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.29206.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.86
//
[ok]

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

Links

Downloads

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:

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:

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:

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:

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