GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pontimonas salivibrio CL-TW6

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_104914353.1 C3B54_RS07945 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_002950575.1:WP_104914353.1
          Length = 324

 Score =  228 bits (580), Expect = 2e-64
 Identities = 137/324 (42%), Positives = 188/324 (58%), Gaps = 8/324 (2%)

Query: 1   MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60
           M  LV GGAGYIG H V  LV  G E VVV+D L +G    +    +  +G +++   + 
Sbjct: 1   MKFLVTGGAGYIGGHTVYSLVNAGHE-VVVIDDLSSGRAEVLPEGVVLVRGSVTNPGALD 59

Query: 61  KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120
           + F  +  VD VIHFA +   G S+EKPL  +D N  GM++LLE M   GV +IVFSST+
Sbjct: 60  EAFSHH--VDGVIHFAGFKHAGVSVEKPLLTYDQNVVGMLRLLEAMERAGVGHIVFSSTS 117

Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180
           A YG  +   I E  P+NP +PYGESKL+ E I++    A G+K+  LRYFNV G+   V
Sbjct: 118 AVYGDVDAPVIHEDAPKNPASPYGESKLVGEWILRDQGVATGLKHCSLRYFNVVGSG--V 175

Query: 181 RLVRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVEY 240
             +   S   LL ++   A G  E   +FG DY+TPDGT +RDY+H   LADAH+   E 
Sbjct: 176 PGIYDTSPYSLLSMVF-AALGRGETPGVFGTDYDTPDGTCIRDYIHVQALADAHVQVAEK 234

Query: 241 LRKGNE-STAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKART 299
           L  G     A+NLGS TG S  Q++    +VTG +   E   RR GDP  ++AS E A  
Sbjct: 235 LVSGQPLQGAYNLGSGTGSSVAQMMTEVARVTGIDFEPEAWPRRAGDPMKVVASGEAAAR 294

Query: 300 VLGWKPQFDNIEKIIASAWAWHSS 323
            +GW  Q  ++ ++++SAW  +S+
Sbjct: 295 DVGWTMQ-QSVAEMVSSAWREYSA 317


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: 323
Number of extensions: 10
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 332
Length of database: 324
Length adjustment: 28
Effective length of query: 304
Effective length of database: 296
Effective search space:    89984
Effective search space used:    89984
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_104914353.1 C3B54_RS07945 (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.2036129.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.8e-99  318.0   0.0    3.4e-99  317.8   0.0    1.0  1  NCBI__GCF_002950575.1:WP_104914353.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002950575.1:WP_104914353.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.8   0.0   3.4e-99   3.4e-99       2     323 ..       3     313 ..       2     320 .. 0.94

  Alignments for each domain:
  == domain 1  score: 317.8 bits;  conditional E-value: 3.4e-99
                             TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 
                                            LvtGgaGyiG h+v +l ++g+evvv+D+ls+g +e+l+++      +lv+g +++  +l+++++ +++d v
  NCBI__GCF_002950575.1:WP_104914353.1   3 FLVTGGAGYIGGHTVYSLVNAGHEVVVIDDLSSGRAEVLPEGV-----VLVRGSVTNPGALDEAFS-HHVDGV 69 
                                           79**************************************998.....8****************7.679*** PP

                             TIGR01179  75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147
                                           iHfa++++ g sv++Pl  Y++nvv+ l+Lleam++agv +++Fss++avYg+ ++ +i+E++p np++pYG+
  NCBI__GCF_002950575.1:WP_104914353.1  70 IHFAGFKHAGVSVEKPLLTYDQNVVGMLRLLEAMERAGVGHIVFSSTSAVYGDVDAPVIHEDAPKNPASPYGE 142
                                           ************************************************************************* PP

                             TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdypt 219
                                           skl+ E+il+d   a ++lk+++LRYFnv+G    g     + + +  l+ + + +a+g+ e+  +fGtdy+t
  NCBI__GCF_002950575.1:WP_104914353.1 143 SKLVGEWILRDQGVA-TGLKHCSLRYFNVVGSGVPGI----YDTSPySLLSM-VFAALGRGETPGVFGTDYDT 209
                                           ************999.***************876653....44555266665.5689**************** PP

                             TIGR01179 220 kDGtcvRDyiHveDlaeaHlaalealeegge.sevynlGagqgfsvkevieavkkvsgkdikveladrRaGDp 291
                                           +DGtc+RDyiHv+ la+aH++  e+l +g+  + +ynlG+g+g sv +++ +v +v+g d++ e  +rRaGDp
  NCBI__GCF_002950575.1:WP_104914353.1 210 PDGTCIRDYIHVQALADAHVQVAEKLVSGQPlQGAYNLGSGTGSSVAQMMTEVARVTGIDFEPEAWPRRAGDP 282
                                           **************************999652679************************************** PP

                             TIGR01179 292 aslvadaskikrelgwkpkyddLeeiiksawd 323
                                            ++va+ + + r +gw+ +   ++e+++saw+
  NCBI__GCF_002950575.1:WP_104914353.1 283 MKVVASGEAAARDVGWTMQQS-VAEMVSSAWR 313
                                           ******************999.*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (324 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.04
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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