Alignments for a candidate for galE in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Desulfovibrio vulgaris Miyazaki F

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate 8499360 DvMF_0137 UDP-glucose 4-epimerase (RefSeq)

Query= curated2:Q9KDV3
         (334 letters)



>FitnessBrowser__Miya:8499360
          Length = 356

 Score =  317 bits (811), Expect = 4e-91
 Identities = 166/348 (47%), Positives = 210/348 (60%), Gaps = 26/348 (7%)

Query: 3   ILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALS----DVTFYHGDIRDDQLLD 58
           +LV GGAGYIGSH V  L+ +G   ++ DNL  GHA A+     D     GD+ D Q L 
Sbjct: 9   VLVCGGAGYIGSHMVRALVARGCTPVIFDNLSTGHADAVDAAAPDCDLVRGDLLDRQTLR 68

Query: 59  TIFTTHSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAA 118
            +F  HS D V+HF+A SLVGESV++P  YY NNV GT  LL  M E  V ++VFSSTAA
Sbjct: 69  RVFAEHSFDAVMHFSARSLVGESVREPALYYANNVTGTLNLLDAMREAGVLRLVFSSTAA 128

Query: 119 TYGEPVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGR 178
            YG PV   I E+ P  P NPYG +KL +E+M      AYGL+ V LRYFNAAGAD  G 
Sbjct: 129 VYGNPVTERIAETHPLAPVNPYGASKLMVERMLADHATAYGLRSVALRYFNAAGADRAGG 188

Query: 179 IGEDHSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEH 238
           IGE HSPE+HLIP +L+  LG    + +FG DY T DG+C+RDYIHV DL +AH  A + 
Sbjct: 189 IGESHSPETHLIPNILRAVLGTGPALTVFGSDYDTPDGTCVRDYIHVNDLCDAHLAALDK 248

Query: 239 --------------LRKDGQSGS--------FNLGNGKGFSVKEVIEVCRQVTGHPIPAE 276
                         L KDG +          +NLGNG GF+V++VI+   +VTG  +P  
Sbjct: 249 LLAAPVGTAALKDGLTKDGLAAEPGGKVALHYNLGNGLGFTVRQVIDAAARVTGREVPYT 308

Query: 277 IAPRRSGDPASLIASSEKAQTILGWEPKYPSLETMVEHAWNWHKEHPH 324
           + PRR GDPA L+A S  A   LGW PK   +  ++E AW WH++  +
Sbjct: 309 VGPRRDGDPARLVADSTLAGRELGWTPKVADIREIIETAWAWHRDQKY 356


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: 359
Number of extensions: 13
Number of successful extensions: 3
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: 356
Length adjustment: 29
Effective length of query: 305
Effective length of database: 327
Effective search space:    99735
Effective search space used:    99735
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 8499360 DvMF_0137 (UDP-glucose 4-epimerase (RefSeq))
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.13234.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.5e-128  413.0   0.0   4.1e-104  333.9   0.0    2.0  2  lcl|FitnessBrowser__Miya:8499360  DvMF_0137 UDP-glucose 4-epimeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499360  DvMF_0137 UDP-glucose 4-epimerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.9   0.0  4.1e-104  4.1e-104       1     247 [.       8     251 ..       8     265 .. 0.98
   2 !   77.4   0.0   4.5e-26   4.5e-26     253     328 ..     279     354 ..     266     356 .] 0.94

  Alignments for each domain:
  == domain 1  score: 333.9 bits;  conditional E-value: 4.1e-104
                         TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidaviHf 77 
                                       ++Lv GgaGyiGsh+vr+l ++g   v++Dnls+g+++a+ a     +  lv+gdl d+++l++v++e+++dav+Hf
  lcl|FitnessBrowser__Miya:8499360   8 NVLVCGGAGYIGSHMVRALVARGCTPVIFDNLSTGHADAVDAAA--PDCDLVRGDLLDRQTLRRVFAEHSFDAVMHF 82 
                                       59***************************************998..69***************************** PP

                         TIGR01179  78 aaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvEr 154
                                       +a+  vgEsv+eP+ YY+nnv++tl+Ll+am++agv +l+Fss+aavYg++ +  i E++pl+p+npYG+sklmvEr
  lcl|FitnessBrowser__Miya:8499360  83 SARSLVGESVREPALYYANNVTGTLNLLDAMREAGVLRLVFSSTAAVYGNPVTERIAETHPLAPVNPYGASKLMVER 159
                                       ***************************************************************************** PP

                         TIGR01179 155 ilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDGtcvRDyiHv 231
                                       +l d ++a ++l+ v+LRYFn+aGAd  g iGe+++++thli+ ++++++g  ++l++fG dy+t+DGtcvRDyiHv
  lcl|FitnessBrowser__Miya:8499360 160 MLADHATA-YGLRSVALRYFNAAGADRAGGIGESHSPETHLIPNILRAVLGTGPALTVFGSDYDTPDGTCVRDYIHV 235
                                       ******99.******************************************************************** PP

                         TIGR01179 232 eDlaeaHlaalealee 247
                                       +Dl +aHlaal++l +
  lcl|FitnessBrowser__Miya:8499360 236 NDLCDAHLAALDKLLA 251
                                       ************9976 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 4.5e-26
                         TIGR01179 253 vynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                        ynlG+g gf v++vi+a+ +v+g+++++++ +rR+GDpa+lvad+  + relgw+pk  d++eii++aw+W++ +
  lcl|FitnessBrowser__Miya:8499360 279 HYNLGNGLGFTVRQVIDAAARVTGREVPYTVGPRRDGDPARLVADSTLAGRELGWTPKVADIREIIETAWAWHRDQ 354
                                       59**********************************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (356 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 3.12
//
[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