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

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.8685.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.16
//
[ok]

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

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Protein sequences (fasta format)
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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