Alignments for a candidate for galE in Methylocella silvestris BL2

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Methylocella silvestris BL2

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_012592648.1 MSIL_RS18775 UDP-glucose 4-epimerase GalE

Query= curated2:Q59083
         (348 letters)



>NCBI__GCF_000021745.1:WP_012592648.1
          Length = 329

 Score =  399 bits (1026), Expect = e-116
 Identities = 198/321 (61%), Positives = 231/321 (71%)

Query: 11  VLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRVM 70
           VLVTGGAGYIG H+  AL D G   V +D+LS G   A+P A  L+ GD G + L+D++ 
Sbjct: 3   VLVTGGAGYIGGHMALALLDQGEEVVVLDNLSTGFAWAVPPAAKLIVGDFGDSALVDQIF 62

Query: 71  RDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVYG 130
            DHR+DA+ HFA  IVVPESV  PL YY NNTA +  LL   ++AG+ + +FSSTAAVYG
Sbjct: 63  ADHRIDAIAHFAAKIVVPESVSDPLAYYLNNTAKARNLLECAVKAGVKQFIFSSTAAVYG 122

Query: 131 APESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTGQ 190
            P   P+ E+    PINPYG SKLM E ML D  AAH LR V+LRYFNVAGADPAGR GQ
Sbjct: 123 EPAENPVFENVALAPINPYGRSKLMVEWMLADVAAAHQLRYVVLRYFNVAGADPAGRLGQ 182

Query: 191 ATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLRR 250
           ++PVATHLIKVA QA LG R  L +FGTDY TPDG+C+RDYI V+DL DAH+LAL HLR 
Sbjct: 183 SSPVATHLIKVAVQAALGHRDGLDVFGTDYPTPDGSCVRDYIQVTDLVDAHLLALAHLRA 242

Query: 251 GGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLGW 310
           GGGSL  NCGYGRG SV EVV  +++VSG         RRPGDP  LVAGADR+R++LGW
Sbjct: 243 GGGSLTCNCGYGRGLSVLEVVEVVKKVSGVDFEVRLKGRRPGDPASLVAGADRVRQELGW 302

Query: 311 VPKHDRLDGIVRSALSWERSL 331
            PKHD L  IV  ALSWER L
Sbjct: 303 TPKHDNLAEIVEQALSWERRL 323


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: 365
Number of extensions: 13
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: 348
Length of database: 329
Length adjustment: 28
Effective length of query: 320
Effective length of database: 301
Effective search space:    96320
Effective search space used:    96320
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_012592648.1 MSIL_RS18775 (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.31325.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-135  437.3   0.0   1.7e-135  437.1   0.0    1.0  1  lcl|NCBI__GCF_000021745.1:WP_012592648.1  MSIL_RS18775 UDP-glucose 4-epime


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012592648.1  MSIL_RS18775 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.1   0.0  1.7e-135  1.7e-135       2     330 ..       3     325 ..       2     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 437.1 bits;  conditional E-value: 1.7e-135
                                 TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 
                                               +LvtGgaGyiG h++ +ll++g evvvlDnls+g+++a++        kl+ gd  d++ +++++++++
  lcl|NCBI__GCF_000021745.1:WP_012592648.1   3 VLVTGGAGYIGGHMALALLDQGEEVVVLDNLSTGFAWAVPPAA-----KLIVGDFGDSALVDQIFADHR 66 
                                               8***************************************999.....6******************** PP

                                 TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139
                                               ida+ Hfaa+i v+Esv++Pl YY nn+  + +Lle+ +kagvk++iFss+aavYge+ ++p+ E+ +l
  lcl|NCBI__GCF_000021745.1:WP_012592648.1  67 IDAIAHFAAKIVVPESVSDPLAYYLNNTAKARNLLECAVKAGVKQFIFSSTAAVYGEPAENPVFENVAL 135
                                               ********************************************************************* PP

                                 TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208
                                               +pinpYGrsklmvE++l d++ a ++l++v+LRYFnvaGAd+ g++G++s+ athlik+++++a+g+r+
  lcl|NCBI__GCF_000021745.1:WP_012592648.1 136 APINPYGRSKLMVEWMLADVAAA-HQLRYVVLRYFNVAGADPAGRLGQSSPVATHLIKVAVQAALGHRD 203
                                               ********************999.********************************************* PP

                                 TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277
                                                l++fGtdypt+DG cvRDyi v+Dl +aHl al  l +gg+s + n+G+g+g sv+ev+e vkkvsg+
  lcl|NCBI__GCF_000021745.1:WP_012592648.1 204 GLDVFGTDYPTPDGSCVRDYIQVTDLVDAHLLALAHLRAGGGSLTCNCGYGRGLSVLEVVEVVKKVSGV 272
                                               ********************************************************************* PP

                                 TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklke 330
                                               d++v+l+ rR+GDpaslva a+++++elgw+pk+d+L+ei+++a++We++l++
  lcl|NCBI__GCF_000021745.1:WP_012592648.1 273 DFEVRLKGRRPGDPASLVAGADRVRQELGWTPKHDNLAEIVEQALSWERRLHN 325
                                               ************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (329 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.15
//
[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