Alignments for a candidate for galE in Thermithiobacillus tepidarius DSM 3134

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Thermithiobacillus tepidarius DSM 3134

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_028990328.1 G579_RS0111685 UDP-glucose 4-epimerase GalE

Query= curated2:Q9KDV3
         (334 letters)



>NCBI__GCF_000423825.1:WP_028990328.1
          Length = 325

 Score =  350 bits (897), Expect = e-101
 Identities = 170/316 (53%), Positives = 213/316 (67%)

Query: 3   ILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALSDVTFYHGDIRDDQLLDTIFT 62
           ILV GGAGYIGSH V  LL+ G QV  LDN   G+  A+       GD+ D +LLD +F 
Sbjct: 4   ILVVGGAGYIGSHMVKMLLQAGHQVTTLDNFSAGYQDAVLGGELVAGDLADRELLDHLFR 63

Query: 63  THSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAATYGE 122
               D V+HFA+   VGESV  P +YY NN   T  LL  M++H V+  +FSSTAA +GE
Sbjct: 64  DRRFDGVMHFASYIQVGESVLDPGKYYRNNFTNTLNLLDAMVQHGVRAFIFSSTAAIFGE 123

Query: 123 PVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGRIGED 182
           P  IPI E  P  P NPYG +K  +E+       AYGL+ V LRYFNAAGADP+G++GE 
Sbjct: 124 PRYIPIDEQHPKAPINPYGRSKWMVEQALADYDHAYGLKSVALRYFNAAGADPDGQLGER 183

Query: 183 HSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEHLRKD 242
           H PE+HLIP+VLQ A G+R  + ++G DY T DG+CIRDYIHV+DL  AH LA E L   
Sbjct: 184 HDPETHLIPLVLQAASGRRPHITVYGRDYDTPDGTCIRDYIHVLDLCQAHLLALEQLWAG 243

Query: 243 GQSGSFNLGNGKGFSVKEVIEVCRQVTGHPIPAEIAPRRSGDPASLIASSEKAQTILGWE 302
           G+S ++NLGNG+GFSV+EVI+  R+VTG  IP     RR+GDPA L+A S +AQ ILGW+
Sbjct: 244 GESAAYNLGNGQGFSVQEVIDTARRVTGREIPVLDGERRAGDPARLVADSRRAQEILGWQ 303

Query: 303 PKYPSLETMVEHAWNW 318
           P+Y  L T++EHAW W
Sbjct: 304 PRYADLATIIEHAWRW 319


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: 411
Number of extensions: 14
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: 325
Length adjustment: 28
Effective length of query: 306
Effective length of database: 297
Effective search space:    90882
Effective search space used:    90882
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 WP_028990328.1 G579_RS0111685 (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.9934.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-139  448.5   0.0   6.3e-139  448.4   0.0    1.0  1  lcl|NCBI__GCF_000423825.1:WP_028990328.1  G579_RS0111685 UDP-glucose 4-epi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000423825.1:WP_028990328.1  G579_RS0111685 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.4   0.0  6.3e-139  6.3e-139       2     328 ..       4     323 ..       3     325 .] 0.99

  Alignments for each domain:
  == domain 1  score: 448.4 bits;  conditional E-value: 6.3e-139
                                 TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 
                                               iLv+GgaGyiGsh+v+ ll++g++v +lDn s g ++a+  +e      lv gdlad+e l++++++++
  lcl|NCBI__GCF_000423825.1:WP_028990328.1   4 ILVVGGAGYIGSHMVKMLLQAGHQVTTLDNFSAGYQDAVLGGE------LVAGDLADRELLDHLFRDRR 66 
                                               9******************************************......******************** PP

                                 TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139
                                               +d v+Hfa++i+vgEsv +P kYY+nn +ntl+Ll+am+++gv+ +iFss+aa++ge++ +pi E++p 
  lcl|NCBI__GCF_000423825.1:WP_028990328.1  67 FDGVMHFASYIQVGESVLDPGKYYRNNFTNTLNLLDAMVQHGVRAFIFSSTAAIFGEPRYIPIDEQHPK 135
                                               ********************************************************************* PP

                                 TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208
                                               +pinpYGrsk mvE+ l d+ +a ++lk v+LRYFn+aGAd++g++Ge++ ++thli+lv+++a+g+r+
  lcl|NCBI__GCF_000423825.1:WP_028990328.1 136 APINPYGRSKWMVEQALADYDHA-YGLKSVALRYFNAAGADPDGQLGERHDPETHLIPLVLQAASGRRP 203
                                               **********************9.********************************************* PP

                                 TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277
                                               +++++G dy+t+DGtc+RDyiHv Dl +aHl ale+l++gges++ynlG+gqgfsv+evi+++++v+g+
  lcl|NCBI__GCF_000423825.1:WP_028990328.1 204 HITVYGRDYDTPDGTCIRDYIHVLDLCQAHLLALEQLWAGGESAAYNLGNGQGFSVQEVIDTARRVTGR 272
                                               ********************************************************************* PP

                                 TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                               +i+v   +rRaGDpa+lvad+ ++++ lgw+p+y dL++ii+ aw+We++l
  lcl|NCBI__GCF_000423825.1:WP_028990328.1 273 EIPVLDGERRAGDPARLVADSRRAQEILGWQPRYADLATIIEHAWRWETRL 323
                                               ************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (325 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 10.14
//
[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