GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Shewanella oneidensis MR-1

Align UTP--glucose-1-phosphate uridylyltransferase; EC 2.7.7.9 (characterized)
to candidate 200830 SO1665 UTP-glucose-1-phosphate uridylyltransferase (NCBI ptt file)

Query= CharProtDB::CH_021667
         (302 letters)



>FitnessBrowser__MR1:200830
          Length = 302

 Score =  408 bits (1048), Expect = e-119
 Identities = 210/298 (70%), Positives = 242/298 (81%), Gaps = 3/298 (1%)

Query: 7   KVKKAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLVTHSSKN 66
           +++KAVIPVAGLGTRMLPATKAIPKEMLP+VDKPLIQYVV+E IAAGI EIVLVTH+SKN
Sbjct: 5   QIRKAVIPVAGLGTRMLPATKAIPKEMLPVVDKPLIQYVVSEAIAAGIKEIVLVTHASKN 64

Query: 67  SIENHFDTSFELEAMLEKRVKRQLLDEVQSICPPHVTIMQVRQGLAKGLGHAVLCAHPVV 126
           SIENHFDTSFELEA LE+RVKRQLL+ VQSICP  VT++ VRQ  AKGLGHA+LCA  VV
Sbjct: 65  SIENHFDTSFELEAQLERRVKRQLLEAVQSICPKDVTVISVRQSQAKGLGHAILCAKSVV 124

Query: 127 GDEPVAVILPDVILDEYESDLSQDNLAEMIRRFDETGHSQIMVEPVAD--VTAYGVVDCK 184
           GD P AV+LPDVI+DE   DL  DNLA M+  FDET   QIMVE V    V  YG+ D  
Sbjct: 125 GDAPFAVLLPDVIIDEASCDLKTDNLASMVSLFDETQVGQIMVEGVPHHLVNQYGIADVN 184

Query: 185 GVELAPGESVPMVGVVEKPKADVAPSNLAIVGRYVLSADIWPLLAKTPPGAGDEIQLTDA 244
           G +L PGES P+V +VEKP  D APSNLA+VGRYVL A IWPLLAKTP GAGDEIQLTDA
Sbjct: 185 GHDLQPGESEPLVELVEKPPVDEAPSNLAVVGRYVLPAAIWPLLAKTPAGAGDEIQLTDA 244

Query: 245 IDMLIEKETVEAYHMKGKSHDCGNKLGYMQAFVEYGIRHNTLGTEFKAWLEEEM-GIK 301
           I ML+++ETV AY+M+GKSHDCGNK GYM+A VEY +RH+ +G +F  +L+  + GIK
Sbjct: 245 IAMLMKEETVNAYYMQGKSHDCGNKQGYMRANVEYALRHSEIGEDFAHYLKTVVKGIK 302


Lambda     K      H
   0.317    0.135    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: 367
Number of extensions: 14
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: 302
Length of database: 302
Length adjustment: 27
Effective length of query: 275
Effective length of database: 275
Effective search space:    75625
Effective search space used:    75625
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: 48 (23.1 bits)

Align candidate 200830 SO1665 (UTP-glucose-1-phosphate uridylyltransferase (NCBI ptt file))
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.2481664.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.8e-114  367.7   0.1   2.1e-114  367.5   0.1    1.0  1  lcl|FitnessBrowser__MR1:200830  SO1665 UTP-glucose-1-phosphate u


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200830  SO1665 UTP-glucose-1-phosphate uridylyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.5   0.1  2.1e-114  2.1e-114       1     261 []       6     275 ..       6     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 367.5 bits;  conditional E-value: 2.1e-114
                       TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklekkn 79 
                                     irkaviP+aGlGtr+LPatkaiPkemlp+vdkPliqyvv ea++aGi+eivlvt+ sk++ie+hfDts+elea+le++ 
  lcl|FitnessBrowser__MR1:200830   6 IRKAVIPVAGLGTRMLPATKAIPKEMLPVVDKPLIQYVVSEAIAAGIKEIVLVTHASKNSIENHFDTSFELEAQLERRV 84 
                                     89***************************************************************************** PP

                       TIGR01099  80 keellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee.....alkqlielyektgas 152
                                     k++ll+ v++i+++ +t++ vrq +akGLGha+l+a+++vgd pfavll+D++++e +      +l+ +++l+++t+  
  lcl|FitnessBrowser__MR1:200830  85 KRQLLEAVQSICPKdVTVISVRQSQAKGLGHAILCAKSVVGDAPFAVLLPDVIIDEASCdlktdNLASMVSLFDETQVG 163
                                     *************99***************************************99876677779************** PP

                       TIGR01099 153 iiaveevpkeevskYGvidgeeveeelye...vkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiqlt 228
                                     +i+ve vp++ v++YG++d+++ + +  e   + +lvekP ++eapsnla+vGrYvl ++i+ ll++t+aG+g+eiqlt
  lcl|FitnessBrowser__MR1:200830 164 QIMVEGVPHHLVNQYGIADVNGHDLQPGEsepLVELVEKPPVDEAPSNLAVVGRYVLPAAIWPLLAKTPAGAGDEIQLT 242
                                     ********************99888877666799********************************************* PP

                       TIGR01099 229 DalrlllekeevlavklkgkryDvGdklgylka 261
                                     Da+++l+++e+v a+ ++gk++D+G+k+gy++a
  lcl|FitnessBrowser__MR1:200830 243 DAIAMLMKEETVNAYYMQGKSHDCGNKQGYMRA 275
                                     *******************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (302 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: 17.73
//
[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:

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