAILTGRNLVG 120

Query: 121 NEPFAVILADDLCISHD-HPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLE 179
           + PFAV+LADD CI  D    VL QM  LY +++CSIVAIEEV  +E  KYGVI GE ++
Sbjct: 121 DNPFAVVLADDFCIGPDGEDGVLAQMVKLYNQFRCSIVAIEEVPADETHKYGVIAGESMK 180

Query: 180 EGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAK 239
           +G+Y I DMVEKP  EDAPSNLA+IGRYILTPDIFEI+ +T  GKN E+QITDAL  QAK
Sbjct: 181 DGLYRITDMVEKPAPEDAPSNLAIIGRYILTPDIFEIIEKTPAGKNGEVQITDALLEQAK 240

Query: 240 RKRIIAYQFKGKRYDCGSVEGYIEASNAYYK 270
              ++AYQFKG+R+DCGS++G++EA+N  Y+
Sbjct: 241 NGCVLAYQFKGRRFDCGSIDGFVEATNYVYE 271


Lambda     K      H
   0.318    0.136    0.391 

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: 295
Number of extensions: 8
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: 273
Length of database: 278
Length adjustment: 25
Effective length of query: 248
Effective length of database: 253
Effective search space:    62744
Effective search space used:    62744
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: 47 (22.7 bits)

Align candidate GFF1978 HP15_1935 (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.20072.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-120  387.7   0.0   1.7e-120  387.5   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1978  HP15_1935 UTP-glucose-1-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1978  HP15_1935 UTP-glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.5   0.0  1.7e-120  1.7e-120       1     261 []       2     265 ..       2     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 387.5 bits;  conditional E-value: 1.7e-120
                           TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleakl 75 
                                         i+k+++P+aG+Gtr+LPatka+Pke+lp+v+kPl+qy veea eaGi+e  +vtgr+kraiedhfD+syele+++
  lcl|FitnessBrowser__Marino:GFF1978   2 IKKCLFPVAGYGTRFLPATKAMPKEILPVVNKPLVQYGVEEAAEAGIHEFGFVTGRGKRAIEDHFDISYELEQQI 76 
                                         89************************************************************************* PP

                           TIGR01099  76 ekknkeellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee...alkqlielye 147
                                           ++keell ++r+++++ ++ ++rq+e+kGLGha+l++++lvgd+pfav+l+Dd +   +    +l+q+++ly+
  lcl|FitnessBrowser__Marino:GFF1978  77 AGSGKEELLTSIRELIDHNSFAFTRQNEMKGLGHAILTGRNLVGDNPFAVVLADDFCIGPDGedgVLAQMVKLYN 151
                                         *********************************************************87655556********** PP

                           TIGR01099 148 ktgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkg 222
                                         ++++si+a+eevp++e++kYGvi+ge++++ ly+++d+vekP pe+apsnlai+GrY+ltp+ife++e+t+aGk+
  lcl|FitnessBrowser__Marino:GFF1978 152 QFRCSIVAIEEVPADETHKYGVIAGESMKDGLYRITDMVEKPAPEDAPSNLAIIGRYILTPDIFEIIEKTPAGKN 226
                                         *************************************************************************** PP

                           TIGR01099 223 geiqltDalrlllekeevlavklkgkryDvGdklgylka 261
                                         ge+q+tDal  ++++ +vla+++kg+r+D+G+  g+++a
  lcl|FitnessBrowser__Marino:GFF1978 227 GEVQITDALLEQAKNGCVLAYQFKGRRFDCGSIDGFVEA 265
                                         ************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (278 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.01
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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