GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galK in Shewanella oneidensis MR-1

Align galactose kinase (characterized)
to candidate 199882 SO0694 galactokinase (NCBI ptt file)

Query= CharProtDB::CH_024146
         (382 letters)



>lcl|FitnessBrowser__MR1:199882 SO0694 galactokinase (NCBI ptt file)
          Length = 381

 Score =  311 bits (797), Expect = 2e-89
 Identities = 157/377 (41%), Positives = 233/377 (61%), Gaps = 4/377 (1%)

Query: 5   EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKV 64
           ++   LF   FG  A    QAPGRVNLIGE+TDYNDGFVLP AI++ TVI+   R+D K 
Sbjct: 6   QRATKLFVQTFGTKADDLYQAPGRVNLIGEYTDYNDGFVLPAAINFHTVIAVKRREDSKF 65

Query: 65  RVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGNVPQG 124
           R +A  +  Q+ E++       H    W NY++G    +        G+D+ + G+VP  
Sbjct: 66  RAVADAFPGQIKEWTFGKETEIHPEDGWVNYLKGFTAAMANTGLIAKGLDLAVVGDVPLA 125

Query: 125 AGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISALGKKD 184
           AGLSSS +L VA GT +     L L    +A   Q  E ++V   C IMD ++ A+G+ D
Sbjct: 126 AGLSSSGALVVAFGTAISDSSQLHLSPMAVAQLAQRGEYRYVASACSIMDHMVCAMGEPD 185

Query: 185 HALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQPALRD 244
           HALLIDC  L ++A+++P+ ++++II+++ ++  + +    RRE+C   A FF   ALR 
Sbjct: 186 HALLIDCLDLDSEAIAIPENLSLIIIDAHIEKQRLATISQQRREECAQAAEFFGLDALRH 245

Query: 245 VTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHASMRDD 304
           + + +  +  ++LD  + +R +H++TEN RT  AA ALEQ ++ +   LMA+SH S+RDD
Sbjct: 246 LDLRQLESAKNKLDETLYRRAKHVVTENKRTQSAARALEQNNISKFSLLMAQSHQSLRDD 305

Query: 305 FEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQYEAKT 364
           FE+T+P+ DTLV+IV  VIG++GG+RMT     GC+VAL+  EL  AV  AV + +  +T
Sbjct: 306 FEVTLPEFDTLVDIVSQVIGERGGIRMT----DGCVVALVDHELTDAVVSAVEQAFFEQT 361

Query: 365 GIKETFYVCKPSQGAGQ 381
           GI  T Y+C  S GAG+
Sbjct: 362 GIDATVYLCSASSGAGR 378


Lambda     K      H
   0.318    0.134    0.389 

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: 334
Number of extensions: 16
Number of successful extensions: 3
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: 382
Length of database: 381
Length adjustment: 30
Effective length of query: 352
Effective length of database: 351
Effective search space:   123552
Effective search space used:   123552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 199882 SO0694 (galactokinase (NCBI ptt file))
to HMM TIGR00131 (galK: galactokinase (EC 2.7.1.6))

# 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/TIGR00131.hmm
# target sequence database:        /tmp/gapView.18953.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00131  [M=388]
Accession:   TIGR00131
Description: gal_kin: galactokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    2.1e-96  309.1   0.0    2.4e-96  308.9   0.0    1.0  1  lcl|FitnessBrowser__MR1:199882  SO0694 galactokinase (NCBI ptt f


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199882  SO0694 galactokinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.9   0.0   2.4e-96   2.4e-96       3     387 ..       7     378 ..       5     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 308.9 bits;  conditional E-value: 2.4e-96
                       TIGR00131   3 evkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldlpl 81 
                                     +++k+F++++++k+d   +aPGRvnliGe++DYndg+vlP ai+++t++avk r+d + + +++ +  +++e  +  + 
  lcl|FitnessBrowser__MR1:199882   7 RATKLFVQTFGTKADDLYQAPGRVNLIGEYTDYNDGFVLPAAINFHTVIAVKRREDSKFRAVADAFPGQIKEWTFGKET 85 
                                     67899************************************************************************** PP

                       TIGR00131  82 dksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldskeillriqkve 160
                                     + +  + W nY+kg    + +      +Gld+ + gdvP +aGLsss al va ++ + +  +l+l+    ++ +q+ e
  lcl|FitnessBrowser__MR1:199882  86 EIHPEDGWVNYLKGFTAAMANTGLI-AKGLDLAVVGDVPLAAGLSSSGALVVAFGTAISDSSQLHLSPMAVAQLAQRGE 163
                                     ***99*********98888776655.55*************************************************** PP

                       TIGR00131 161 ehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaakvlakk 239
                                      ++v   c +mD ++ ++Ge dhall+++  L+ +++ +p+ +++l+i+++ ++++   +    Rr+e+ +aa+++   
  lcl|FitnessBrowser__MR1:199882 164 YRYVASACSIMDHMVCAMGEPDHALLIDCLDLDSEAIAIPE-NLSLIIIDAHIEKQRLATISQQRREECAQAAEFFGLD 241
                                     *****************************************.**************8889999**************99 PP

                       TIGR00131 240 sekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldddyeitvpe 318
                                         aLr +   + +      +kl++   + Rakhvv+en+R+  a+++l+++++ ++  Lm++s++sl+dd+e+t pe
  lcl|FitnessBrowser__MR1:199882 242 ----ALRHLDLRQLE---SAKNKLDETLYR-RAKHVVTENKRTQSAARALEQNNISKFSLLMAQSHQSLRDDFEVTLPE 312
                                     ....9**99998888...777888888888.************************************************ PP

                       TIGR00131 319 idelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskealge 387
                                      d+lv ++ +v+G  +G R+t     GC+valv +e  ++v  a+ + + ++t++ ++ +++ ++ ++g+
  lcl|FitnessBrowser__MR1:199882 313 FDTLVDIVSQVIGeRGGIRMTD----GCVVALVDHELTDAVVSAVEQAFFEQTGIDATVYLCSASSGAGR 378
                                     *************999*****5....9****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (381 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.44
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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