Alignments for a candidate for galU in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Pseudomonas fluorescens FW300-N1B4

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate Pf1N1B4_5948 UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)

Query= BRENDA::O25363
         (273 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948
          Length = 277

 Score =  375 bits (964), Expect = e-109
 Identities = 177/266 (66%), Positives = 221/266 (83%)

Query: 1   MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKR 60
           MI+KCLFPAAGYGTRFLP TK +PKEMLPIV+KPLIQYAVEEA +AG + MAIVTGR KR
Sbjct: 1   MIRKCLFPAAGYGTRFLPATKAMPKEMLPIVNKPLIQYAVEEARDAGLQHMAIVTGRGKR 60

Query: 61  SLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIG 120
           +LED+FD S+E+EHQI+GT+KE  L+  R +I+ C FSY RQ +MKGLGHAIL+G +LIG
Sbjct: 61  ALEDHFDVSFELEHQIRGTDKERYLEGTRELIDTCTFSYTRQVEMKGLGHAILSGRSLIG 120

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

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

Query: 241 KRIIAYQFKGKRYDCGSVEGYIEASN 266
             ++AY+FKG+R+DCG  EGYIEA+N
Sbjct: 241 GCVLAYKFKGQRFDCGGAEGYIEATN 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: 281
Number of extensions: 5
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: 277
Length adjustment: 25
Effective length of query: 248
Effective length of database: 252
Effective search space:    62496
Effective search space used:    62496
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 Pf1N1B4_5948 (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.28864.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.6e-123  397.4   0.0   1.8e-123  397.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948  UTP--glucose-1-phosphate uridyly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948  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 !  397.2   0.0  1.8e-123  1.8e-123       1     261 []       2     264 ..       2     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 397.2 bits;  conditional E-value: 1.8e-123
                                      TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedh 64 
                                                    irk+++PaaG+Gtr+LPatka+Pkemlpiv+kPliqy+veea +aG++++++vtgr+kra+edh
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948   2 IRKCLFPAAGYGTRFLPATKAMPKEMLPIVNKPLIQYAVEEARDAGLQHMAIVTGRGKRALEDH 65 
                                                    89************************************************************** PP

                                      TIGR01099  65 fDtsyeleaklekknkeellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllg 128
                                                    fD+s+ele++++ ++ke++l+  r++++++t+ y+rq e+kGLGha+l +++l+gdepfav+l+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948  66 FDVSFELEHQIRGTDKERYLEGTRELIDTCTFSYTRQVEMKGLGHAILSGRSLIGDEPFAVVLA 129
                                                    **************************************************************** PP

                                      TIGR01099 129 Ddlvseeee..alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPk 190
                                                    Ddl+ + e   +l+q+i+ly+++++si+a++evp+e+++kYGvi+ge + e +y+v+++vekP+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948 130 DDLCLNLEGdgVLAQMIKLYQQFRCSIVAIQEVPREQTQKYGVIAGELIREGIYRVNSMVEKPR 193
                                                    ****9988778***************************************************** PP

                                      TIGR01099 191 peeapsnlaivGrYvltpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGd 254
                                                    pe+apsnlai+GrY+ltp+if+l+++t++Gkggeiq+tDal +++++ +vla+k+kg+r+D+G 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948 194 PEDAPSNLAIIGRYILTPDIFDLIADTEPGKGGEIQITDALMKQAQNGCVLAYKFKGQRFDCGG 257
                                                    **************************************************************** PP

                                      TIGR01099 255 klgylka 261
                                                    ++gy++a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5948 258 AEGYIEA 264
                                                    *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (277 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: 10.05
//
[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