GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galE in Marinobacter adhaerens HP15

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate GFF2094 HP15_2048 UDP-glucose 4-epimerase

Query= curated2:Q59083
         (348 letters)



>lcl|FitnessBrowser__Marino:GFF2094 HP15_2048 UDP-glucose
           4-epimerase
          Length = 342

 Score =  349 bits (895), Expect = e-101
 Identities = 180/319 (56%), Positives = 221/319 (69%), Gaps = 1/319 (0%)

Query: 10  RVLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRV 69
           +VLVTGGAGYIGSHV+  L  AG   V  D+LS G R A+ A   LV GD+     ++ +
Sbjct: 2   KVLVTGGAGYIGSHVVRQLGQAGHDIVVFDNLSTGYRWAVTAG-ELVVGDLADEAAIEDL 60

Query: 70  MRDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVY 129
              H+ +AV+HFA +IVVPESV  PL YY NNT N+L LL A  +  +  +VFSSTAAVY
Sbjct: 61  FSRHQFEAVLHFAANIVVPESVANPLKYYSNNTRNTLNLLKAVEKHEVPYMVFSSTAAVY 120

Query: 130 GAPESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTG 189
           G PE   + ED P  PINPYGASK+M+E+M+ D  AA  L  VILRYFNVAGA+P G  G
Sbjct: 121 GMPEQTVLTEDLPLAPINPYGASKMMSERMIMDLAAASSLNYVILRYFNVAGANPEGLLG 180

Query: 190 QATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLR 249
           QATP ATHLIKVAC+ +  +R  +++FGTDYDT DGTCIRDYIHV DLA AHV+AL ++ 
Sbjct: 181 QATPEATHLIKVACECVTEQREGMSVFGTDYDTRDGTCIRDYIHVEDLAKAHVMALDYMA 240

Query: 250 RGGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLG 309
            GG S +MNCGYGRG +VREV+  ++  SG   P T   RR GDP  L+A    IR+ LG
Sbjct: 241 DGGHSKVMNCGYGRGFTVREVIDVVKAQSGVDFPVTETGRRAGDPAALMADNTLIRQTLG 300

Query: 310 WVPKHDRLDGIVRSALSWE 328
           W P +D LD IV +AL+WE
Sbjct: 301 WQPDYDNLDTIVGTALAWE 319


Lambda     K      H
   0.319    0.136    0.401 

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: 364
Number of extensions: 12
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: 348
Length of database: 342
Length adjustment: 29
Effective length of query: 319
Effective length of database: 313
Effective search space:    99847
Effective search space used:    99847
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: 49 (23.5 bits)

Align candidate GFF2094 HP15_2048 (UDP-glucose 4-epimerase)
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.22852.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-143  463.7   0.1   1.5e-143  463.5   0.1    1.0  1  lcl|FitnessBrowser__Marino:GFF2094  HP15_2048 UDP-glucose 4-epimeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2094  HP15_2048 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.5   0.1  1.5e-143  1.5e-143       1     327 [.       2     321 ..       2     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 463.5 bits;  conditional E-value: 1.5e-143
                           TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidavi 75 
                                         k+LvtGgaGyiGshvvrql ++g+++vv+Dnls+g ++a++a+e      lv gdlad++++e+++++++++av+
  lcl|FitnessBrowser__Marino:GFF2094   2 KVLVTGGAGYIGSHVVRQLGQAGHDIVVFDNLSTGYRWAVTAGE------LVVGDLADEAAIEDLFSRHQFEAVL 70 
                                         79******************************************......************************* PP

                           TIGR01179  76 HfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrskl 150
                                         Hfaa i v+Esv++PlkYY+nn+ ntl+Ll+a++k++v  ++Fss+aavYg++e+++++E+ pl+pinpYG+sk+
  lcl|FitnessBrowser__Marino:GFF2094  71 HFAANIVVPESVANPLKYYSNNTRNTLNLLKAVEKHEVPYMVFSSTAAVYGMPEQTVLTEDLPLAPINPYGASKM 145
                                         *************************************************************************** PP

                           TIGR01179 151 mvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDGtcv 225
                                         m+Er++ dl+ a ++l++viLRYFnvaGA++eg +G+a+++athlik+++e+++ +re +++fGtdy+t+DGtc+
  lcl|FitnessBrowser__Marino:GFF2094 146 MSERMIMDLAAA-SSLNYVILRYFNVAGANPEGLLGQATPEATHLIKVACECVTEQREGMSVFGTDYDTRDGTCI 219
                                         *********999.************************************************************** PP

                           TIGR01179 226 RDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadask 300
                                         RDyiHveDla+aH+ al+++++gg+s+v n+G+g+gf v+evi+ vk+ sg+d++v+++ rRaGDpa+l+ad+  
  lcl|FitnessBrowser__Marino:GFF2094 220 RDYIHVEDLAKAHVMALDYMADGGHSKVMNCGYGRGFTVREVIDVVKAQSGVDFPVTETGRRAGDPAALMADNTL 294
                                         *************************************************************************** PP

                           TIGR01179 301 ikrelgwkpkyddLeeiiksawdWekk 327
                                         i+++lgw+p yd+L++i+ +a++We  
  lcl|FitnessBrowser__Marino:GFF2094 295 IRQTLGWQPDYDNLDTIVGTALAWEAI 321
                                         ************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (342 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: 7.05
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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