Alignments for a candidate for galU in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Shewanella loihica PV-4

Align UTP--glucose-1-phosphate uridylyltransferase; EC 2.7.7.9 (characterized)
to candidate 5208917 Shew_1418 UTP-glucose-1-phosphate uridylyltransferase GalU (RefSeq)

Query= CharProtDB::CH_021667
         (302 letters)



>FitnessBrowser__PV4:5208917
          Length = 306

 Score =  422 bits (1084), Expect = e-123
 Identities = 211/288 (73%), Positives = 240/288 (83%), Gaps = 2/288 (0%)

Query: 10  KAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLVTHSSKNSIE 69
           K VIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQY+VNEC++AG+ EIVLVTH+SKN+IE
Sbjct: 14  KVVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYIVNECVSAGVKEIVLVTHASKNAIE 73

Query: 70  NHFDTSFELEAMLEKRVKRQLLDEVQSICPPHVTIMQVRQGLAKGLGHAVLCAHPVVGDE 129
           NHFDTS+ELE+ LEKRVKRQLLDEVQSICP  VTIM VRQG AKGLGHAVLCA P +G+ 
Sbjct: 74  NHFDTSYELESTLEKRVKRQLLDEVQSICPKDVTIMHVRQGEAKGLGHAVLCAKPCIGNN 133

Query: 130 PVAVILPDVILDEYESDLSQDNLAEMIRRFDETGHSQIMVEPVA--DVTAYGVVDCKGVE 187
           P AV+LPDVILDEY +D S +NLA MI+ +  T  SQIMV PVA  +V  YG+ DC GV 
Sbjct: 134 PFAVVLPDVILDEYSADQSSENLAAMIKHYKATQASQIMVAPVALDEVNKYGIADCGGVN 193

Query: 188 LAPGESVPMVGVVEKPKADVAPSNLAIVGRYVLSADIWPLLAKTPPGAGDEIQLTDAIDM 247
           + PGES  +  +VEKP  D APSNLA+VGRYVLS  IW LLAKTP GAGDEIQLTDAIDM
Sbjct: 194 IEPGESSVIKAMVEKPAIDEAPSNLAVVGRYVLSEKIWDLLAKTPAGAGDEIQLTDAIDM 253

Query: 248 LIEKETVEAYHMKGKSHDCGNKLGYMQAFVEYGIRHNTLGTEFKAWLE 295
           LIE +TVEA++M GKSHDCG+KLGYM AFVEYG+R+  LG EF+  L+
Sbjct: 254 LIESDTVEAFNMTGKSHDCGDKLGYMAAFVEYGLRNEKLGKEFRQQLD 301


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: 363
Number of extensions: 13
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: 306
Length adjustment: 27
Effective length of query: 275
Effective length of database: 279
Effective search space:    76725
Effective search space used:    76725
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 5208917 Shew_1418 (UTP-glucose-1-phosphate uridylyltransferase GalU (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.25071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   7.1e-119  382.1   0.4   8.2e-119  381.9   0.4    1.0  1  lcl|FitnessBrowser__PV4:5208917  Shew_1418 UTP-glucose-1-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208917  Shew_1418 UTP-glucose-1-phosphate uridylyltransferase GalU (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.9   0.4  8.2e-119  8.2e-119       2     261 .]      13     281 ..      12     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 381.9 bits;  conditional E-value: 8.2e-119
                        TIGR01099   2 rkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklekkn 79 
                                      +k+viP+aGlGtr+LPatkaiPkemlp+vdkPliqy+v+e+v aG++eivlvt+ sk+aie+hfDtsyele++lek+ 
  lcl|FitnessBrowser__PV4:5208917  13 MKVVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYIVNECVSAGVKEIVLVTHASKNAIENHFDTSYELESTLEKRV 90 
                                      79**************************************************************************** PP

                        TIGR01099  80 keellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee.....alkqlielyektga 151
                                      k++ll+ev++i+++ +ti++vrq eakGLGhavl+a++++g++pfav+l+D++++e ++     +l+ +i+ y+ t+a
  lcl|FitnessBrowser__PV4:5208917  91 KRQLLDEVQSICPKdVTIMHVRQGEAKGLGHAVLCAKPCIGNNPFAVVLPDVILDEYSAdqsseNLAAMIKHYKATQA 168
                                      *************99***************************************9887667788************** PP

                        TIGR01099 152 siiaveevpkeevskYGvidgeeveeelye...vkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiq 226
                                      s+i+v  v+ +ev+kYG++d+ +v+ e  e   +k++vekP  +eapsnla+vGrYvl+ +i++ll++t+aG+g+eiq
  lcl|FitnessBrowser__PV4:5208917 169 SQIMVAPVALDEVNKYGIADCGGVNIEPGEssvIKAMVEKPAIDEAPSNLAVVGRYVLSEKIWDLLAKTPAGAGDEIQ 246
                                      **********************99877666667********************************************* PP

                        TIGR01099 227 ltDalrlllekeevlavklkgkryDvGdklgylka 261
                                      ltDa+++l+e+++v+a++++gk++D+Gdklgy+ a
  lcl|FitnessBrowser__PV4:5208917 247 LTDAIDMLIESDTVEAFNMTGKSHDCGDKLGYMAA 281
                                      ********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (306 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: 8.56
//
[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