Alignments for a candidate for galE in Herbaspirillum seropedicae SmR1

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.17856.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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 11.78
//
[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