GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Herbaspirillum seropedicae SmR1

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate HSERO_RS10045 HSERO_RS10045 UDP-glucose 4-epimerase

Query= curated2:P55180
         (339 letters)



>FitnessBrowser__HerbieS:HSERO_RS10045
          Length = 343

 Score =  447 bits (1150), Expect = e-130
 Identities = 213/327 (65%), Positives = 260/327 (79%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           ILVTGGAGYIGSHTCVEL+++GY +VVLDNL NS A  ++R+ +I+G+   F + D+ DR
Sbjct: 6   ILVTGGAGYIGSHTCVELIHAGYAVVVLDNLCNSRASVIDRIAQISGQRPHFVQGDIRDR 65

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
             +D +F  + IEAVIHFAGLKAVGESVA PL+YY NN+ G+ +L EAM  +GVK IVFS
Sbjct: 66  AVLDGIFKSHRIEAVIHFAGLKAVGESVAQPLRYYDNNVHGSNVLFEAMAAHGVKNIVFS 125

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           SSATVYG P + PITE+FPL ATNPYG++KLM+EQIL DLH AD  W +ALLRYFNP GA
Sbjct: 126 SSATVYGDPASVPITEEFPLSATNPYGRSKLMVEQILGDLHVADPSWRIALLRYFNPVGA 185

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H SG IGEDP+GIPNNL+P++AQVA G+   LSV+G+DYPT DGTGVRDYIHVVDLA GH
Sbjct: 186 HESGLIGEDPSGIPNNLLPFIAQVADGRRAALSVYGSDYPTPDGTGVRDYIHVVDLALGH 245

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           +K L K+    G   YNLGTG G SVLEM+ AFE+  G ++PY+  DRRPGDIA C+A  
Sbjct: 246 LKTLRKLEQGPGVYTYNLGTGRGNSVLEMLAAFEQACGNKLPYQLVDRRPGDIACCYAAT 305

Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQS 329
            +A+RELGW A+RG+E MCAD+WRWQ+
Sbjct: 306 ERAERELGWRAQRGIEAMCADTWRWQA 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: 450
Number of extensions: 8
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: 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 HSERO_RS10045 HSERO_RS10045 (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.18954.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.2e-142  457.8   0.0   9.6e-142  457.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS10045  HSERO_RS10045 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS10045  HSERO_RS10045 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.6   0.0  9.6e-142  9.6e-142       2     327 ..       6     333 ..       5     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: 457.6 bits;  conditional E-value: 9.6e-142
                                  TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavle 67 
                                                iLvtGgaGyiGsh++++l ++g+ vvvlDnl+++ ++++ ++ +i+  + ++v+gd++d++ l+ +++
  lcl|FitnessBrowser__HerbieS:HSERO_RS10045   6 ILVTGGAGYIGSHTCVELIHAGYAVVVLDNLCNSRASVIDRIAQISgqRPHFVQGDIRDRAVLDGIFK 73 
                                                9********************************************99999****************** PP

                                  TIGR01179  68 eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisE 135
                                                +++i+aviHfa+l+avgEsv++Pl+YY+nnv+++ +L eam+++gvk+++Fsssa+vYg++ +vpi+E
  lcl|FitnessBrowser__HerbieS:HSERO_RS10045  74 SHRIEAVIHFAGLKAVGESVAQPLRYYDNNVHGSNVLFEAMAAHGVKNIVFSSSATVYGDPASVPITE 141
                                                ******************************************************************** PP

                                  TIGR01179 136 esplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaev 202
                                                e+pl+++npYGrsklmvE+il dl+ ad+++++++LRYFn++GA+e+g iGe++++++ +l++ +a+v
  lcl|FitnessBrowser__HerbieS:HSERO_RS10045 142 EFPLSATNPYGRSKLMVEQILGDLHVADPSWRIALLRYFNPVGAHESGLIGEDPSGIPnNLLPFIAQV 209
                                                **********************************************************9********* PP

                                  TIGR01179 203 avgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkeviea 270
                                                a g+r +l+++G dypt+DGt+vRDyiHv Dla +Hl++l++le+g ++ +ynlG+g+g+sv+e++ a
  lcl|FitnessBrowser__HerbieS:HSERO_RS10045 210 ADGRRAALSVYGSDYPTPDGTGVRDYIHVVDLALGHLKTLRKLEQGPGVYTYNLGTGRGNSVLEMLAA 277
                                                ******************************************************************** PP

                                  TIGR01179 271 vkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekk 327
                                                +++++g++++++l drR+GD+a+++a +++++relgw+++++ +e +++++w+W+  
  lcl|FitnessBrowser__HerbieS:HSERO_RS10045 278 FEQACGNKLPYQLVDRRPGDIACCYAATERAERELGWRAQRG-IEAMCADTWRWQAL 333
                                                ******************************************.***********975 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: 00:00:00.00
# Mc/sec: 12.03
//
[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:

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