Alignments for a candidate for galU in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Pseudomonas fluorescens GW456-L13

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate PfGW456L13_2923 UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)

Query= BRENDA::O25363
         (273 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923
          Length = 279

 Score =  367 bits (941), Expect = e-106
 Identities = 172/266 (64%), Positives = 218/266 (81%)

Query: 1   MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKR 60
           MIKKCLFPAAGYGTRFLP TK +PKEMLP+V+KPLIQY VEEA++AG   ++IVTGR KR
Sbjct: 1   MIKKCLFPAAGYGTRFLPATKAMPKEMLPVVNKPLIQYGVEEALDAGLTEISIVTGRGKR 60

Query: 61  SLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIG 120
           +LED+FD SYE+E+QI+GT+KE  L  IR ++++C FSY RQ +MKGLGHAILTG  LIG
Sbjct: 61  ALEDHFDISYELENQIKGTDKEKYLVGIRKLLDECSFSYTRQTEMKGLGHAILTGRPLIG 120

Query: 121 NEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEE 180
           +EPFAV+LADDLC++ +   VL QM  LY++++CSIVAI+EV   E +KYGVI GE + +
Sbjct: 121 DEPFAVVLADDLCVNLEGDGVLTQMVKLYKQFRCSIVAIQEVDPSETNKYGVIAGEMIRD 180

Query: 181 GVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKR 240
            +Y +  MVEKP  EDAPSNLA+IGRYILTPDIF+++ +T+PGK  EIQITDAL  QA+ 
Sbjct: 181 DIYRVHSMVEKPKPEDAPSNLAIIGRYILTPDIFDLIEQTEPGKGGEIQITDALMKQAQN 240

Query: 241 KRIIAYQFKGKRYDCGSVEGYIEASN 266
             ++AY+FKGKR+DCG  EGYI+A+N
Sbjct: 241 GCVMAYKFKGKRFDCGGAEGYIDATN 266


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: 303
Number of extensions: 9
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: 273
Length of database: 279
Length adjustment: 25
Effective length of query: 248
Effective length of database: 254
Effective search space:    62992
Effective search space used:    62992
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 PfGW456L13_2923 (UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9))
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.15553.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   7.5e-125  401.7   0.0   8.5e-125  401.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923  UTP--glucose-1-phosphate uridyly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923  UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.6   0.0  8.5e-125  8.5e-125       1     261 []       2     264 ..       2     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 401.6 bits;  conditional E-value: 8.5e-125
                                               TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtg 55 
                                                             i+k+++PaaG+Gtr+LPatka+Pkemlp+v+kPliqy veea++aG++ei +vtg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923   2 IKKCLFPAAGYGTRFLPATKAMPKEMLPVVNKPLIQYGVEEALDAGLTEISIVTG 56 
                                                             89***************************************************** PP

                                               TIGR01099  56 rskraiedhfDtsyeleaklekknkeellkevrkiaelatilyvrqkeakGLGha 110
                                                             r+kra+edhfD+syele++++ ++ke++l  +rk+ +++++ y+rq e+kGLGha
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923  57 RGKRALEDHFDISYELENQIKGTDKEKYLVGIRKLLDECSFSYTRQTEMKGLGHA 111
                                                             ******************************************************* PP

                                               TIGR01099 111 vllaeelvgdepfavllgDdlvseeee..alkqlielyektgasiiaveevpkee 163
                                                             +l++++l+gdepfav+l+Ddl+++ e   +l q+++ly+++++si+a++ev+ +e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923 112 ILTGRPLIGDEPFAVVLADDLCVNLEGdgVLTQMVKLYKQFRCSIVAIQEVDPSE 166
                                                             ***********************998888************************** PP

                                               TIGR01099 164 vskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetk 218
                                                             ++kYGvi+ge++ +++y+v+++vekPkpe+apsnlai+GrY+ltp+if+l+e+t+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923 167 TNKYGVIAGEMIRDDIYRVHSMVEKPKPEDAPSNLAIIGRYILTPDIFDLIEQTE 221
                                                             ******************************************************* PP

                                               TIGR01099 219 aGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261
                                                             +Gkggeiq+tDal +++++ +v+a+k+kgkr+D+G ++gy++a
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2923 222 PGKGGEIQITDALMKQAQNGCVMAYKFKGKRFDCGGAEGYIDA 264
                                                             ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (279 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: 6.85
//
[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