Alignments for a candidate for galE in Thiohalomonas denitrificans HLD2

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Thiohalomonas denitrificans HLD2

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_092991400.1 BLP65_RS00130 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_900102855.1:WP_092991400.1
          Length = 340

 Score =  289 bits (739), Expect = 8e-83
 Identities = 155/321 (48%), Positives = 211/321 (65%), Gaps = 6/321 (1%)

Query: 2   AILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAV-HPDAIFYQGDLSDQDFMR 60
           A+LV GGAGYIGSH+V +L E G E+V+V+D+L TG   +V H D I   GD  D+D + 
Sbjct: 6   AVLVTGGAGYIGSHVVRQLAEVG-ERVIVLDNLSTGFAESVLHGDLIV--GDTGDRDTVL 62

Query: 61  KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120
            + +E   VDAV+HFAA+++V ES+  PLKY+ NNT+    LLE   E GVK+ VFSSTA
Sbjct: 63  AILREYR-VDAVMHFAAHTVVPESVRDPLKYYGNNTSSTRNLLECCQEAGVKHFVFSSTA 121

Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180
           A YG P+     E TP  PINPYG SKLM E ++    Q   + YV  RYFNVAG +   
Sbjct: 122 AVYGTPDGGLASEETPTRPINPYGRSKLMSEWMLHDLSQVTDLNYVTFRYFNVAGCDPYA 181

Query: 181 RLVR-TRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVE 239
           R+ + T + T L+ +  + A G R ++ IFG DY TPDGT VRD++H  DLA+AH L +E
Sbjct: 182 RIGQSTPNATLLIKVACETAIGKRAQLKIFGTDYPTPDGTGVRDFIHVEDLAEAHRLGLE 241

Query: 240 YLRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKART 299
           YLR G +S+ FN G   G+S  ++L++ ++VTGK +  E+  RRPGDP  LIA S +   
Sbjct: 242 YLRNGGDSSVFNCGYGHGYSVREVLDSVQRVTGKSLTIEEVARRPGDPPRLIADSGRLHQ 301

Query: 300 VLGWKPQFDNIEKIIASAWAW 320
            LGWKP++D+++ I+ +AW W
Sbjct: 302 RLGWKPRYDDLDFIVETAWNW 322


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: 349
Number of extensions: 19
Number of successful extensions: 4
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: 340
Length adjustment: 28
Effective length of query: 304
Effective length of database: 312
Effective search space:    94848
Effective search space used:    94848
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_092991400.1 BLP65_RS00130 (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.31292.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-140  453.0   0.0   2.8e-140  452.8   0.0    1.0  1  lcl|NCBI__GCF_900102855.1:WP_092991400.1  BLP65_RS00130 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900102855.1:WP_092991400.1  BLP65_RS00130 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.8   0.0  2.8e-140  2.8e-140       1     328 [.       6     326 ..       6     330 .. 0.99

  Alignments for each domain:
  == domain 1  score: 452.8 bits;  conditional E-value: 2.8e-140
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 
                                               ++LvtGgaGyiGshvvrql e g +v+vlDnls+g++e++ +++      l+ gd  d+ ++ a+l+e 
  lcl|NCBI__GCF_900102855.1:WP_092991400.1   6 AVLVTGGAGYIGSHVVRQLAEVGERVIVLDNLSTGFAESVLHGD------LIVGDTGDRDTVLAILREY 68 
                                               59*****************************************9......******************* PP

                                 TIGR01179  70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138
                                               ++dav+Hfaa + v+Esv++PlkYY nn+++t +Lle++q+agvk+++Fss+aavYg+++    sEe+p
  lcl|NCBI__GCF_900102855.1:WP_092991400.1  69 RVDAVMHFAAHTVVPESVRDPLKYYGNNTSSTRNLLECCQEAGVKHFVFSSTAAVYGTPDGGLASEETP 137
                                               ********************************************************************* PP

                                 TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207
                                               + pinpYGrsklm+E++l+dl+++ ++l++v  RYFnvaG d+  +iG++++nat lik+++e+a+gkr
  lcl|NCBI__GCF_900102855.1:WP_092991400.1 138 TRPINPYGRSKLMSEWMLHDLSQV-TDLNYVTFRYFNVAGCDPYARIGQSTPNATLLIKVACETAIGKR 205
                                               ************************.******************************************** PP

                                 TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276
                                                +l+ifGtdypt+DGt+vRD+iHveDlaeaH   le+l +gg+s+v+n+G+g+g+sv+ev++ v++v+g
  lcl|NCBI__GCF_900102855.1:WP_092991400.1 206 AQLKIFGTDYPTPDGTGVRDFIHVEDLAEAHRLGLEYLRNGGDSSVFNCGYGHGYSVREVLDSVQRVTG 274
                                               ********************************************************************* PP

                                 TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                               k++++e+ +rR+GDp++l+ad+ + +++lgwkp+yddL+ i+++aw+We++ 
  lcl|NCBI__GCF_900102855.1:WP_092991400.1 275 KSLTIEEVARRPGDPPRLIADSGRLHQRLGWKPRYDDLDFIVETAWNWERRV 326
                                               *************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (340 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.21
//
[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