Alignments for a candidate for galE in Steroidobacter denitrificans DSM 18526

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Steroidobacter denitrificans DSM 18526

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_066920863.1 ACG33_RS10030 UDP-glucose 4-epimerase GalE

Query= curated2:Q59083
         (348 letters)



>NCBI__GCF_001579945.1:WP_066920863.1
          Length = 331

 Score =  362 bits (929), Expect = e-105
 Identities = 184/321 (57%), Positives = 226/321 (70%), Gaps = 1/321 (0%)

Query: 11  VLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRVM 70
           +L+TGGAGYIGSHV   L +     V +D+LS G R A+     L+ GD G  EL+ RV+
Sbjct: 3   ILITGGAGYIGSHVARQLGERQEKIVILDNLSTGFRSAVLHG-ELIVGDTGDRELVARVL 61

Query: 71  RDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVYG 130
           R+H +D VMHFA   +VPESV  PL YY NNT ++  LL    +AG+   VFSSTAAVYG
Sbjct: 62  REHDIDTVMHFAAHTIVPESVSDPLKYYGNNTCSTRNLLQCSQQAGVQHFVFSSTAAVYG 121

Query: 131 APESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTGQ 190
            PE     ED+PT PINPYG SKLM+E MLRD  AA  LR V+LRYFNVAG+DP GR GQ
Sbjct: 122 IPEGGIAAEDSPTQPINPYGTSKLMSEWMLRDLAAASTLRHVVLRYFNVAGSDPGGRIGQ 181

Query: 191 ATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLRR 250
           +T  AT L KVAC+A +G+R  ++IFGTDYDTPDGT +RDYIHV DLA AHV AL +LR 
Sbjct: 182 STLKATLLTKVACEAAVGKRAHISIFGTDYDTPDGTGVRDYIHVEDLAAAHVKALDYLRA 241

Query: 251 GGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLGW 310
           GG  + +NCGYG G SVRE++ T++ ++G  +      RR GDPP L+A A R+RE LGW
Sbjct: 242 GGAPVTLNCGYGHGYSVRELIATVDRLNGTPLKTLEEPRRAGDPPTLIARAQRVREVLGW 301

Query: 311 VPKHDRLDGIVRSALSWERSL 331
           +P+HD LD IVRS L+WER L
Sbjct: 302 IPRHDDLDTIVRSQLAWERRL 322


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: 391
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: 331
Length adjustment: 28
Effective length of query: 320
Effective length of database: 303
Effective search space:    96960
Effective search space used:    96960
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 WP_066920863.1 ACG33_RS10030 (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.20768.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-132  427.9   0.0   1.2e-132  427.7   0.0    1.0  1  lcl|NCBI__GCF_001579945.1:WP_066920863.1  ACG33_RS10030 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066920863.1  ACG33_RS10030 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.7   0.0  1.2e-132  1.2e-132       2     328 ..       3     322 ..       2     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 427.7 bits;  conditional E-value: 1.2e-132
                                 TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 
                                               iL+tGgaGyiGshv+rql e++ ++v+lDnls+g+++a+ ++e      l+ gd  d+e +++vl+e++
  lcl|NCBI__GCF_001579945.1:WP_066920863.1   3 ILITGGAGYIGSHVARQLGERQEKIVILDNLSTGFRSAVLHGE------LIVGDTGDRELVARVLREHD 65 
                                               9******************************************......******************** PP

                                 TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139
                                               id+v+Hfaa + v+Esv++PlkYY nn+ +t +Ll++ q+agv++++Fss+aavYg +e     E+sp+
  lcl|NCBI__GCF_001579945.1:WP_066920863.1  66 IDTVMHFAAHTIVPESVSDPLKYYGNNTCSTRNLLQCSQQAGVQHFVFSSTAAVYGIPEGGIAAEDSPT 134
                                               ********************************************************************* PP

                                 TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208
                                               +pinpYG+sklm+E++l+dl+ a + l++v+LRYFnvaG d+ g+iG+++ +at l k+++e+avgkr 
  lcl|NCBI__GCF_001579945.1:WP_066920863.1 135 QPINPYGTSKLMSEWMLRDLAAA-STLRHVVLRYFNVAGSDPGGRIGQSTLKATLLTKVACEAAVGKRA 202
                                               ********************999.********************************************* PP

                                 TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277
                                               +++ifGtdy+t+DGt+vRDyiHveDla+aH++al++l +gg   ++n+G+g+g+sv+e+i +v+++ g+
  lcl|NCBI__GCF_001579945.1:WP_066920863.1 203 HISIFGTDYDTPDGTGVRDYIHVEDLAAAHVKALDYLRAGGAPVTLNCGYGHGYSVRELIATVDRLNGT 271
                                               ********************************************************************* PP

                                 TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                               ++k+ +++rRaGDp++l+a a++++++lgw p++ddL++i++s ++We++l
  lcl|NCBI__GCF_001579945.1:WP_066920863.1 272 PLKTLEEPRRAGDPPTLIARAQRVREVLGWIPRHDDLDTIVRSQLAWERRL 322
                                               ************************************************986 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.33
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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