Alignments for a candidate for galE in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Phaeobacter inhibens BS107

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate GFF3394 PGA1_c34470 UDP-glucose 4-epimerase ExoB

Query= curated2:Q59745
         (327 letters)



>FitnessBrowser__Phaeo:GFF3394
          Length = 327

 Score =  330 bits (847), Expect = 2e-95
 Identities = 163/317 (51%), Positives = 215/317 (67%), Gaps = 1/317 (0%)

Query: 6   VLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREFVRWGPAEEGDIRDRARLDEVLA 65
           +LV GGAGYIGSH C  L   G+ PV +DN   G ++ V++GP E+GD+ DRARLDEV A
Sbjct: 4   ILVTGGAGYIGSHACKALRAAGFTPVTYDNLVTGWQDAVKFGPFEKGDLSDRARLDEVFA 63

Query: 66  KHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFSSTCATYGL 125
           K++PAA++HFAAL +VGE++ +P  ++ NNV G+LTL+ AA AA    FVFSSTCATYG 
Sbjct: 64  KYQPAAVMHFAALSQVGEAMSEPGRYWANNVGGSLTLIEAAVAADCLDFVFSSTCATYGE 123

Query: 126 PQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGADFEGRIGEW 185
             +V LDE+  QVP+N YG +K  VE  L D+     LRSV+ RYFN AGAD E  +GE+
Sbjct: 124 HDNVVLDESTPQVPLNAYGASKRAVEDILRDFGASHGLRSVIFRYFNVAGADPEAEVGEF 183

Query: 186 HQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVRAVEYLLKG 245
           H+PETH +PL +DA  G+R    +FG+DY+T DGTCVRDY+HV DL DAHV  +++L  G
Sbjct: 184 HRPETHLVPLVLDAIDGKRDALTIFGTDYDTPDGTCVRDYVHVCDLVDAHVLGLKWLKDG 243

Query: 246 GDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDKARDVLGWV 305
             S   NLGTGTG +V+E++   E  + +  P     RR GD   LV+ + +A  +LGW 
Sbjct: 244 KGSQVFNLGTGTGFSVREVMDKAEATTGKSVPHSIGPRRAGDCTKLVSGSVRAATLLGWE 303

Query: 306 P-QYDLSEIIRSAWDWH 321
           P + DL  +I  AW WH
Sbjct: 304 PTRSDLETMIADAWGWH 320


Lambda     K      H
   0.319    0.137    0.415 

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: 383
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: 327
Length of database: 327
Length adjustment: 28
Effective length of query: 299
Effective length of database: 299
Effective search space:    89401
Effective search space used:    89401
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate GFF3394 PGA1_c34470 (UDP-glucose 4-epimerase ExoB)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# 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/TIGR01179.hmm
# target sequence database:        /tmp/gapView.14953.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.7e-126  406.4   0.0   4.6e-126  406.1   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3394  PGA1_c34470 UDP-glucose 4-epimer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3394  PGA1_c34470 UDP-glucose 4-epimerase ExoB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.1   0.0  4.6e-126  4.6e-126       2     326 ..       4     321 ..       3     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 406.1 bits;  conditional E-value: 4.6e-126
                          TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidaviHf 77 
                                        iLvtGgaGyiGsh +++l+++g+  v++Dnl++g ++a+k +       + +gdl+d+++l++v+++ ++ av+Hf
  lcl|FitnessBrowser__Phaeo:GFF3394   4 ILVTGGAGYIGSHACKALRAAGFTPVTYDNLVTGWQDAVKFGP------FEKGDLSDRARLDEVFAKYQPAAVMHF 73 
                                        9*****************************************9......*************************** PP

                          TIGR01179  78 aaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvE 153
                                        aal +vgE+++eP +Y++nnv ++l+L+ea ++a + +++Fss++a+Yge+++v++ E++p+ p n YG+sk++vE
  lcl|FitnessBrowser__Phaeo:GFF3394  74 AALSQVGEAMSEPGRYWANNVGGSLTLIEAAVAADCLDFVFSSTCATYGEHDNVVLDESTPQVPLNAYGASKRAVE 149
                                        **************************************************************************** PP

                          TIGR01179 154 rilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDGtcvRDyi 229
                                         il+d+  + ++l+ vi RYFnvaGAd+e e+Ge ++++thl++lv++++ gkr++l+ifGtdy+t+DGtcvRDy+
  lcl|FitnessBrowser__Phaeo:GFF3394 150 DILRDFGAS-HGLRSVIFRYFNVAGADPEAEVGEFHRPETHLVPLVLDAIDGKRDALTIFGTDYDTPDGTCVRDYV 224
                                        ******888.****************************************************************** PP

                          TIGR01179 230 HveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrel 305
                                        Hv+Dl +aH+  l++l++g++s+v+nlG+g+gfsv+ev++++++ +gk+++ ++ +rRaGD ++lv+ + ++ + l
  lcl|FitnessBrowser__Phaeo:GFF3394 225 HVCDLVDAHVLGLKWLKDGKGSQVFNLGTGTGFSVREVMDKAEATTGKSVPHSIGPRRAGDCTKLVSGSVRAATLL 300
                                        **************************************************************************** PP

                          TIGR01179 306 gwkpkyddLeeiiksawdWek 326
                                        gw+p++ dLe++i++aw W+k
  lcl|FitnessBrowser__Phaeo:GFF3394 301 GWEPTRSDLETMIADAWGWHK 321
                                        *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (327 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.40
//
[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