Alignments for a candidate for galE in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Rhodococcus qingshengii djl-6-2

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_003942257.1 C1M55_RS14120 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_002893965.1:WP_003942257.1
          Length = 329

 Score =  268 bits (684), Expect = 2e-76
 Identities = 154/318 (48%), Positives = 198/318 (62%), Gaps = 3/318 (0%)

Query: 1   MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60
           M +LV GGAGY+GS     L+E+G E VVV+D L TG+  AV   A F +GD+       
Sbjct: 1   MKLLVTGGAGYVGSVCSTVLLERGHE-VVVIDDLSTGNADAVPAGAEFIEGDVGALAADV 59

Query: 61  KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120
                +P  D V+HFAA SLVGES+  P KY+  N    ++LLE +   G   +VFSSTA
Sbjct: 60  LGSAGSPVFDGVLHFAAQSLVGESVLHPEKYWRGNVVTTIELLEAIRVSGTPRLVFSSTA 119

Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180
           ATYG PE+ PI+ET P  P NPYG +KL ++  +     A+G+    LRYFNVAGA    
Sbjct: 120 ATYGEPEQSPIVETAPTRPTNPYGATKLAIDHAITSYSIAHGLGATSLRYFNVAGAYKSA 179

Query: 181 RLVRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVEY 240
              R   ETHL+P++LQVA   R+KI +FG D+ TPDGT VRDY+H  DLA+AHLLA+E 
Sbjct: 180 GENRV-IETHLIPLVLQVALEQRDKISVFGTDWPTPDGTAVRDYIHVLDLAEAHLLALES 238

Query: 241 LRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKARTV 300
              G E   +NLGS  GFS  +++ A  +VTG  I  E A RR GDP +LIASS+KA   
Sbjct: 239 SVPG-EHRIYNLGSGAGFSVREVIAACARVTGLPINVEDASRRLGDPAVLIASSDKAIAE 297

Query: 301 LGWKPQFDNIEKIIASAW 318
           LGW P   +++ I+A AW
Sbjct: 298 LGWTPTRTDLDVIVADAW 315


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: 319
Number of extensions: 14
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: 329
Length adjustment: 28
Effective length of query: 304
Effective length of database: 301
Effective search space:    91504
Effective search space used:    91504
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_003942257.1 C1M55_RS14120 (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.1641550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-112  361.7   0.0   1.7e-112  361.5   0.0    1.0  1  NCBI__GCF_002893965.1:WP_003942257.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_003942257.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.5   0.0  1.7e-112  1.7e-112       1     326 [.       2     319 ..       2     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 361.5 bits;  conditional E-value: 1.7e-112
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladk.ekleavleeekid 72 
                                           k+LvtGgaGy+Gs     lle+g+evvv+D+ls+g+++a++a+      +++egd+    + +     +  +d
  NCBI__GCF_002893965.1:WP_003942257.1   2 KLLVTGGAGYVGSVCSTVLLERGHEVVVIDDLSTGNADAVPAGA-----EFIEGDVGALaADVLGSAGSPVFD 69 
                                           69*****************************************9.....5******8641445555668889* PP

                             TIGR01179  73 aviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpY 145
                                            v+Hfaa+  vgEsv +P kY++ nvv t+eLlea++  g  +l+Fss+aa+Yge+e++pi E++p+ p+npY
  NCBI__GCF_002893965.1:WP_003942257.1  70 GVLHFAAQSLVGESVLHPEKYWRGNVVTTIELLEAIRVSGTPRLVFSSTAATYGEPEQSPIVETAPTRPTNPY 142
                                           ************************************************************************* PP

                             TIGR01179 146 GrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyp 218
                                           G++kl++++ ++ ++ a ++l  ++LRYFnvaGA ++   Ge+   +thli+lv++va+ +r+k+++fGtd+p
  NCBI__GCF_002893965.1:WP_003942257.1 143 GATKLAIDHAITSYSIA-HGLGATSLRYFNVAGAYKS--AGENRVIETHLIPLVLQVALEQRDKISVFGTDWP 212
                                           **************999.****************986..6********************************* PP

                             TIGR01179 219 tkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDp 291
                                           t+DGt+vRDyiHv DlaeaHl ale     ge ++ynlG+g gfsv+evi a+ +v+g +i+ve a rR GDp
  NCBI__GCF_002893965.1:WP_003942257.1 213 TPDGTAVRDYIHVLDLAEAHLLALESSVP-GEHRIYNLGSGAGFSVREVIAACARVTGLPINVEDASRRLGDP 284
                                           *************************9995.899**************************************** PP

                             TIGR01179 292 aslvadaskikrelgwkpkyddLeeiiksawdWek 326
                                           a+l+a+++k+ +elgw+p+++dL+ i+++aw++ +
  NCBI__GCF_002893965.1:WP_003942257.1 285 AVLIASSDKAIAELGWTPTRTDLDVIVADAWQFLQ 319
                                           *******************************9865 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.49
//
[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 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