Alignments for a candidate for galU in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Burkholderia phytofirmans PsJN

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate BPHYT_RS31105 BPHYT_RS31105 UTP--glucose-1-phosphate uridylyltransferase

Query= BRENDA::Q8PK83
         (297 letters)



>FitnessBrowser__BFirm:BPHYT_RS31105
          Length = 293

 Score =  304 bits (779), Expect = 1e-87
 Identities = 155/272 (56%), Positives = 200/272 (73%), Gaps = 1/272 (0%)

Query: 4   RIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNRYKH 63
           ++ KA+FPVAGLGTRFLPATK  PKEMLPI+DKPLIQYAV+EA+ AG   +IFVT R K 
Sbjct: 3   KVTKAIFPVAGLGTRFLPATKASPKEMLPIVDKPLIQYAVEEAMAAGITEMIFVTGRSKR 62

Query: 64  SIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAKAVV 123
           +I D+FDK+YE+E +LE  GK + LELVR   P  V   +V Q EALGLGHAV+CA+ +V
Sbjct: 63  AIEDHFDKSYEIEAELEARGKDKLLELVRSIKPSHVDCFYVRQPEALGLGHAVMCAEKLV 122

Query: 124 GNEPFAVLLPDDLMWNRGDAALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDAFDG 183
           G+ PFAV+L DDL++      +TQM  V +    SVI VE++P ++T SYGIV    ++ 
Sbjct: 123 GDNPFAVILADDLLYGT-PPVMTQMIEVFDHYHSSVIGVEEIPAEETRSYGIVDGKKWED 181

Query: 184 RKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAELLKE 243
              +++ IVEKP+P +APSNL VVGRYVL P+IF+ L A   GAGGE+QLTDAI  LL +
Sbjct: 182 SIIKMSRIVEKPEPSMAPSNLGVVGRYVLKPRIFEHLRALKPGAGGELQLTDAIQSLLAD 241

Query: 244 EQVDAFRFEGRRFDCGAHIGLIEATVHFALEH 275
           EQV A+++ G RFDCG+ +G ++ATV FAL H
Sbjct: 242 EQVLAYKYHGTRFDCGSKLGYLKATVEFALRH 273


Lambda     K      H
   0.319    0.137    0.393 

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: 263
Number of extensions: 6
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: 297
Length of database: 293
Length adjustment: 26
Effective length of query: 271
Effective length of database: 267
Effective search space:    72357
Effective search space used:    72357
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS31105 BPHYT_RS31105 (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.25328.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.4e-119  383.2   0.0   3.8e-119  383.0   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS31105  BPHYT_RS31105 UTP--glucose-1-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS31105  BPHYT_RS31105 UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.0   0.0  3.8e-119  3.8e-119       1     261 []       4     265 ..       4     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 383.0 bits;  conditional E-value: 3.8e-119
                                TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsye 70 
                                              + ka++P+aGlGtr+LPatka PkemlpivdkPliqy+veea++aGi+e+++vtgrskraiedhfD+sye
  lcl|FitnessBrowser__BFirm:BPHYT_RS31105   4 VTKAIFPVAGLGTRFLPATKASPKEMLPIVDKPLIQYAVEEAMAAGITEMIFVTGRSKRAIEDHFDKSYE 73 
                                              679******************************************************************* PP

                                TIGR01099  71 leaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeeal 139
                                              +ea+le ++k++ll+ vr+i ++ ++++yvrq ea GLGhav++ae+lvgd+pfav+l+Ddl+  + +++
  lcl|FitnessBrowser__BFirm:BPHYT_RS31105  74 IEAELEARGKDKLLELVRSIKPShVDCFYVRQPEALGLGHAVMCAEKLVGDNPFAVILADDLLYGTPPVM 143
                                              *********************988********************************************** PP

                                TIGR01099 140 kqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpe 209
                                               q+ie+++++++s+i+vee+p+ee+++YG++dg++ e+++++++ +vekP+p  apsnl +vGrYvl+p+
  lcl|FitnessBrowser__BFirm:BPHYT_RS31105 144 TQMIEVFDHYHSSVIGVEEIPAEETRSYGIVDGKKWEDSIIKMSRIVEKPEPSMAPSNLGVVGRYVLKPR 213
                                              ********************************************************************** PP

                                TIGR01099 210 ifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261
                                              ife+l+ +k+G+gge+qltDa++ ll +e+vla+k +g+r+D+G+klgylka
  lcl|FitnessBrowser__BFirm:BPHYT_RS31105 214 IFEHLRALKPGAGGELQLTDAIQSLLADEQVLAYKYHGTRFDCGSKLGYLKA 265
                                              **************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (293 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: 11.22
//
[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