Alignments for a candidate for galK in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Shewanella amazonensis SB2B

Align galactose kinase (characterized)
to candidate 6936347 Sama_0536 galactokinase (RefSeq)

Query= CharProtDB::CH_024146
         (382 letters)



>FitnessBrowser__SB2B:6936347
          Length = 382

 Score =  314 bits (804), Expect = 3e-90
 Identities = 161/377 (42%), Positives = 229/377 (60%), Gaps = 3/377 (0%)

Query: 5   EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKV 64
           ++   LF   FG  A    QAPGRVN+IGEHTDYNDGFVLP AI++ TVI+   R+D + 
Sbjct: 6   QRATKLFVQTFGTKADAYYQAPGRVNIIGEHTDYNDGFVLPAAINFHTVIAVKKREDDRF 65

Query: 65  RVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGNVPQG 124
           RV+   +  +L E+             W NY++G  + +        G+D+ +  ++P G
Sbjct: 66  RVVTEAFPGELREWRFGEEGEVTAGGDWVNYLKGFTQAVGQAGLKAKGLDLAVVSSIPMG 125

Query: 125 AGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISALGKKD 184
           AG SSS +LE+A GT L     L L    IA   Q  E++F G  CG+MD + SAL + D
Sbjct: 126 AGFSSSGALEIAFGTALNDTCQLHLSPMAIAQLAQRGESRFHGSTCGVMDHMTSALAEAD 185

Query: 185 HALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQPALRD 244
            ALLIDC  L  +AV +P  ++++I++S     L+   Y  R ++C   A FF   +LRD
Sbjct: 186 SALLIDCLDLDIEAVLIPDNLSLIIVHSPLDPKLLEEAYKARADECRDAAEFFGLDSLRD 245

Query: 245 VTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHASMRDD 304
           + ++E  A +  LD  + KR RH+++EN RT  A  AL++GD+ R+ ELMA SHAS+RDD
Sbjct: 246 LELDELKAASDVLDETLYKRARHVISENLRTQSAGRALKRGDVARLSELMALSHASLRDD 305

Query: 305 FEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQYEAKT 364
           FE+ VP+++TLV+I+   IGD+GGVRMT    G  +VAL+  +L  AV  AV  +Y AKT
Sbjct: 306 FELMVPEVETLVQIMAQAIGDRGGVRMTD---GCSVVALVEHDLTDAVVHAVESEYPAKT 362

Query: 365 GIKETFYVCKPSQGAGQ 381
           G++   Y+C PS GAG+
Sbjct: 363 GLEPVLYMCAPSAGAGR 379


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: 314
Number of extensions: 13
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: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 6936347 Sama_0536 (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.17312.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
      4e-94  301.6   0.0    4.5e-94  301.4   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6936347  Sama_0536 galactokinase (RefSeq)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936347  Sama_0536 galactokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.4   0.0   4.5e-94   4.5e-94       3     387 ..       7     379 ..       5     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 301.4 bits;  conditional E-value: 4.5e-94
                         TIGR00131   3 evkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldl 79 
                                       +++k+F++++++k+d   +aPGRvn+iGeh+DYndg+vlP ai+++t++avk+r+d + +++++ +  +l e ++  
  lcl|FitnessBrowser__SB2B:6936347   7 RATKLFVQTFGTKADAYYQAPGRVNIIGEHTDYNDGFVLPAAINFHTVIAVKKREDDRFRVVTEAFPGELREWRFGE 83 
                                       67899************************************************************************ PP

                         TIGR00131  80 pldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldskeillri 156
                                       + +     dW nY+kg  + + +   +++ Gld+ + + +P gaG sss ale+a ++ l++  +l+l+   i++ +
  lcl|FitnessBrowser__SB2B:6936347  84 EGEVTAGGDWVNYLKGFTQAVGQAGLKAK-GLDLAVVSSIPMGAGFSSSGALEIAFGTALNDTCQLHLSPMAIAQLA 159
                                       *999999**************99999988.*********************************************** PP

                         TIGR00131 157 qkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaa 233
                                       q+ e +f G  cG mD ++s+l e d all+++  L+ ++v +p  +++l+i+ +    +l +  Y  R  e+ +aa
  lcl|FitnessBrowser__SB2B:6936347 160 QRGESRFHGSTCGVMDHMTSALAEADSALLIDCLDLDIEAVLIPD-NLSLIIVHSPLDPKLLEEAYKARADECRDAA 235
                                       *********************************************.******************************* PP

                         TIGR00131 234 kvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldd 310
                                       +++       +LrD+   e +   a +  l++   k Ra+hv+senlR+  a ++lk +d+ +l +Lm+ s+asl+d
  lcl|FitnessBrowser__SB2B:6936347 236 EFFGLD----SLRDLELDELK---AASDVLDETLYK-RARHVISENLRTQSAGRALKRGDVARLSELMALSHASLRD 304
                                       ****99....9*****99999...777777777777.**************************************** PP

                         TIGR00131 311 dyeitvpeidelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskealg 386
                                       d+e+ vpe+++lv ++a+++G  +G+R+t    G  +valv+++  ++v +a+  +Y++kt+l+   +++ ++ ++g
  lcl|FitnessBrowser__SB2B:6936347 305 DFELMVPEVETLVQIMAQAIGdRGGVRMTD---GCSVVALVEHDLTDAVVHAVESEYPAKTGLEPVLYMCAPSAGAG 378
                                       *********************99******7...44589************************************998 PP

                         TIGR00131 387 e 387
                                       +
  lcl|FitnessBrowser__SB2B:6936347 379 R 379
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (382 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: 10.60
//
[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