Alignments for a candidate for galE in Nitriliruptor alkaliphilus DSM 45188

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Nitriliruptor alkaliphilus DSM 45188

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_052665615.1 NITAL_RS08115 UDP-glucose 4-epimerase GalE

Query= SwissProt::P21977
         (332 letters)



>NCBI__GCF_000969705.1:WP_052665615.1
          Length = 325

 Score =  278 bits (710), Expect = 2e-79
 Identities = 156/318 (49%), Positives = 202/318 (63%), Gaps = 4/318 (1%)

Query: 1   MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60
           M +LV GGAG+IG+     L+  G E V V+D L TGHR AV   A     D +D   + 
Sbjct: 1   MRVLVTGGAGFIGATTTAALLGAGHE-VTVLDDLSTGHRDAVPAGAELVVADATDPTAVG 59

Query: 61  KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120
            V  +    DA IHFAA    GESM  P ++F  NTAG  +LLEV+ +  V   V SSTA
Sbjct: 60  PVVGDGR-FDACIHFAALIEAGESMRHPERFFTVNTAGTARLLEVLIDHAVPRFVLSSTA 118

Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180
           A YG PE  PI E  P  P N YGESKL++E ++ W  + +G++   LRYFN AGA    
Sbjct: 119 AVYGEPERTPIDEDHPLAPTNAYGESKLLIERMLAWHHRIHGLRTAALRYFNAAGAT-PG 177

Query: 181 RLVRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVEY 240
           R  R   ETHL+P++LQVA G R+++ IFG DY TPDGT +RDYVH  DLADAH+ AVE 
Sbjct: 178 RGERHDPETHLIPLVLQVAAGERDQVSIFGSDYPTPDGTAIRDYVHVADLADAHVRAVER 237

Query: 241 LRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKARTV 300
           L +    T  NLGS TGFS  ++++AAR+VTG  IP  +ADRR GDP  L+AS+ +AR +
Sbjct: 238 LDQLGTCTV-NLGSGTGFSVREVIDAARRVTGHAIPVIEADRRAGDPARLVASATRAREL 296

Query: 301 LGWKPQFDNIEKIIASAW 318
           LGW+P   ++++I+A AW
Sbjct: 297 LGWEPAITDLDRIVADAW 314


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: 15
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_052665615.1 NITAL_RS08115 (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.1016467.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-116  374.0   0.0   3.2e-116  373.7   0.0    1.0  1  NCBI__GCF_000969705.1:WP_052665615.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000969705.1:WP_052665615.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.7   0.0  3.2e-116  3.2e-116       1     325 [.       2     317 ..       2     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 373.7 bits;  conditional E-value: 3.2e-116
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekida 73 
                                           ++LvtGgaG+iG+ ++ +ll +g+ev vlD+ls+g+++a++a+      +lv +d +d +++  v+ + ++da
  NCBI__GCF_000969705.1:WP_052665615.1   2 RVLVTGGAGFIGATTTAALLGAGHEVTVLDDLSTGHRDAVPAGA-----ELVVADATDPTAVGPVVGDGRFDA 69 
                                           69*****************************************9.....5*********************** PP

                             TIGR01179  74 viHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYG 146
                                            iHfaali+ gEs+++P ++++ n+ +t +Lle++ +++v +++ ss+aavYge+e++pi E++pl+p+n YG
  NCBI__GCF_000969705.1:WP_052665615.1  70 CIHFAALIEAGESMRHPERFFTVNTAGTARLLEVLIDHAVPRFVLSSTAAVYGEPERTPIDEDHPLAPTNAYG 142
                                           ************************************************************************* PP

                             TIGR01179 147 rsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdypt 219
                                           +skl +Er+l   +++ ++l++++LRYFn+aGA++    Ge++ ++thli+lv++va+g+r++++ifG dypt
  NCBI__GCF_000969705.1:WP_052665615.1 143 ESKLLIERMLAWHHRI-HGLRTAALRYFNAAGATPGR--GERHDPETHLIPLVLQVAAGERDQVSIFGSDYPT 212
                                           ****************.*****************986..********************************** PP

                             TIGR01179 220 kDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpa 292
                                           +DGt++RDy+Hv Dla+aH++a+e l +  ++ + nlG+g+gfsv+evi+a+++v+g+ i+v +adrRaGDpa
  NCBI__GCF_000969705.1:WP_052665615.1 213 PDGTAIRDYVHVADLADAHVRAVERLDQ-LGTCTVNLGSGTGFSVREVIDAARRVTGHAIPVIEADRRAGDPA 284
                                           **************************97.667788************************************** PP

                             TIGR01179 293 slvadaskikrelgwkpkyddLeeiiksawdWe 325
                                           +lva+a ++++ lgw+p  +dL+ i+++aw+ +
  NCBI__GCF_000969705.1:WP_052665615.1 285 RLVASATRARELLGWEPAITDLDRIVADAWNAT 317
                                           ******************************865 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 13.51
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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