Alignments for a candidate for galE in Nitratifractor salsuginis DSM 16511

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Nitratifractor salsuginis DSM 16511

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate WP_013554342.1 NITSA_RS07120 UDP-glucose 4-epimerase GalE

Query= metacyc::BSU38860-MONOMER
         (339 letters)



>NCBI__GCF_000186245.1:WP_013554342.1
          Length = 343

 Score =  444 bits (1141), Expect = e-129
 Identities = 216/335 (64%), Positives = 267/335 (79%), Gaps = 3/335 (0%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           I VTGGAGYIGSHTCVELLN+GY+++V DNLSN+S E L RV++ITGK LTF + D+ D 
Sbjct: 11  IFVTGGAGYIGSHTCVELLNAGYDVIVYDNLSNASKEVLRRVEKITGKPLTFVKGDIRDG 70

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
           + ++   A    +AVIHFAGLKAVGESV  PL+YY NN+ GT  L ++M+K G+K IVFS
Sbjct: 71  DTLEE--AMQGCDAVIHFAGLKAVGESVEKPLEYYDNNVCGTVTLLKSMQKIGLKAIVFS 128

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTAD-NEWSVALLRYFNPFG 181
           SSATVYG PE  P+TE+ PL  TNPYGQTKL++E+ILRDL+ AD + W +++LRYFNP G
Sbjct: 129 SSATVYGDPEFLPLTEEHPLRTTNPYGQTKLVIEEILRDLYRADPSSWRISILRYFNPVG 188

Query: 182 AHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEG 241
           AH SG IGEDP GIPNNLMP+V+QVAVG+ ++L VFG DY T DGTGVRDYIHVVDLA G
Sbjct: 189 AHESGLIGEDPRGIPNNLMPFVSQVAVGRRDELQVFGGDYDTHDGTGVRDYIHVVDLARG 248

Query: 242 HVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFAD 301
           H+ AL+ + ++   +A NLGTG GYSVL++VKAFEK SGK+VPYR   RRPGDIATC+A+
Sbjct: 249 HLAALKTLESAPQCEAVNLGTGKGYSVLDVVKAFEKASGKKVPYRITTRRPGDIATCYAN 308

Query: 302 PAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336
           P KAK  LGWEA+ GLE+MC D+W +QS+N  G +
Sbjct: 309 PGKAKELLGWEAQYGLEKMCEDTWNFQSNNPEGIR 343


Lambda     K      H
   0.315    0.134    0.395 

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: 467
Number of extensions: 13
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: 339
Length of database: 343
Length adjustment: 29
Effective length of query: 310
Effective length of database: 314
Effective search space:    97340
Effective search space used:    97340
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_013554342.1 NITSA_RS07120 (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.1391.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-139  449.7   0.0   2.9e-139  449.5   0.0    1.0  1  lcl|NCBI__GCF_000186245.1:WP_013554342.1  NITSA_RS07120 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000186245.1:WP_013554342.1  NITSA_RS07120 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.5   0.0  2.9e-139  2.9e-139       1     331 [.      10     341 ..      10     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: 449.5 bits;  conditional E-value: 2.9e-139
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavle 67 
                                               ki vtGgaGyiGsh++++ll++g++v+v+Dnls++ske+l+++ekit   +++v+gd++d  +le++++
  lcl|NCBI__GCF_000186245.1:WP_013554342.1  10 KIFVTGGAGYIGSHTCVELLNAGYDVIVYDNLSNASKEVLRRVEKITgkPLTFVKGDIRDGDTLEEAMQ 78 
                                               699*******************************************9999****************985 PP

                                 TIGR01179  68 eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEe 136
                                                   daviHfa+l+avgEsv++Pl+YY+nnv +t++Ll++mqk+g+k ++Fsssa+vYg++e +p++Ee
  lcl|NCBI__GCF_000186245.1:WP_013554342.1  79 --GCDAVIHFAGLKAVGESVEKPLEYYDNNVCGTVTLLKSMQKIGLKAIVFSSSATVYGDPEFLPLTEE 145
                                               ..79***************************************************************** PP

                                 TIGR01179 137 splnpinpYGrsklmvErilkdlkkad.kelkvviLRYFnvaGAdeegeiGeasknat.hliklvaeva 203
                                               +pl ++npYG++kl++E+il+dl +ad +++++ iLRYFn++GA+e+g iGe++++++ +l++ v +va
  lcl|NCBI__GCF_000186245.1:WP_013554342.1 146 HPLRTTNPYGQTKLVIEEILRDLYRADpSSWRISILRYFNPVGAHESGLIGEDPRGIPnNLMPFVSQVA 214
                                               ************************999357****************************9********** PP

                                 TIGR01179 204 vgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavk 272
                                               vg+r++l++fG+dy+t+DGt+vRDyiHv Dla +Hlaal++le+  + e+ nlG+g+g+sv++v++a++
  lcl|NCBI__GCF_000186245.1:WP_013554342.1 215 VGRRDELQVFGGDYDTHDGTGVRDYIHVVDLARGHLAALKTLESAPQCEAVNLGTGKGYSVLDVVKAFE 283
                                               ********************************************************************* PP

                                 TIGR01179 273 kvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                               k+sgk+++++++ rR+GD+a+++a++ k+k+ lgw+++y+ Le++++++w+++++++eg
  lcl|NCBI__GCF_000186245.1:WP_013554342.1 284 KASGKKVPYRITTRRPGDIATCYANPGKAKELLGWEAQYG-LEKMCEDTWNFQSNNPEG 341
                                               ****************************************.*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (343 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: 00:00:00.01
# Mc/sec: 9.50
//
[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