Alignments for a candidate for galE in Desulfovibrio vulgaris Hildenborough

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.25690.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: 8.28
//
[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