Alignments for a candidate for galE in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Dechlorosoma suillum PS

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate Dsui_0398 Dsui_0398 UDP-glucose-4-epimerase

Query= curated2:P55180
         (339 letters)



>FitnessBrowser__PS:Dsui_0398
          Length = 337

 Score =  423 bits (1087), Expect = e-123
 Identities = 205/332 (61%), Positives = 248/332 (74%)

Query: 1   MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60
           M ILVTGG GYIGSHTCVELL +G+ + +LDNLSNS A+   R+  + G    F E D+ 
Sbjct: 1   MHILVTGGLGYIGSHTCVELLQAGHGVTILDNLSNSRADVAERIAGLGGAAPIFIEGDVR 60

Query: 61  DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120
           DR+ +  +F E  ++AVIHFAGLKAVGESVA PL+YY  N+ G+ +L EAM + GVK +V
Sbjct: 61  DRQLLCRIFREQTVDAVIHFAGLKAVGESVAQPLRYYECNVGGSLVLFEAMAEAGVKTLV 120

Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180
           FSSSATVYG P   PI EDFPL ATNPYG++KLMLE++L D+  AD++W +A LRYFNP 
Sbjct: 121 FSSSATVYGDPHAVPIREDFPLRATNPYGRSKLMLEEVLADMAAADSQWRIARLRYFNPV 180

Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240
           GAH SG +GE PNGIPNNLMPYVAQVA G   +LSVFGNDYPT DGTGVRD+IHVVDLA+
Sbjct: 181 GAHESGLLGEAPNGIPNNLMPYVAQVAAGLRARLSVFGNDYPTPDGTGVRDFIHVVDLAQ 240

Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300
           GH+ AL  +    G    NLGTG GYSVL++V+AFE  SG+ +P+ F  RRPGDIA C+A
Sbjct: 241 GHLAALAALARGEGMLTVNLGTGRGYSVLDLVRAFEAASGRTIPFDFVPRRPGDIAACYA 300

Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNV 332
           DPA A   LGW A+R L  MC D+WRWQ + V
Sbjct: 301 DPALAASLLGWTARRDLAAMCRDTWRWQQTAV 332


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: 407
Number of extensions: 10
Number of successful extensions: 2
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: 337
Length adjustment: 28
Effective length of query: 311
Effective length of database: 309
Effective search space:    96099
Effective search space used:    96099
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 Dsui_0398 Dsui_0398 (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.22412.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.5e-136  438.7   0.0   6.5e-136  438.5   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0398  Dsui_0398 UDP-glucose-4-epimeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0398  Dsui_0398 UDP-glucose-4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.5   0.0  6.5e-136  6.5e-136       2     328 ..       3     331 ..       2     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.5 bits;  conditional E-value: 6.5e-136
                         TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekidaviH 76 
                                       iLvtGg GyiGsh++++ll++g+ v +lDnls++ +++ +++  +   +  ++egd++d++ l ++++e+++daviH
  lcl|FitnessBrowser__PS:Dsui_0398   3 ILVTGGLGYIGSHTCVELLQAGHGVTILDNLSNSRADVAERIAGLGgaAPIFIEGDVRDRQLLCRIFREQTVDAVIH 79 
                                       9******************************************99888899************************** PP

                         TIGR01179  77 faaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvE 153
                                       fa+l+avgEsv++Pl+YYe nv ++l+L eam++agvk+l+Fsssa+vYg++++vpi E++pl ++npYGrsklm+E
  lcl|FitnessBrowser__PS:Dsui_0398  80 FAGLKAVGESVAQPLRYYECNVGGSLVLFEAMAEAGVKTLVFSSSATVYGDPHAVPIREDFPLRATNPYGRSKLMLE 156
                                       ***************************************************************************** PP

                         TIGR01179 154 rilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGtcvRDyi 229
                                       ++l d++ ad++++++ LRYFn++GA+e+g +Gea+++++ +l+++va+va+g r +l++fG+dypt+DGt+vRD+i
  lcl|FitnessBrowser__PS:Dsui_0398 157 EVLADMAAADSQWRIARLRYFNPVGAHESGLLGEAPNGIPnNLMPYVAQVAAGLRARLSVFGNDYPTPDGTGVRDFI 233
                                       ****************************************9************************************ PP

                         TIGR01179 230 HveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelg 306
                                       Hv Dla++Hlaal al++g+++ + nlG+g+g+sv+++++a++++sg++i++ + +rR+GD+a+++ad++ + + lg
  lcl|FitnessBrowser__PS:Dsui_0398 234 HVVDLAQGHLAALAALARGEGMLTVNLGTGRGYSVLDLVRAFEAASGRTIPFDFVPRRPGDIAACYADPALAASLLG 310
                                       ***************************************************************************** PP

                         TIGR01179 307 wkpkyddLeeiiksawdWekkl 328
                                       w++++d L+ +++++w+W+++ 
  lcl|FitnessBrowser__PS:Dsui_0398 311 WTARRD-LAAMCRDTWRWQQTA 331
                                       ***999.************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (337 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: 7.26
//
[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