Alignments for a candidate for galE in Clostridium acetobutylicum ATCC 824

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Clostridium acetobutylicum ATCC 824

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate NP_349562.1 CA_C2960 UDP-galactose 4-epimerase

Query= SwissProt::Q7WTB1
         (330 letters)



>NCBI__GCF_000008765.1:NP_349562.1
          Length = 329

 Score =  371 bits (953), Expect = e-107
 Identities = 179/328 (54%), Positives = 235/328 (71%)

Query: 1   MKVLVIGGAGYIGSHAVRELVKEGNDVLVLDALYTGHRKAVDPKAKFYQGDIEDTFLVSK 60
           M +LV GGAGYIGSH V EL++ G +V+++D L +GH +AV+ KAKFY+GDI D+  + K
Sbjct: 1   MSILVCGGAGYIGSHTVHELIESGKEVVIVDNLQSGHLQAVNKKAKFYKGDIRDSEFLDK 60

Query: 61  ILRDEKIDAVMHFAAYSLVPESVKKPLKYYDNNVTGMISLLQAMNDANVKYLVFSSSAAT 120
           +  + KI +++HFAA SLV ES++KPL Y++NNV GM  LL++M   N+K +VFSS+AA 
Sbjct: 61  VFSENKIQSIIHFAANSLVGESMEKPLLYFNNNVYGMQILLESMVKHNIKNIVFSSTAAV 120

Query: 121 YGIPKKLPITEDTPLNPINPYGETKMMMEKIMAWADKADGIKYTALRYFNVAGASSDGSI 180
           YG PKK+PI E    NP N YGETK+ MEK+M W+ KA GI Y ALRYFNVAGA  DGSI
Sbjct: 121 YGEPKKIPILESDDTNPTNTYGETKLTMEKMMKWSSKAYGINYVALRYFNVAGALDDGSI 180

Query: 181 GEDHAPETHLIPNILKSAISGDGKFTIFGDDYDTKDGTNVRDYVQVEDLIDAHILALKHM 240
           GEDH PETHLIP IL+  +      T+FG DY T DGT +RDY+ V DL  AHI A++++
Sbjct: 181 GEDHNPETHLIPLILQVPLKKRPFITVFGTDYPTPDGTCIRDYIHVIDLAAAHIKAVEYL 240

Query: 241 MKTNKSDVFNLGTAHGYSNLEILESAKKVTGIDIPYTMGPRRGGDPDSLVADSTKARTVL 300
               KS +FNLG   G+S  E++++A++VT  +I   +G RR GDP  LVA S KA+ VL
Sbjct: 241 ENGGKSSIFNLGNGVGFSVKEMIDAAREVTKQNIKVVLGERRSGDPAQLVASSQKAKEVL 300

Query: 301 GWKPKHENVDDVIATAWKWHKSHPKGYE 328
           GW PK  NV D+I  AWKWH++HP G++
Sbjct: 301 GWSPKFTNVKDIIKDAWKWHETHPNGFD 328


Lambda     K      H
   0.315    0.134    0.395 

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: 362
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: 330
Length of database: 329
Length adjustment: 28
Effective length of query: 302
Effective length of database: 301
Effective search space:    90902
Effective search space used:    90902
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate NP_349562.1 CA_C2960 (UDP-galactose 4-epimerase)
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.30577.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-138  447.1   0.1   1.7e-138  447.0   0.1    1.0  1  lcl|NCBI__GCF_000008765.1:NP_349562.1  CA_C2960 UDP-galactose 4-epimera


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_349562.1  CA_C2960 UDP-galactose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.0   0.1  1.7e-138  1.7e-138       2     331 ..       3     326 ..       2     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 447.0 bits;  conditional E-value: 1.7e-138
                              TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekida 73 
                                            iLv GgaGyiGsh+v++l e+gkevv++Dnl +g+ +a+++       k+++gd++d+e l++v++e+ki++
  lcl|NCBI__GCF_000008765.1:NP_349562.1   3 ILVCGGAGYIGSHTVHELIESGKEVVIVDNLQSGHLQAVNKKA-----KFYKGDIRDSEFLDKVFSENKIQS 69 
                                            9**************************************9988.....6*********************** PP

                              TIGR01179  74 viHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpY 145
                                            +iHfaa   vgEs+++Pl Y++nnv +   Lle+m+k+++k+++Fss+aavYge++k+pi E+  +np+n Y
  lcl|NCBI__GCF_000008765.1:NP_349562.1  70 IIHFAANSLVGESMEKPLLYFNNNVYGMQILLESMVKHNIKNIVFSSTAAVYGEPKKIPILESDDTNPTNTY 141
                                            ************************************************************************ PP

                              TIGR01179 146 GrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdy 217
                                            G++kl++E+++k  +ka +++++v+LRYFnvaGA  +g+iGe+++++thli+l+++v + kr+ +++fGtdy
  lcl|NCBI__GCF_000008765.1:NP_349562.1 142 GETKLTMEKMMKWSSKA-YGINYVALRYFNVAGALDDGSIGEDHNPETHLIPLILQVPLKKRPFITVFGTDY 212
                                            *****************.****************************************************** PP

                              TIGR01179 218 ptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaG 289
                                            pt+DGtc+RDyiHv Dla+aH++a+e+le+gg+s+++nlG+g gfsvke+i+a+++v+ ++ikv l +rR+G
  lcl|NCBI__GCF_000008765.1:NP_349562.1 213 PTPDGTCIRDYIHVIDLAAAHIKAVEYLENGGKSSIFNLGNGVGFSVKEMIDAAREVTKQNIKVVLGERRSG 284
                                            ************************************************************************ PP

                              TIGR01179 290 DpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                            Dpa+lva+++k+k++lgw+pk++++++iik+aw+W++++++g
  lcl|NCBI__GCF_000008765.1:NP_349562.1 285 DPAQLVASSQKAKEVLGWSPKFTNVKDIIKDAWKWHETHPNG 326
                                            *************************************99875 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: 9.35
//
[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