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

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.10994.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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.27
//
[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