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.27489.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: 6.63
//
[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:

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