Alignments for a candidate for galU in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Sinorhizobium meliloti 1021

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 SMc04023 SMc04023 UTP--glucose-1-phosphate uridylyltransferase

Query= SwissProt::Q05852
         (292 letters)



>FitnessBrowser__Smeli:SMc04023
          Length = 295

 Score =  276 bits (705), Expect = 5e-79
 Identities = 143/289 (49%), Positives = 195/289 (67%), Gaps = 9/289 (3%)

Query: 2   KKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSK 61
           +KVRKA+ P AGLGTRFLPATKA+PKEML +VDKP IQY+++EA+EAGIE +I VTG+SK
Sbjct: 5   RKVRKAVFPVAGLGTRFLPATKAVPKEMLTVVDKPVIQYVVDEALEAGIEHLIFVTGRSK 64

Query: 62  RAIEDHFDYSPELERNLEEKGKT---ELLEKVKKASNLADIHYIRQKEPKGLGHAVWCAR 118
             IED+FD   EL++ L E+ K    ELLE +   +      + RQ+ P GLGHAVWCAR
Sbjct: 65  AVIEDYFDIQVELDQTLRERNKKAEIELLEAMLPKAGTTS--FTRQQAPLGLGHAVWCAR 122

Query: 119 NFIGDEPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTS 178
           + +G+EPFA+LL D I++ E   L+ +++ YE++  +++ V++   ++ H+YGI+    +
Sbjct: 123 DLVGNEPFALLLPDMIMKGEKGCLKGMVELYEESGGNVVAVEECAPDQAHKYGIVGVGET 182

Query: 179 EGRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKLN 238
            G  +++   VEKP KGTAPSN  I GRY+  PEIF  LE Q+ GAG EIQLTD + KL 
Sbjct: 183 VGDGFRITRMVEKPAKGTAPSNFFINGRYILQPEIFPILETQERGAGNEIQLTDGMVKLA 242

Query: 239 EIQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFMEGLL 287
           E Q   AY F G  YD G K GFI   + FA++  ++R    P +EG L
Sbjct: 243 EAQPFAAYHFRGDTYDCGAKDGFILANVAFALERGDIR----PIVEGPL 287


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: 249
Number of extensions: 4
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: 292
Length of database: 295
Length adjustment: 26
Effective length of query: 266
Effective length of database: 269
Effective search space:    71554
Effective search space used:    71554
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 SMc04023 SMc04023 (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.5624.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.7e-105  337.7   0.0   3.1e-105  337.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc04023  SMc04023 UTP--glucose-1-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04023  SMc04023 UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.4   0.0  3.1e-105  3.1e-105       1     260 [.       7     267 ..       7     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 337.4 bits;  conditional E-value: 3.1e-105
                           TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleakl 75 
                                         +rkav+P+aGlGtr+LPatka+Pkeml++vdkP+iqyvv+ea+eaGie++++vtgrsk  ied+fD+++el+++l
  lcl|FitnessBrowser__Smeli:SMc04023   7 VRKAVFPVAGLGTRFLPATKAVPKEMLTVVDKPVIQYVVDEALEAGIEHLIFVTGRSKAVIEDYFDIQVELDQTL 81 
                                         79************************************************************************* PP

                           TIGR01099  76 ekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeealkqlielyekt 149
                                         +++nk+ +++ ++++ ++  t  ++rq+   GLGhav++a++lvg+epfa ll+D +++ e+ +lk ++elye+ 
  lcl|FitnessBrowser__Smeli:SMc04023  82 RERNKKAEIELLEAMLPKaGTTSFTRQQAPLGLGHAVWCARDLVGNEPFALLLPDMIMKGEKGCLKGMVELYEES 156
                                         ****************9967899**************************************************** PP

                           TIGR01099 150 gasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkgge 224
                                         g +++avee + ++ +kYG++ + e+  + ++++ +vekP + +apsn+ i GrY+l+peif +le++++G+g+e
  lcl|FitnessBrowser__Smeli:SMc04023 157 GGNVVAVEECAPDQAHKYGIVGVGETVGDGFRITRMVEKPAKGTAPSNFFINGRYILQPEIFPILETQERGAGNE 231
                                         *************************************************************************** PP

                           TIGR01099 225 iqltDalrlllekeevlavklkgkryDvGdklgylk 260
                                         iqltD++ +l+e++ + a++++g +yD+G k g++ 
  lcl|FitnessBrowser__Smeli:SMc04023 232 IQLTDGMVKLAEAQPFAAYHFRGDTYDCGAKDGFIL 267
                                         **********************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (295 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: 9.21
//
[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