Alignments for a candidate for galE in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Cupriavidus basilensis 4G11

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate RR42_RS35875 RR42_RS35875 UDP-galactose-4-epimerase

Query= curated2:P55180
         (339 letters)



>FitnessBrowser__Cup4G11:RR42_RS35875
          Length = 339

 Score =  415 bits (1066), Expect = e-120
 Identities = 202/333 (60%), Positives = 241/333 (72%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           +L+TG  GYI SHT V LL +GY ++ LDNL NS+   + R+ +ITG+   F E D+ DR
Sbjct: 5   LLLTGATGYIASHTWVALLEAGYHVIGLDNLCNSNRAVVERLAQITGQRPHFVEGDVRDR 64

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
             +D +FAE+ I   IHFA LKAVGESV+ PL YY NNL G   LC  M   GVK++VFS
Sbjct: 65  ALLDRLFAEHRISGAIHFAALKAVGESVSKPLDYYDNNLNGLLTLCSVMNTAGVKQLVFS 124

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           SSATVYG P T PI EDFPL ATNPYGQTKLM EQILRDL  +D  W +A LRYFNP GA
Sbjct: 125 SSATVYGNPHTVPILEDFPLSATNPYGQTKLMSEQILRDLELSDPAWRIAYLRYFNPVGA 184

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H SG IGEDP G+PNNLMPYVAQVA G+ E+L V G DYPT DGTGVRDYIHV DLA GH
Sbjct: 185 HESGLIGEDPGGVPNNLMPYVAQVAGGRREKLQVHGGDYPTVDGTGVRDYIHVCDLAAGH 244

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           + AL  + +       NLGTG GYSVLE+V A+++ SG+ VPY   DRRPGDIA+C+ADP
Sbjct: 245 LAALVYLRDQQQCLTVNLGTGRGYSVLEVVAAYQRASGRPVPYVIGDRRPGDIASCYADP 304

Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
           A A++ +GW A+  ++ MC DSWRWQS N  G+
Sbjct: 305 ALAQKLIGWRAQHDIDRMCEDSWRWQSMNPLGF 337


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: 425
Number of extensions: 5
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: 339
Length adjustment: 28
Effective length of query: 311
Effective length of database: 311
Effective search space:    96721
Effective search space used:    96721
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 RR42_RS35875 RR42_RS35875 (UDP-galactose-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.18964.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-133  430.6   0.0   1.9e-133  430.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS35875  RR42_RS35875 UDP-galactose-4-epi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS35875  RR42_RS35875 UDP-galactose-4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.4   0.0  1.9e-133  1.9e-133       2     329 ..       5     334 ..       4     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 430.4 bits;  conditional E-value: 1.9e-133
                                 TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavlee 68 
                                               +L+tG++Gyi sh+ ++lle+g++v+ lDnl+++++ ++++l +it  + ++vegd++d++ l+++++e
  lcl|FitnessBrowser__Cup4G11:RR42_RS35875   5 LLLTGATGYIASHTWVALLEAGYHVIGLDNLCNSNRAVVERLAQITgqRPHFVEGDVRDRALLDRLFAE 73 
                                               79*******************************************99999******************* PP

                                 TIGR01179  69 ekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEes 137
                                               ++i   iHfaal+avgEsv++Pl YY+nn+++ l+L+++m++agvk+l+Fsssa+vYg++++vpi E++
  lcl|FitnessBrowser__Cup4G11:RR42_RS35875  74 HRISGAIHFAALKAVGESVSKPLDYYDNNLNGLLTLCSVMNTAGVKQLVFSSSATVYGNPHTVPILEDF 142
                                               ********************************************************************* PP

                                 TIGR01179 138 plnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavg 205
                                               pl+++npYG++klm+E+il+dl+ +d++++++ LRYFn++GA+e+g iGe++ + + +l+++va+va g
  lcl|FitnessBrowser__Cup4G11:RR42_RS35875 143 PLSATNPYGQTKLMSEQILRDLELSDPAWRIAYLRYFNPVGAHESGLIGEDPGGVPnNLMPYVAQVAGG 211
                                               ********************************************************9************ PP

                                 TIGR01179 206 krekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkv 274
                                               +rekl+++G+dypt DGt+vRDyiHv+Dla++Hlaal +l ++++  + nlG+g+g+sv+ev+ a +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS35875 212 RREKLQVHGGDYPTVDGTGVRDYIHVCDLAAGHLAALVYLRDQQQCLTVNLGTGRGYSVLEVVAAYQRA 280
                                               ********************************************************************* PP

                                 TIGR01179 275 sgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                               sg+++++ + drR+GD+as++ad++ +++ +gw++++d ++ +++++w+W++ ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS35875 281 SGRPVPYVIGDRRPGDIASCYADPALAQKLIGWRAQHD-IDRMCEDSWRWQSMNP 334
                                               ************************************99.************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (339 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: 11.85
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 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