Alignments for a candidate for galK in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Shewanella loihica PV-4

Align galactose kinase (characterized)
to candidate 5210845 Shew_3271 galactokinase (RefSeq)

Query= CharProtDB::CH_024146
         (382 letters)



>FitnessBrowser__PV4:5210845
          Length = 388

 Score =  372 bits (956), Expect = e-108
 Identities = 186/377 (49%), Positives = 248/377 (65%)

Query: 5   EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKV 64
           ++   LF   FG  A    QAPGRVNLIGEHTDYNDGFVLP AI+++TVI+   RDD K 
Sbjct: 6   QRANKLFVQTFGTTADDLYQAPGRVNLIGEHTDYNDGFVLPAAINFRTVIAVKQRDDDKF 65

Query: 65  RVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGNVPQG 124
           R ++  +  ++  +          N  W NY++G    +        G+D+ + G+VP G
Sbjct: 66  RAVSDAFPGKIYTWHFGQEGEMDPNDSWINYLKGFTAAVSASGLPAKGMDLAVVGSVPLG 125

Query: 125 AGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISALGKKD 184
           AGLSSSA+LE+A GT L     L L    +A   Q  ENQ+VGC CGIMDQ+ISA+ +++
Sbjct: 126 AGLSSSAALEIAFGTALNDCSQLRLSPLAVAQMAQRGENQYVGCACGIMDQMISAMAQEE 185

Query: 185 HALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQPALRD 244
           HALLIDC  L  + V +P+ ++++I+NSN  R LV SEYN RREQCE  A  F   +LR 
Sbjct: 186 HALLIDCEDLDCEPVPIPESLSLIIVNSNVPRGLVDSEYNLRREQCEQVAEHFGIESLRH 245

Query: 245 VTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHASMRDD 304
           + +        EL  +  +R RH+L+EN RT  AA ALE G++ ++ ELMA+SH SMRDD
Sbjct: 246 LELRTLEGAKDELPEVCYRRARHVLSENRRTQNAAHALEAGNIAKLSELMAQSHQSMRDD 305

Query: 305 FEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQYEAKT 364
           FEITVP+ID LVEI+ AV+GD+GGVRMTGGGFGGC+VAL+  +L  AV +AV  QY+A T
Sbjct: 306 FEITVPEIDKLVEIIDAVVGDRGGVRMTGGGFGGCVVALVDHDLTDAVVEAVERQYQAAT 365

Query: 365 GIKETFYVCKPSQGAGQ 381
           G++ + Y+C  SQGA +
Sbjct: 366 GLEASVYLCSASQGASR 382


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: 376
Number of extensions: 11
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: 382
Length of database: 388
Length adjustment: 30
Effective length of query: 352
Effective length of database: 358
Effective search space:   126016
Effective search space used:   126016
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 5210845 Shew_3271 (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.4713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   5.5e-122  393.3   0.0   6.3e-122  393.1   0.0    1.0  1  lcl|FitnessBrowser__PV4:5210845  Shew_3271 galactokinase (RefSeq)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210845  Shew_3271 galactokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.1   0.0  6.3e-122  6.3e-122       3     386 ..       7     381 ..       5     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 393.1 bits;  conditional E-value: 6.3e-122
                        TIGR00131   3 evkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldlp 80 
                                      +++k+F++++++ +d   +aPGRvnliGeh+DYndg+vlP ai++ t++avk+rdd + + +++ +  k+   ++ ++
  lcl|FitnessBrowser__PV4:5210845   7 RANKLFVQTFGTTADDLYQAPGRVNLIGEHTDYNDGFVLPAAINFRTVIAVKQRDDDKFRAVSDAFPGKIYTWHFGQE 84 
                                      67899************************************************************************* PP

                        TIGR00131  81 ldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldskeillriqk 158
                                       + + ++ W nY+kg    +      ++ G+d+ + g vP gaGLsssaale+a ++ l++  +l l+    ++++q+
  lcl|FitnessBrowser__PV4:5210845  85 GEMDPNDSWINYLKGFTAAVSASGLPAK-GMDLAVVGSVPLGAGLSSSAALEIAFGTALNDCSQLRLSPLAVAQMAQR 161
                                      *****9*********9999988776666.************************************************* PP

                        TIGR00131 159 veehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaakvl 236
                                       e+++vG+ cG+mDq++s++ +e+hall++++ L+ +pv++p+  ++l+i+n+nv++ l++seYnlRr+++e+ a+ +
  lcl|FitnessBrowser__PV4:5210845 162 GENQYVGCACGIMDQMISAMAQEEHALLIDCEDLDCEPVPIPE-SLSLIIVNSNVPRGLVDSEYNLRREQCEQVAEHF 238
                                      *******************************************.9********************************* PP

                        TIGR00131 237 akksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldddyei 314
                                        +    +Lr +     +       +l  +v  +Ra+hv+sen R+ +a+++l+ +++ +l +Lm++s++s++dd+ei
  lcl|FitnessBrowser__PV4:5210845 239 GIE----SLRHLELRTLE---GAKDELP-EVCYRRARHVLSENRRTQNAAHALEAGNIAKLSELMAQSHQSMRDDFEI 308
                                      *99....99999998888...4445555.55556******************************************** PP

                        TIGR00131 315 tvpeidelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskealg 386
                                      tvpeid+lve+i +v G  +G+R+tG+GfGGC+valv ++  ++v +a+  +Y++ t+l+++ +++ +++++ 
  lcl|FitnessBrowser__PV4:5210845 309 TVPEIDKLVEIIDAVVGdRGGVRMTGGGFGGCVVALVDHDLTDAVVEAVERQYQAATGLEASVYLCSASQGAS 381
                                      *****************99***************************************************986 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: 00:00:00.02
# Mc/sec: 7.48
//
[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