Alignments for a candidate for galE in Hippea alviniae EP5-r

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Hippea alviniae EP5-r

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_022671112.1 G415_RS0107775 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_000420385.1:WP_022671112.1
          Length = 342

 Score =  267 bits (683), Expect = 2e-76
 Identities = 150/330 (45%), Positives = 209/330 (63%), Gaps = 13/330 (3%)

Query: 2   AILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHP-----DAIFYQGDLSDQ 56
           +IL+ GGAGYIGSH+V  L+E     + V+D+L TG ++ +       D  F   DLS+ 
Sbjct: 6   SILITGGAGYIGSHVVKLLLENSNSDITVIDNLSTGFKSTIDELKKIRDFDFIYADLSNW 65

Query: 57  DFMRKVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVF 116
           D ++ VFK     DA+IHFAA  +V ES+++PLKY+ NNTA    L+++  E  VK  +F
Sbjct: 66  DEIKGVFKAK-QFDAIIHFAASIIVPESVKEPLKYYLNNTANTTNLVKLAVEYKVKKFIF 124

Query: 117 SSTAATYGIPEEIPILETTPQN----PINPYGESKLMMETIMKWSDQAY-GIKYVPLRYF 171
           SSTAA YG P    I +   +N    PINPYG+SKL  E I++ + +A    KYV  RYF
Sbjct: 125 SSTAAVYGEPTIKEIGDGIDENFKTEPINPYGQSKLFSERIIQDTAKANPDFKYVIFRYF 184

Query: 172 NVAGANLMVRL-VRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDL 230
           NVAGA+  + +  +T++ THL+ +  +   G R+K+ IFGDDY T DGT VRDY+H  DL
Sbjct: 185 NVAGASPDLTIGQKTKNATHLIKVAAETTVGKRDKMFIFGDDYPTKDGTGVRDYIHVMDL 244

Query: 231 ADAHLLAVEYLRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDIL 290
           ADAH+  +EYL K NES  FN+G   G S  +++E  +KVTG +   E A RR GDP IL
Sbjct: 245 ADAHIKGLEYLEK-NESDIFNVGYGKGASVKEVIETMKKVTGIDFKVETAQRRLGDPAIL 303

Query: 291 IASSEKARTVLGWKPQFDNIEKIIASAWAW 320
           IA ++K    +GWKP++D++E I  +A+ W
Sbjct: 304 IAKNDKIINKMGWKPKYDSLETICKTAYEW 333


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: 340
Number of extensions: 19
Number of successful extensions: 6
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: 342
Length adjustment: 28
Effective length of query: 304
Effective length of database: 314
Effective search space:    95456
Effective search space used:    95456
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_022671112.1 G415_RS0107775 (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.111711.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-144  466.5   0.3   2.1e-144  466.4   0.3    1.0  1  NCBI__GCF_000420385.1:WP_022671112.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022671112.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.4   0.3  2.1e-144  2.1e-144       2     330 ..       7     339 ..       6     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: 466.4 bits;  conditional E-value: 2.1e-144
                             TIGR01179   2 iLvtGgaGyiGshvvrqllekgke.vvvlDnlskgskealkalekitevklvegdladkekleavleeekida 73 
                                           iL+tGgaGyiGshvv+ lle++ + + v+Dnls+g+k+++ +l+ki+++ ++ +dl++  +++ v++++++da
  NCBI__GCF_000420385.1:WP_022671112.1   7 ILITGGAGYIGSHVVKLLLENSNSdITVIDNLSTGFKSTIDELKKIRDFDFIYADLSNWDEIKGVFKAKQFDA 79 
                                           9****************99887655************************************************ PP

                             TIGR01179  74 viHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekv....pisEesplnpi 142
                                           +iHfaa+i v+EsvkePlkYY nn+ nt++L+++ ++++vkk+iFss+aavYge++       i E+++++pi
  NCBI__GCF_000420385.1:WP_022671112.1  80 IIHFAASIIVPESVKEPLKYYLNNTANTTNLVKLAVEYKVKKFIFSSTAAVYGEPTIKeigdGIDENFKTEPI 152
                                           ******************************************************98651222579******** PP

                             TIGR01179 143 npYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGt 215
                                           npYG+skl +Eri++d++ka++++k+vi RYFnvaGA+++ +iG+++knathlik++ae+ vgkr+k+ ifG+
  NCBI__GCF_000420385.1:WP_022671112.1 153 NPYGQSKLFSERIIQDTAKANPDFKYVIFRYFNVAGASPDLTIGQKTKNATHLIKVAAETTVGKRDKMFIFGD 225
                                           ************************************************************************* PP

                             TIGR01179 216 dyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRa 288
                                           dyptkDGt+vRDyiHv+Dla+aH++ le+le ++es+++n+G+g+g svkevie++kkv+g d+kve a+rR 
  NCBI__GCF_000420385.1:WP_022671112.1 226 DYPTKDGTGVRDYIHVMDLADAHIKGLEYLE-KNESDIFNVGYGKGASVKEVIETMKKVTGIDFKVETAQRRL 297
                                           ******************************9.6**************************************** PP

                             TIGR01179 289 GDpaslvadaskikrelgwkpkyddLeeiiksawdWekklke 330
                                           GDpa l+a+++ki +++gwkpkyd Le+i+k+a++Wek+ +e
  NCBI__GCF_000420385.1:WP_022671112.1 298 GDPAILIAKNDKIINKMGWKPKYDSLETICKTAYEWEKRFNE 339
                                           **************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (342 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: 16.33
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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