Alignments for a candidate for galU in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Phaeobacter inhibens BS107

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 GFF3395 PGA1_c34480 UTP--glucose-1-phosphate uridylyltransferase CelA

Query= SwissProt::Q05852
         (292 letters)



>FitnessBrowser__Phaeo:GFF3395
          Length = 297

 Score =  285 bits (729), Expect = 9e-82
 Identities = 142/285 (49%), Positives = 200/285 (70%), Gaps = 4/285 (1%)

Query: 2   KKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKSK 61
           +KV KAI P AGLGTRFLPATK++PKE++ +VD+P +QY I+EA EAGI++ I VT + K
Sbjct: 3   RKVTKAIFPVAGLGTRFLPATKSVPKEIMTLVDRPLVQYAIDEAREAGIKEFIFVTSRGK 62

Query: 62  RAIEDHFDYSPELERNLEEKGKTELLEKVKKASNLAD--IHYIRQKEPKGLGHAVWCARN 119
            A+ED+FD+SP LE+ L +KGK +LL+ + KA+N+    I YIRQ +  GLGHAVWCAR 
Sbjct: 63  GALEDYFDHSPMLEQELRKKGKDDLLD-ILKATNMDSGAIAYIRQHQALGLGHAVWCARR 121

Query: 120 FIGDEPFAVLLGDDIVQAETPGLRQLMDEYEKTLSSIIGVQQVPEEETHRYGIIDPLTSE 179
            I +EPFAV+L DD++ AETP L+Q+++ YE+T  +++   +VP E+T  YG++D     
Sbjct: 122 LIANEPFAVILPDDVIAAETPCLKQMVEAYEETGGNMVAAMEVPPEQTSSYGVLDVRDDM 181

Query: 180 GRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAI-QKLN 238
           G    V   VEKP    APSNLA++GRY+  P +   L +++ GAGGEIQLTDAI + + 
Sbjct: 182 GSVVSVNGMVEKPKAEEAPSNLAVIGRYILAPSVLRNLNKKKQGAGGEIQLTDAIAEDIA 241

Query: 239 EIQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKELRDQLVPFM 283
               V+ Y F G+R+D G K GF+  T+ FA+  +ELRD L+ ++
Sbjct: 242 ADVPVYGYRFRGQRFDCGSKAGFLQATVAFALAREELRDDLMCYI 286


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: 240
Number of extensions: 8
Number of successful extensions: 3
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: 297
Length adjustment: 26
Effective length of query: 266
Effective length of database: 271
Effective search space:    72086
Effective search space used:    72086
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 GFF3395 PGA1_c34480 (UTP--glucose-1-phosphate uridylyltransferase CelA)
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.27891.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.1e-105  338.0   0.0   2.5e-105  337.8   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3395  PGA1_c34480 UTP--glucose-1-phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3395  PGA1_c34480 UTP--glucose-1-phosphate uridylyltransferase CelA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.8   0.0  2.5e-105  2.5e-105       1     261 []       5     267 ..       5     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 337.8 bits;  conditional E-value: 2.5e-105
                          TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleakle 76 
                                        + ka++P+aGlGtr+LPatk++Pke++++vd+Pl+qy+++ea eaGi+e ++vt+r+k a+ed+fD+s  le++l+
  lcl|FitnessBrowser__Phaeo:GFF3395   5 VTKAIFPVAGLGTRFLPATKSVPKEIMTLVDRPLVQYAIDEAREAGIKEFIFVTSRGKGALEDYFDHSPMLEQELR 80 
                                        679************************************************************************* PP

                          TIGR01099  77 kknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeeealkqlielyektga 151
                                        kk+k++ll+ +++       i y+rq++a GLGhav++a++l+++epfav+l+Dd++++e+++lkq++e+ye+tg 
  lcl|FitnessBrowser__Phaeo:GFF3395  81 KKGKDDLLDILKATNMDsGAIAYIRQHQALGLGHAVWCARRLIANEPFAVILPDDVIAAETPCLKQMVEAYEETGG 156
                                        ***********98764449********************************************************* PP

                          TIGR01099 152 siiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiql 227
                                        +++a +evp e++s+YGv+d++    ++++v+ +vekPk+eeapsnla++GrY+l p++ + l++ k+G+ggeiql
  lcl|FitnessBrowser__Phaeo:GFF3395 157 NMVAAMEVPPEQTSSYGVLDVRDDMGSVVSVNGMVEKPKAEEAPSNLAVIGRYILAPSVLRNLNKKKQGAGGEIQL 232
                                        **************************************************************************** PP

                          TIGR01099 228 tDalrllleke.evlavklkgkryDvGdklgylka 261
                                        tDa++  + ++  v++++++g+r+D+G+k g+l+a
  lcl|FitnessBrowser__Phaeo:GFF3395 233 TDAIAEDIAADvPVYGYRFRGQRFDCGSKAGFLQA 267
                                        ****987765527********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (297 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: 9.47
//
[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