GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Shewanella amazonensis SB2B

Align UTP--glucose-1-phosphate uridylyltransferase; EC 2.7.7.9 (characterized)
to candidate 6938102 Sama_2223 UTP--glucose-1-phosphate uridylyltransferase (RefSeq)

Query= CharProtDB::CH_021667
         (302 letters)



>FitnessBrowser__SB2B:6938102
          Length = 302

 Score =  418 bits (1075), Expect = e-122
 Identities = 211/293 (72%), Positives = 241/293 (82%), Gaps = 2/293 (0%)

Query: 6   TKVKKAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLVTHSSK 65
           TK++KAVIPVAGLGTRMLPATKAIPKEMLP+VDKPLIQYVV+E +AAGI EIVLVTH+SK
Sbjct: 4   TKIRKAVIPVAGLGTRMLPATKAIPKEMLPVVDKPLIQYVVSEAVAAGIKEIVLVTHASK 63

Query: 66  NSIENHFDTSFELEAMLEKRVKRQLLDEVQSICPPHVTIMQVRQGLAKGLGHAVLCAHPV 125
           NSIENHFDTSFELEA LE+RVKRQLLDEVQ+ICP  VT++ VRQ  AKGLGHA+LCA PV
Sbjct: 64  NSIENHFDTSFELEAQLERRVKRQLLDEVQAICPKDVTVISVRQAQAKGLGHAILCARPV 123

Query: 126 VGDEPVAVILPDVILDEYESDLSQDNLAEMIRRFDETGHSQIMVEPVAD--VTAYGVVDC 183
           VGDEP AV+LPDVI+D  +SDL+ +NLA M+R FDET   QIMVE V    V  YG+ D 
Sbjct: 124 VGDEPFAVLLPDVIIDGAKSDLTSENLAAMVRLFDETSTGQIMVEAVPHEMVNQYGIADV 183

Query: 184 KGVELAPGESVPMVGVVEKPKADVAPSNLAIVGRYVLSADIWPLLAKTPPGAGDEIQLTD 243
           KG ++  G+SVP+  +VEKP  D APSNLA+VGRYVL ADIWPLLA+TP GAGDEIQLTD
Sbjct: 184 KGHQMVNGDSVPLEALVEKPAVDEAPSNLAVVGRYVLPADIWPLLARTPAGAGDEIQLTD 243

Query: 244 AIDMLIEKETVEAYHMKGKSHDCGNKLGYMQAFVEYGIRHNTLGTEFKAWLEE 296
           AI ML+E   V AY M GKSHDCGNK GYMQA VEY +RH  LG EF  +L++
Sbjct: 244 AIAMLMESAQVNAYGMVGKSHDCGNKQGYMQANVEYALRHPELGKEFAKYLKQ 296


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: 378
Number of extensions: 19
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 6938102 Sama_2223 (UTP--glucose-1-phosphate uridylyltransferase (RefSeq))
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.26400.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-115  371.0   0.2   2.1e-115  370.8   0.2    1.0  1  lcl|FitnessBrowser__SB2B:6938102  Sama_2223 UTP--glucose-1-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938102  Sama_2223 UTP--glucose-1-phosphate uridylyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.8   0.2  2.1e-115  2.1e-115       1     261 []       6     275 ..       6     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 370.8 bits;  conditional E-value: 2.1e-115
                         TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklek 77 
                                       irkaviP+aGlGtr+LPatkaiPkemlp+vdkPliqyvv eav+aGi+eivlvt+ sk++ie+hfDts+elea+le+
  lcl|FitnessBrowser__SB2B:6938102   6 IRKAVIPVAGLGTRMLPATKAIPKEMLPVVDKPLIQYVVSEAVAAGIKEIVLVTHASKNSIENHFDTSFELEAQLER 82 
                                       89*************************************************************************** PP

                         TIGR01099  78 knkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee.....alkqlielyek 148
                                       + k++ll+ev++i+++ +t++ vrq +akGLGha+l+a+++vgdepfavll+D++++  ++     +l+ +++l+++
  lcl|FitnessBrowser__SB2B:6938102  83 RVKRQLLDEVQAICPKdVTVISVRQAQAKGLGHAILCARPVVGDEPFAVLLPDVIIDGAKSdltseNLAAMVRLFDE 159
                                       ***************99***************************************98877788889********** PP

                         TIGR01099 149 tgasiiaveevpkeevskYGvidgee...veeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkg 222
                                       t + +i+ve vp+e v++YG++d+++   v+ + + +++lvekP ++eapsnla+vGrYvl ++i+ ll++t+aG+g
  lcl|FitnessBrowser__SB2B:6938102 160 TSTGQIMVEAVPHEMVNQYGIADVKGhqmVNGDSVPLEALVEKPAVDEAPSNLAVVGRYVLPADIWPLLARTPAGAG 236
                                       *********************998763347788888***************************************** PP

                         TIGR01099 223 geiqltDalrlllekeevlavklkgkryDvGdklgylka 261
                                       +eiqltDa+++l+e+ +v a+ + gk++D+G+k+gy++a
  lcl|FitnessBrowser__SB2B:6938102 237 DEIQLTDAIAMLMESAQVNAYGMVGKSHDCGNKQGYMQA 275
                                       *************************************97 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: 10.21
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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