GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galK in Pedobacter sp. GW460-11-11-14-LB5

Align Galactokinase; EC 2.7.1.6; Galactose kinase (uncharacterized)
to candidate CA265_RS09565 CA265_RS09565 galactokinase

Query= curated2:Q896X8
         (392 letters)



>FitnessBrowser__Pedo557:CA265_RS09565
          Length = 388

 Score =  390 bits (1002), Expect = e-113
 Identities = 204/383 (53%), Positives = 262/383 (68%), Gaps = 2/383 (0%)

Query: 8   MNINELKKEFIKIYGEGSMRNFFSPGRVNLIGEHIDYNGGHVFPCALNFGTLGCVRKRKD 67
           MNIN L+++F + Y + +   +F+PGRVNLIGEHIDYNGG V PCA+  GT   +    D
Sbjct: 1   MNIN-LQEKFAEQYHKKADAIYFTPGRVNLIGEHIDYNGGLVMPCAITLGTWVAIAPNND 59

Query: 68  NKVNLASTNIPLKVSINLEDIKYEKKHGWGNYPKGVIKEIIDKGYKVGGMDILISGNIPN 127
           N     S N  ++ ++    I  +    W NYP GVI E I  G ++ G+D L  GNIP 
Sbjct: 60  NLFRFKSLNFDVQTAVTSNTINEKDGSLWANYPVGVINEFIKDGKEINGLDFLFYGNIPI 119

Query: 128 GSGLSSSASLELLIAIMINNIFNDGKLDKVELIKLSQKAENDFVGLNCGIMDQFAVAMGK 187
           GSGLSSSAS+E+  A  +N   N G  DK++L+K++++ ENDF+GLN GIMDQFAVA G+
Sbjct: 120 GSGLSSSASIEIATAYALNTYINLG-YDKLDLVKIAKRVENDFIGLNSGIMDQFAVAFGE 178

Query: 188 KDMAILLDCNTLEYKYAPVDLGNYVITIMNTNKRRELSDSKYNERRLECEKALKLINKEK 247
           K+ AI+LDC TL+YK   VDLGNYV+ I+NTNK REL+DSKYNER  EC+ ALKL+N+E 
Sbjct: 179 KNKAIVLDCETLKYKMVDVDLGNYVLAIINTNKPRELADSKYNERVAECQTALKLLNEEI 238

Query: 248 KINYLCELSLEEFESLKYLIKDNRVLNRATHVVYENERVKRAYYLLSKRNLKEFGKLLAE 307
            ++YLCEL+ E+F    +LI D  +LNRATHVV EN+RV  A   L+  NL EFG+L+  
Sbjct: 239 TLHYLCELTAEKFALHSHLITDQTILNRATHVVKENDRVHLAAKALNGGNLAEFGRLMYA 298

Query: 308 SHFSLRDLYEVTGKELDAIVGEALNVSGCIGARMIGAGFGGCAIALVEKSKLDLFKKKVS 367
           SH SLR LYEV+GKELDA+V    +    IGARM GAGFGGCAIAL+EK   + F K ++
Sbjct: 299 SHESLRTLYEVSGKELDAVVDFCADYEHVIGARMTGAGFGGCAIALLEKGFEEDFAKNLT 358

Query: 368 NNYNKIIGYKPGFYTSEIGEGTY 390
           + Y + IGY    Y SEIG G Y
Sbjct: 359 DYYVEKIGYPAAIYISEIGNGPY 381


Lambda     K      H
   0.318    0.139    0.400 

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: 495
Number of extensions: 21
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: 392
Length of database: 388
Length adjustment: 31
Effective length of query: 361
Effective length of database: 357
Effective search space:   128877
Effective search space used:   128877
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate CA265_RS09565 CA265_RS09565 (galactokinase)
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.20664.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.4e-110  353.4   0.2   8.8e-110  353.1   0.2    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS09565  CA265_RS09565 galactokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS09565  CA265_RS09565 galactokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.1   0.2  8.8e-110  8.8e-110       3     383 ..       4     378 ..       2     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 353.1 bits;  conditional E-value: 8.8e-110
                                  TIGR00131   3 evkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadn 70 
                                                +++++Fa++y++k+d + ++PGRvnliGehiDYn+g v+P+ai+++t va++  +d+  +  + n+d 
  lcl|FitnessBrowser__Pedo557:CA265_RS09565   4 NLQEKFAEQYHKKADAIYFTPGRVNLIGEHIDYNGGLVMPCAITLGTWVAIAPNNDNLFRFKSLNFDV 71 
                                                6899***************************************************************7 PP

                                  TIGR00131  71 klaerkldlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaav 138
                                                ++a ++    +++++ s WanY+ gv++++ +  ++++ Gld ++ g++P g+GLsssa++e+a a  
  lcl|FitnessBrowser__Pedo557:CA265_RS09565  72 QTAVTS--NTINEKDGSLWANYPVGVINEFIKDGKEIN-GLDFLFYGNIPIGSGLSSSASIEIATAYA 136
                                                776655..5677777799******************99.***************************** PP

                                  TIGR00131 139 lknlgkleldskeillriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleial 206
                                                l+ + +l  d+ + ++ +++ve+ f+G n+G+mDq+a+++Ge++ a+++++++Lk++ v ++  +  l
  lcl|FitnessBrowser__Pedo557:CA265_RS09565 137 LNTYINLGYDKLDLVKIAKRVENDFIGLNSGIMDQFAVAFGEKNKAIVLDCETLKYKMVDVDLGNYVL 204
                                                ***************************************************************9**** PP

                                  TIGR00131 207 viantnvksnlapseYnlRrqeveeaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakh 274
                                                 i+ntn++++la+s+Yn R+ e+++a+k l+++     L +++ e+fa    +++ ++  +  +Ra h
  lcl|FitnessBrowser__Pedo557:CA265_RS09565 205 AIINTNKPRELADSKYNERVAECQTALKLLNEEITLHYLCELTAEKFA---LHSHLITDQTILNRATH 269
                                                ************************************************...66777777776678*** PP

                                  TIGR00131 275 vvsenlRvlkavkllkdedlkelGkLmnesqasldddyeitvpeidelvesialvnGsiGsRltGaGf 342
                                                vv+en Rv  a+k+l+ ++l e+G+Lm +s++sl+ +ye++  e+d  v   a+ + +iG+R+tGaGf
  lcl|FitnessBrowser__Pedo557:CA265_RS09565 270 VVKENDRVHLAAKALNGGNLAEFGRLMYASHESLRTLYEVSGKELDAVVDFCADYEHVIGARMTGAGF 337
                                                ******************************************************************** PP

                                  TIGR00131 343 GGCtvalvpnenvekvrkalaekYekktdlklefavivske 383
                                                GGC +al+++++ e++ k l++ Y +k +  +  ++ ++++
  lcl|FitnessBrowser__Pedo557:CA265_RS09565 338 GGCAIALLEKGFEEDFAKNLTDYYVEKIGYPAAIYISEIGN 378
                                                ******************************99999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (388 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: 9.83
//
[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