Alignments for a candidate for galE in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Burkholderia phytofirmans PsJN

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate BPHYT_RS07405 BPHYT_RS07405 UDP-glucose 4-epimerase

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



>FitnessBrowser__BFirm:BPHYT_RS07405
          Length = 340

 Score =  448 bits (1152), Expect = e-130
 Identities = 215/333 (64%), Positives = 255/333 (76%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           ILVTGGAG+IGSHTCVELLN GY++VV+DNL NS+ E+L RV++ITGK + F+E D  D 
Sbjct: 7   ILVTGGAGFIGSHTCVELLNGGYDVVVVDNLVNSNRESLKRVEQITGKRVAFHETDSRDE 66

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
            A+  +F  + +   IHFA LKAVGESV+ P++YY NNL     L   M    VK+ VFS
Sbjct: 67  SALQRIFDAHPVSGAIHFAALKAVGESVSKPIEYYDNNLGSLLTLLSVMRARDVKQFVFS 126

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           SSATVYGVP+TSPI E FPL ATNPYGQTKL+ EQILRDL  +D  W +A LRYFNP GA
Sbjct: 127 SSATVYGVPKTSPIDESFPLSATNPYGQTKLIAEQILRDLEVSDPSWRIATLRYFNPVGA 186

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H SG IGEDP G+PNNLMPYVAQVAVGKLE+L VFG DY T DGTGVRDYIHVVDLA GH
Sbjct: 187 HESGLIGEDPGGVPNNLMPYVAQVAVGKLEKLRVFGGDYDTPDGTGVRDYIHVVDLARGH 246

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           + AL+ ++    +   NLGTG GYSVL++V++FEK SGK VPY    RRPGD+A+CFADP
Sbjct: 247 LAALDALVARDASFVVNLGTGQGYSVLDVVRSFEKASGKPVPYEIVARRPGDVASCFADP 306

Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
           A A++ LGW A+ G+E MCAD WRWQS+N  GY
Sbjct: 307 AAAEKLLGWRAQYGIERMCADHWRWQSTNPAGY 339


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: 442
Number of extensions: 7
Number of successful extensions: 1
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: 340
Length adjustment: 28
Effective length of query: 311
Effective length of database: 312
Effective search space:    97032
Effective search space used:    97032
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 BPHYT_RS07405 BPHYT_RS07405 (UDP-glucose 4-epimerase)
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.25530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.1e-136  439.5   0.0   3.4e-136  439.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07405  BPHYT_RS07405 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07405  BPHYT_RS07405 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.4   0.0  3.4e-136  3.4e-136       2     331 ..       7     338 ..       6     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 439.4 bits;  conditional E-value: 3.4e-136
                                TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleee 69 
                                              iLvtGgaG+iGsh++++ll+ g++vvv+Dnl+++++e+lk++e+it  +v++ e+d +d+++l+++++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07405   7 ILVTGGAGFIGSHTCVELLNGGYDVVVVDNLVNSNRESLKRVEQITgkRVAFHETDSRDESALQRIFDAH 76 
                                              9********************************************9999********************* PP

                                TIGR01179  70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139
                                               +   iHfaal+avgEsv++P++YY+nn+ + l+Ll++m++  vk+++Fsssa+vYg ++++pi E++pl
  lcl|FitnessBrowser__BFirm:BPHYT_RS07405  77 PVSGAIHFAALKAVGESVSKPIEYYDNNLGSLLTLLSVMRARDVKQFVFSSSATVYGVPKTSPIDESFPL 146
                                              ********************************************************************** PP

                                TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkre 208
                                              +++npYG++kl++E+il+dl+ +d++++++ LRYFn++GA+e+g iGe++ + + +l+++va+vavgk+e
  lcl|FitnessBrowser__BFirm:BPHYT_RS07405 147 SATNPYGQTKLIAEQILRDLEVSDPSWRIATLRYFNPVGAHESGLIGEDPGGVPnNLMPYVAQVAVGKLE 216
                                              ******************************************************9*************** PP

                                TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkd 278
                                              kl++fG+dy+t+DGt+vRDyiHv Dla +Hlaal+al + + s v nlG+gqg+sv++v++ ++k+sgk+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07405 217 KLRVFGGDYDTPDGTGVRDYIHVVDLARGHLAALDALVARDASFVVNLGTGQGYSVLDVVRSFEKASGKP 286
                                              ********************************************************************** PP

                                TIGR01179 279 ikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                              +++e+ +rR+GD+as++ad++ +++ lgw+++y+ +e ++++ w+W+++++ g
  lcl|FitnessBrowser__BFirm:BPHYT_RS07405 287 VPYEIVARRPGDVASCFADPAAAEKLLGWRAQYG-IERMCADHWRWQSTNPAG 338
                                              **********************************.*************99876 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 9.88
//
[ok]

This GapMind analysis is from Sep 17 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