GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Desulfovibrio vulgaris Hildenborough

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate 206802 DVU1360 UDP-glucose 4-epimerase

Query= curated2:Q9KDV3
         (334 letters)



>MicrobesOnline__882:206802
          Length = 331

 Score =  334 bits (856), Expect = 2e-96
 Identities = 163/319 (51%), Positives = 212/319 (66%)

Query: 3   ILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALSDVTFYHGDIRDDQLLDTIFT 62
           +LV GGAGYIGSH V  L+E G   I+ DNL  GHA ++ DV    GD+ D Q L  +F 
Sbjct: 10  VLVCGGAGYIGSHMVRALVEHGYVPIIFDNLSTGHAESVGDVDLVRGDLLDRQALRRLFA 69

Query: 63  THSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAATYGE 122
            HS D V+HF+A SLVGES+  P  Y+ NNV+GT  LL+ M E  V ++VFSS+AA +G 
Sbjct: 70  EHSFDAVMHFSAKSLVGESMTDPGIYFVNNVVGTINLLEAMREAGVSRLVFSSSAAVFGN 129

Query: 123 PVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGRIGED 182
           P+   I E  P  P NPYG +KL IE+       AYG++ V LRYFNAAGAD  G IGE 
Sbjct: 130 PLTARIAEDHPRQPVNPYGRSKLMIEQALRDYANAYGMRSVSLRYFNAAGADEAGDIGES 189

Query: 183 HSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEHLRKD 242
           H PE+HLIP VL+ ALG    + IFGDDY T DG+C+RDYIHV DL +AH  A  +++  
Sbjct: 190 HKPETHLIPNVLRAALGTGPELKIFGDDYDTPDGTCVRDYIHVADLCDAHLRALSYMQLK 249

Query: 243 GQSGSFNLGNGKGFSVKEVIEVCRQVTGHPIPAEIAPRRSGDPASLIASSEKAQTILGWE 302
             + +FNLGNG GFSVK+V+E   +VTG  +P  +APRR GDPA L+A S  A+  LGW+
Sbjct: 250 PGAHAFNLGNGNGFSVKQVVEAAWRVTGRDVPHSMAPRRPGDPAWLVADSTLAERELGWK 309

Query: 303 PKYPSLETMVEHAWNWHKE 321
           P +  ++ +++ AW WH++
Sbjct: 310 PSFTDIDAIIDSAWRWHQK 328


Lambda     K      H
   0.317    0.135    0.411 

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: 355
Number of extensions: 10
Number of successful extensions: 1
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: 334
Length of database: 331
Length adjustment: 28
Effective length of query: 306
Effective length of database: 303
Effective search space:    92718
Effective search space used:    92718
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: 49 (23.5 bits)

Align candidate 206802 DVU1360 (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.32056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.9e-136  439.6   0.0   3.2e-136  439.4   0.0    1.0  1  lcl|MicrobesOnline__882:206802  DVU1360 UDP-glucose 4-epimerase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206802  DVU1360 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.4   0.0  3.2e-136  3.2e-136       1     327 [.       9     328 ..       9     331 .] 0.99

  Alignments for each domain:
  == domain 1  score: 439.4 bits;  conditional E-value: 3.2e-136
                       TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidaviHfaa 79 
                                     ++Lv GgaGyiGsh+vr+l e+g+  +++Dnls+g++e++ +++      lv+gdl d+++l+++++e+++dav+Hf+a
  lcl|MicrobesOnline__882:206802   9 NVLVCGGAGYIGSHMVRALVEHGYVPIIFDNLSTGHAESVGDVD------LVRGDLLDRQALRRLFAEHSFDAVMHFSA 81 
                                     59**************************************9999......***************************** PP

                       TIGR01179  80 liavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvErilkd 158
                                     +  vgEs+++P  Y+ nnvv+t++Lleam++agv +l+Fsssaav+g++ +  i E++p +p+npYGrsklm+E+ l+d
  lcl|MicrobesOnline__882:206802  82 KSLVGESMTDPGIYFVNNVVGTINLLEAMREAGVSRLVFSSSAAVFGNPLTARIAEDHPRQPVNPYGRSKLMIEQALRD 160
                                     ******************************************************************************* PP

                       TIGR01179 159 lkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDGtcvRDyiHveDlaea 237
                                     +++a ++++ v+LRYFn+aGAde g+iGe++k++thli+ v+++a+g  ++l+ifG+dy+t+DGtcvRDyiHv Dl +a
  lcl|MicrobesOnline__882:206802 161 YANA-YGMRSVSLRYFNAAGADEAGDIGESHKPETHLIPNVLRAALGTGPELKIFGDDYDTPDGTCVRDYIHVADLCDA 238
                                     ****.************************************************************************** PP

                       TIGR01179 238 HlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLee 316
                                     Hl+al +++ + +++++nlG+g+gfsvk+v+ea+ +v+g+d++ ++a+rR+GDpa lvad+  ++relgwkp+++d++ 
  lcl|MicrobesOnline__882:206802 239 HLRALSYMQLKPGAHAFNLGNGNGFSVKQVVEAAWRVTGRDVPHSMAPRRPGDPAWLVADSTLAERELGWKPSFTDIDA 317
                                     ******************************************************************************* PP

                       TIGR01179 317 iiksawdWekk 327
                                     ii saw+W++k
  lcl|MicrobesOnline__882:206802 318 IIDSAWRWHQK 328
                                     *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (331 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: 7.34
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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