GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galK in Shewanella sp. ANA-3

Align galactose kinase (characterized)
to candidate 7026436 Shewana3_3578 galactokinase (RefSeq)

Query= CharProtDB::CH_024146
         (382 letters)



>FitnessBrowser__ANA3:7026436
          Length = 381

 Score =  305 bits (782), Expect = 1e-87
 Identities = 157/377 (41%), Positives = 230/377 (61%), Gaps = 4/377 (1%)

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

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

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

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

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

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

Query: 365 GIKETFYVCKPSQGAGQ 381
           GI  T Y+C  S GAG+
Sbjct: 362 GIDATVYLCSASAGAGR 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: 353
Number of extensions: 18
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 7026436 Shewana3_3578 (galactokinase (RefSeq))
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.30893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.2e-96  309.9   0.0    1.4e-96  309.7   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026436  Shewana3_3578 galactokinase (Ref


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026436  Shewana3_3578 galactokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.7   0.0   1.4e-96   1.4e-96       3     387 ..       7     378 ..       5     379 .. 0.95

  Alignments for each domain:
  == domain 1  score: 309.7 bits;  conditional E-value: 1.4e-96
                         TIGR00131   3 evkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldl 79 
                                       +++k+F++++++k+d   +aPGRvnliGe++DYndg+vlP ai+++t++avk r+d++ + +++ +  +++e ++  
  lcl|FitnessBrowser__ANA3:7026436   7 RATKLFVQTFGTKADDLYQAPGRVNLIGEYTDYNDGFVLPAAINFHTVIAVKRREDNKFRAVADAFPGQIKEWSFGK 83 
                                       67899**********************************************************************99 PP

                         TIGR00131  80 pldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldskeillri 156
                                         + +  + W nY+kg   v+      + +Gld+ + gdvP +aGLsss al va ++ + +  +l+l+    ++ +
  lcl|FitnessBrowser__ANA3:7026436  84 DTEINPEDGWVNYLKGL-TVAMANTGLIAKGLDLAVVGDVPLAAGLSSSGALVVAFGTAISDSSQLHLSPMAVAQLA 159
                                       99988889*******85.555555666777*********************************************** PP

                         TIGR00131 157 qkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaa 233
                                       q+ e ++v   c +mD ++ ++Ge dhall+++  L+ +p+ +p+ +++l+i+++ ++++   +    Rr+e+ +aa
  lcl|FitnessBrowser__ANA3:7026436 160 QRGEYRYVSSACSIMDHMVCAMGEPDHALLIDCLDLDSEPIAIPE-NLSLIIIDAHIEKQRLAAINQQRREECAQAA 235
                                       *********************************************.***********99977777789********* PP

                         TIGR00131 234 kvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldd 310
                                        ++       aLr + + + +       +l+    + Rakhvv+en+R+  a+++l++++l ++  Lm++s++sl+d
  lcl|FitnessBrowser__ANA3:7026436 236 DFFGLD----ALRHLDQRQLE---SAKDQLDDTLYR-RAKHVVTENKRTQSAARALEQNNLSKFSLLMAQSHQSLRD 304
                                       *****9....*******9999...666778888777.**************************************** PP

                         TIGR00131 311 dyeitvpeidelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskealg 386
                                       d+e+t pe d+lv ++ +v+G  +G R+t     GC+valv +e  ++v  a+   + ++t++ ++ +++ ++ ++g
  lcl|FitnessBrowser__ANA3:7026436 305 DFEVTLPEFDTLVDIVSQVIGeRGGIRMTD----GCVVALVDHELTDAVVSAVEHAFYEQTGIDATVYLCSASAGAG 377
                                       *********************999*****5....9****************************************99 PP

                         TIGR00131 387 e 387
                                       +
  lcl|FitnessBrowser__ANA3:7026436 378 R 378
                                       7 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.83
//
[ok]

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

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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