Alignments for a candidate for galE in Thermovibrio ammonificans HB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Thermovibrio ammonificans HB-1

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_013537410.1 THEAM_RS03320 UDP-glucose 4-epimerase GalE

Query= curated2:Q59745
         (327 letters)



>NCBI__GCF_000185805.1:WP_013537410.1
          Length = 324

 Score =  336 bits (862), Expect = 4e-97
 Identities = 168/316 (53%), Positives = 214/316 (67%), Gaps = 1/316 (0%)

Query: 6   VLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREFVRWGPAEEGDIRDRARLDEVLA 65
           +LV GGAGYIGSHT   L  KG+  +  DN S GHRE V +G   E D+ ++ +L E++ 
Sbjct: 3   ILVTGGAGYIGSHTVELLGRKGHIVLTVDNLSRGHREAVLFGELAEVDLSEKEKLKELIN 62

Query: 66  KHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFSSTCATYGL 125
             +P A++HFAA IEVGESVKDP SFY NN    L LL A   +G+  F+FSST A YG 
Sbjct: 63  SFRPDAVIHFAAFIEVGESVKDPKSFYRNNTCNALNLLEAVVESGVKNFIFSSTAAVYGN 122

Query: 126 PQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGADFEGRIGEW 185
           PQ VP+ E H + PINPYG +K  VE+ L D+     L  V LRYFNAAGAD +GRIGE 
Sbjct: 123 PQKVPIPEEHPKNPINPYGASKLAVERMLQDFHTAYGLNYVALRYFNAAGADPKGRIGES 182

Query: 186 HQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVRAVEYLLKG 245
           H PETH IPL + AA G R  FK+FG+DY T DGTC+RD+IHV DLA+AH++A+EYL +G
Sbjct: 183 HNPETHLIPLILKAAKGERDSFKIFGTDYPTPDGTCIRDFIHVCDLAEAHLKALEYLAEG 242

Query: 246 GDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDKARDVLGWV 305
           G+S ALN G GTG +VKE++   + V+ R F VE   RR GD   LVA+  +  + L W 
Sbjct: 243 GESCALNCGYGTGHSVKEVVETAKRVTGREFKVEEAPRRPGDPPILVADTRRIEEKLNWK 302

Query: 306 PQY-DLSEIIRSAWDW 320
           P++ DL  II++AW+W
Sbjct: 303 PKFNDLEYIIQTAWNW 318


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: 366
Number of extensions: 15
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: 324
Length adjustment: 28
Effective length of query: 299
Effective length of database: 296
Effective search space:    88504
Effective search space used:    88504
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 WP_013537410.1 THEAM_RS03320 (UDP-glucose 4-epimerase GalE)
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.30398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-146  471.9   0.0   5.3e-146  471.6   0.0    1.0  1  lcl|NCBI__GCF_000185805.1:WP_013537410.1  THEAM_RS03320 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185805.1:WP_013537410.1  THEAM_RS03320 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.6   0.0  5.3e-146  5.3e-146       1     327 [.       2     321 ..       2     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 471.6 bits;  conditional E-value: 5.3e-146
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 
                                               +iLvtGgaGyiGsh+v  l +kg+ v+++Dnls+g++ea+  +e      l e dl++kekl++++++ 
  lcl|NCBI__GCF_000185805.1:WP_013537410.1   2 RILVTGGAGYIGSHTVELLGRKGHIVLTVDNLSRGHREAVLFGE------LAEVDLSEKEKLKELINSF 64 
                                               69******************************************......9****************** PP

                                 TIGR01179  70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138
                                               ++daviHfaa+i+vgEsvk+P  +Y+nn+ n+l+Llea+++ gvk++iFss+aavYg+++kvpi Ee+p
  lcl|NCBI__GCF_000185805.1:WP_013537410.1  65 RPDAVIHFAAFIEVGESVKDPKSFYRNNTCNALNLLEAVVESGVKNFIFSSTAAVYGNPQKVPIPEEHP 133
                                               ********************************************************************* PP

                                 TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207
                                                npinpYG+skl+vEr+l+d+++a ++l++v+LRYFn+aGAd++g+iGe+++++thli+l++++a g+r
  lcl|NCBI__GCF_000185805.1:WP_013537410.1 134 KNPINPYGASKLAVERMLQDFHTA-YGLNYVALRYFNAAGADPKGRIGESHNPETHLIPLILKAAKGER 201
                                               ************************.******************************************** PP

                                 TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276
                                               ++++ifGtdypt+DGtc+RD+iHv+DlaeaHl+ale+l+egges ++n+G+g+g+svkev+e++k+v+g
  lcl|NCBI__GCF_000185805.1:WP_013537410.1 202 DSFKIFGTDYPTPDGTCIRDFIHVCDLAEAHLKALEYLAEGGESCALNCGYGTGHSVKEVVETAKRVTG 270
                                               ********************************************************************* PP

                                 TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekk 327
                                               +++kve+a+rR+GDp+ lvad+ +i+++l+wkpk++dLe ii++aw+We +
  lcl|NCBI__GCF_000185805.1:WP_013537410.1 271 REFKVEEAPRRPGDPPILVADTRRIEEKLNWKPKFNDLEYIIQTAWNWELN 321
                                               ************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (324 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: 9.29
//
[ok]

This GapMind analysis is from Sep 24 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