GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Methanospirillum lacunae Ki8-1

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 WP_109969550.1 DK846_RS13790 UTP--glucose-1-phosphate uridylyltransferase GalU

Query= SwissProt::Q05852
         (292 letters)



>NCBI__GCF_003173355.1:WP_109969550.1
          Length = 294

 Score =  266 bits (680), Expect = 4e-76
 Identities = 143/287 (49%), Positives = 187/287 (65%), Gaps = 6/287 (2%)

Query: 1   MKKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKS 60
           ++KVRK +IPAAGLGTRFLP TKA PKEMLP+VDKP IQY++EEAV +GI+DIIIVTG++
Sbjct: 2   VQKVRKVVIPAAGLGTRFLPITKAQPKEMLPVVDKPVIQYVVEEAVASGIDDIIIVTGRN 61

Query: 61  KRAIEDHFDYSPELERNLEEKGKTELLEKVKKASNLADIHYIRQKEPKGLGHAVWCARNF 120
           KRAIEDHFD   ELE        +   +     S++ +IHYIRQ+EP+GLG A+  +   
Sbjct: 62  KRAIEDHFDRCIELEHVFPSNQGSGASDAYVDLSDIPNIHYIRQREPRGLGDAILLSEKH 121

Query: 121 IGDEPFAVLLGDDIVQA---ETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLT 177
             DEPF VLLGD I  A   E     Q++  Y K   SII V+ VPE++   YGIID   
Sbjct: 122 CNDEPFVVLLGDTITIAPENEKTCTSQMIHAYTKYGQSIIAVEPVPEKKIPDYGIIDGNL 181

Query: 178 SEGRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKL 237
            +   Y++KN VEKP    APSNL  +G Y+FTPEIF  L++   G GGEIQLTDAI+KL
Sbjct: 182 IDKNFYEIKNIVEKPTISDAPSNLGAIGCYLFTPEIFSCLKQTTPGKGGEIQLTDAIKKL 241

Query: 238 NEIQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFME 284
           +    +       +RYD+G+K+G++    E A+  KE  D L+  ++
Sbjct: 242 SHSIGMIT---NCRRYDIGDKIGWMKAFFELALSRKEFHDDLMSILQ 285


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: 278
Number of extensions: 14
Number of successful extensions: 4
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: 294
Length adjustment: 26
Effective length of query: 266
Effective length of database: 268
Effective search space:    71288
Effective search space used:    71288
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 WP_109969550.1 DK846_RS13790 (UTP--glucose-1-phosphate uridylyltransferase GalU)
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.1601190.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-106  340.4   0.0   4.6e-106  340.1   0.0    1.0  1  NCBI__GCF_003173355.1:WP_109969550.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003173355.1:WP_109969550.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.1   0.0  4.6e-106  4.6e-106       1     261 []       5     265 ..       5     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 340.1 bits;  conditional E-value: 4.6e-106
                             TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyelea 73 
                                           +rk+viPaaGlGtr+LP+tka+Pkemlp+vdkP+iqyvveeav++Gi++i++vtgr+kraiedhfD+ +ele+
  NCBI__GCF_003173355.1:WP_109969550.1   5 VRKVVIPAAGLGTRFLPITKAQPKEMLPVVDKPVIQYVVEEAVASGIDDIIIVTGRNKRAIEDHFDRCIELEH 77 
                                           79*********************************************************************** PP

                             TIGR01099  74 klekknkeellkevrkiaelatilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee...alkqli 143
                                            + +++ + + +   ++++  +i+y+rq+e +GLG+a+ll+e++  depf+vllgD+++ + e+   ++ q+i
  NCBI__GCF_003173355.1:WP_109969550.1  78 VFPSNQGSGASDAYVDLSDIPNIHYIRQREPRGLGDAILLSEKHCNDEPFVVLLGDTITIAPENektCTSQMI 150
                                           **********************************************************9766555569***** PP

                             TIGR01099 144 elyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifellee 216
                                           ++y+k+g+siiave vp++++  YG+idg+ ++++ ye+k++vekP+  +apsnl  +G Y++tpeif+ l++
  NCBI__GCF_003173355.1:WP_109969550.1 151 HAYTKYGQSIIAVEPVPEKKIPDYGIIDGNLIDKNFYEIKNIVEKPTISDAPSNLGAIGCYLFTPEIFSCLKQ 223
                                           ************************************************************************* PP

                             TIGR01099 217 tkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261
                                           t +GkggeiqltDa+++l    + +++  +++ryD+Gdk+g++ka
  NCBI__GCF_003173355.1:WP_109969550.1 224 TTPGKGGEIQLTDAIKKLS---HSIGMITNCRRYDIGDKIGWMKA 265
                                           *****************94...45788899*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (294 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.80
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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:

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:

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:

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