GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Dietzia timorensis ID05-A0528

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_067471624.1 BJL86_RS07645 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_001659785.1:WP_067471624.1
          Length = 325

 Score =  292 bits (747), Expect = 9e-84
 Identities = 166/332 (50%), Positives = 212/332 (63%), Gaps = 16/332 (4%)

Query: 1   MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60
           M +LV GGAGY+GS     L+ +G E VVV+D L TG+R  V P+A F +GDL   D  R
Sbjct: 1   MRVLVTGGAGYVGSCCAAELISRGHE-VVVLDDLSTGNRDGVPPEATFIEGDLIS-DSAR 58

Query: 61  KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120
            +      VDAVIH AA SLVGES+E+P +Y+  N    + LL+ M E  VK IVFSSTA
Sbjct: 59  AL----EGVDAVIHCAARSLVGESVEQPAEYWHGNVVSTLALLDAMREADVKNIVFSSTA 114

Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180
           ATYG PE++PI E  P  P N YG +KL ++  +     AYG     LRYFNVAGA+L  
Sbjct: 115 ATYGEPEQVPITEDMPTRPTNTYGATKLAIDMAITSYCVAYGFAATSLRYFNVAGAHLGF 174

Query: 181 RLVRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVEY 240
              R   ETHL+P++LQVA G REKI +FGDD+ T DGT  RDY+H  DLADAH+LA+E 
Sbjct: 175 GENRV-VETHLIPLVLQVAAGHREKIFVFGDDWPTTDGTCARDYIHVGDLADAHVLALES 233

Query: 241 LRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKARTV 300
              G E   FNLGS  GFS  Q+++  R VTG EIPA+ + RR GDP  L+ASSE+A++V
Sbjct: 234 NAAG-EHRIFNLGSGEGFSVQQVIDVCRTVTGHEIPAQVSPRRAGDPATLVASSEQAKSV 292

Query: 301 LGWKPQFDNIEKIIASAWAW--------HSSH 324
           LGW+P   ++  ++  AW +        HS+H
Sbjct: 293 LGWQPSRTDLTTVVEDAWEFLRALGDRAHSAH 324


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: 289
Number of extensions: 9
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: 325
Length adjustment: 28
Effective length of query: 304
Effective length of database: 297
Effective search space:    90288
Effective search space used:    90288
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_067471624.1 BJL86_RS07645 (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.3432728.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-116  373.5   0.0   4.6e-116  373.2   0.0    1.0  1  NCBI__GCF_001659785.1:WP_067471624.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001659785.1:WP_067471624.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.2   0.0  4.6e-116  4.6e-116       1     325 [.       2     313 ..       2     319 .. 0.96

  Alignments for each domain:
  == domain 1  score: 373.2 bits;  conditional E-value: 4.6e-116
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekida 73 
                                           ++LvtGgaGy+Gs  + +l ++g+evvvlD+ls+g+++ ++ +      +++egdl   ++  +  + e +da
  NCBI__GCF_001659785.1:WP_067471624.1   2 RVLVTGGAGYVGSCCAAELISRGHEVVVLDDLSTGNRDGVPPEA-----TFIEGDLISDSA--R--ALEGVDA 65 
                                           69***************************************998.....7*****976542..3..34689** PP

                             TIGR01179  74 viHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYG 146
                                           viH aa+  vgEsv++P++Y++ nvv+tl Ll+am++a vk+++Fss+aa+Yge+e+vpi+E++p+ p+n YG
  NCBI__GCF_001659785.1:WP_067471624.1  66 VIHCAARSLVGESVEQPAEYWHGNVVSTLALLDAMREADVKNIVFSSTAATYGEPEQVPITEDMPTRPTNTYG 138
                                           ************************************************************************* PP

                             TIGR01179 147 rsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdypt 219
                                           ++kl+++  ++ +  a +++  ++LRYFnvaGA+     Ge+   +thli+lv++va+g+rek+ +fG+d+pt
  NCBI__GCF_001659785.1:WP_067471624.1 139 ATKLAIDMAITSYCVA-YGFAATSLRYFNVAGAHLG--FGENRVVETHLIPLVLQVAAGHREKIFVFGDDWPT 208
                                           *************999.****************985..8********************************** PP

                             TIGR01179 220 kDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpa 292
                                           +DGtc RDyiHv Dla+aH+ ale  ++ ge +++nlG+g+gfsv++vi+ +++v+g++i++++++rRaGDpa
  NCBI__GCF_001659785.1:WP_067471624.1 209 TDGTCARDYIHVGDLADAHVLALESNAA-GEHRIFNLGSGEGFSVQQVIDVCRTVTGHEIPAQVSPRRAGDPA 280
                                           ************************9885.899***************************************** PP

                             TIGR01179 293 slvadaskikrelgwkpkyddLeeiiksawdWe 325
                                           +lva+++++k++lgw+p+++dL +++++aw++ 
  NCBI__GCF_001659785.1:WP_067471624.1 281 TLVASSEQAKSVLGWQPSRTDLTTVVEDAWEFL 313
                                           ******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (325 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: 24.90
//
[ok]

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

Links

Downloads

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:

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