Alignments for a candidate for galE in Clostridium kluyveri DSM 555

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Clostridium kluyveri DSM 555

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_012101939.1 CKL_RS07610 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_000016505.1:WP_012101939.1
          Length = 328

 Score =  369 bits (947), Expect = e-107
 Identities = 187/331 (56%), Positives = 248/331 (74%), Gaps = 4/331 (1%)

Query: 1   MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60
           M+ILV GGAGYIGSHM   L+E+G+E +VV+D+   GH++AV    + YQGDL D++ + 
Sbjct: 1   MSILVCGGAGYIGSHMAAELLERGKE-IVVLDNFEKGHKSAVLGGKV-YQGDLRDENAVD 58

Query: 61  KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120
           KVF+EN ++++VI FAAYSLVGES+E+PLKYF+NN  G + LL+ M + GVKYIVFSSTA
Sbjct: 59  KVFEEN-NIESVIDFAAYSLVGESVEEPLKYFENNVVGTLNLLKSMRKYGVKYIVFSSTA 117

Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180
           ATYG P+ IPI E     P NPYGESKL +E ++KWSD+AYGIKY  LRYFN AGA++  
Sbjct: 118 ATYGEPKNIPIFEDDSTYPTNPYGESKLTVEKLLKWSDRAYGIKYAALRYFNAAGAHISG 177

Query: 181 RLVRTRS-ETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVE 239
            +    + ETHL+PIILQVA   R+KI IFGDDY+T DGT +RDYVH  DLA+AHLLA+ 
Sbjct: 178 LIGEDHNPETHLIPIILQVALKKRDKIFIFGDDYSTEDGTCIRDYVHVMDLANAHLLALN 237

Query: 240 YLRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKART 299
            + +  +S  +NLG+  GFS  +++E +RKVTG++I AE A RR GDP+ LIASS+KA  
Sbjct: 238 KIIEDGKSGIYNLGNGRGFSVKEVIEVSRKVTGQKIKAEIAPRREGDPETLIASSKKAEE 297

Query: 300 VLGWKPQFDNIEKIIASAWAWHSSHPKGYDD 330
            L WKP+++++E II +AW WH  H  G+++
Sbjct: 298 ELNWKPKYNSLETIIDTAWKWHKEHLNGFEE 328


Lambda     K      H
   0.318    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: 386
Number of extensions: 13
Number of successful extensions: 5
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: 332
Length of database: 328
Length adjustment: 28
Effective length of query: 304
Effective length of database: 300
Effective search space:    91200
Effective search space used:    91200
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_012101939.1 CKL_RS07610 (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.1166324.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-141  455.7   0.1   4.3e-141  455.5   0.1    1.0  1  NCBI__GCF_000016505.1:WP_012101939.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016505.1:WP_012101939.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.5   0.1  4.3e-141  4.3e-141       2     330 ..       3     324 ..       2     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 455.5 bits;  conditional E-value: 4.3e-141
                             TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 
                                           iLv GgaGyiGsh++ +lle+gke+vvlDn  kg+k+a+  ++      +++gdl+d++++++v+ee++i++v
  NCBI__GCF_000016505.1:WP_012101939.1   3 ILVCGGAGYIGSHMAAELLERGKEIVVLDNFEKGHKSAVLGGK------VYQGDLRDENAVDKVFEENNIESV 69 
                                           9******************************************......9*********************** PP

                             TIGR01179  75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147
                                           i faa+  vgEsv+ePlkY+ennvv+tl+Ll++m+k+gvk ++Fss+aa+Yge++++pi E+ ++ p+npYG+
  NCBI__GCF_000016505.1:WP_012101939.1  70 IDFAAYSLVGESVEEPLKYFENNVVGTLNLLKSMRKYGVKYIVFSSTAATYGEPKNIPIFEDDSTYPTNPYGE 142
                                           ************************************************************************* PP

                             TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptk 220
                                           skl+vE++lk   +a +++k+++LRYFn+aGA+ +g iGe+++++thli+++++va+ kr+k+ ifG+dy t+
  NCBI__GCF_000016505.1:WP_012101939.1 143 SKLTVEKLLKWSDRA-YGIKYAALRYFNAAGAHISGLIGEDHNPETHLIPIILQVALKKRDKIFIFGDDYSTE 214
                                           **********99999.********************************************************* PP

                             TIGR01179 221 DGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpas 293
                                           DGtc+RDy+Hv+Dla+aHl al+++ e g+s +ynlG+g+gfsvkevie  +kv+g++ik+e+a+rR+GDp +
  NCBI__GCF_000016505.1:WP_012101939.1 215 DGTCIRDYVHVMDLANAHLLALNKIIEDGKSGIYNLGNGRGFSVKEVIEVSRKVTGQKIKAEIAPRREGDPET 287
                                           ************************************************************************* PP

                             TIGR01179 294 lvadaskikrelgwkpkyddLeeiiksawdWekklke 330
                                           l+a+++k+++el+wkpky+ Le+ii +aw+W+k++ +
  NCBI__GCF_000016505.1:WP_012101939.1 288 LIASSKKAEEELNWKPKYNSLETIIDTAWKWHKEHLN 324
                                           *********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (328 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: 00:00:00.00
# Mc/sec: 15.77
//
[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