Align galactose kinase (characterized)
to candidate 14882 b0757 galactokinase (NCBI)
Query= CharProtDB::CH_024146 (382 letters) >FitnessBrowser__Keio:14882 Length = 382 Score = 761 bits (1964), Expect = 0.0 Identities = 382/382 (100%), Positives = 382/382 (100%) Query: 1 MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRD 60 MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRD Sbjct: 1 MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRD 60 Query: 61 DRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGN 120 DRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGN Sbjct: 61 DRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGN 120 Query: 121 VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL 180 VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL Sbjct: 121 VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL 180 Query: 181 GKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP 240 GKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP Sbjct: 181 GKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP 240 Query: 241 ALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHAS 300 ALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHAS Sbjct: 241 ALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHAS 300 Query: 301 MRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQY 360 MRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQY Sbjct: 301 MRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQY 360 Query: 361 EAKTGIKETFYVCKPSQGAGQC 382 EAKTGIKETFYVCKPSQGAGQC Sbjct: 361 EAKTGIKETFYVCKPSQGAGQC 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: 576 Number of extensions: 8 Number of successful extensions: 1 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 14882 b0757 (galactokinase (NCBI))
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.11934.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-180 584.6 0.1 5e-180 584.4 0.1 1.0 1 lcl|FitnessBrowser__Keio:14882 b0757 galactokinase (NCBI) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14882 b0757 galactokinase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 584.4 0.1 5e-180 5e-180 2 388 .] 5 382 .] 4 382 .] 0.99 Alignments for each domain: == domain 1 score: 584.4 bits; conditional E-value: 5e-180 TIGR00131 2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldlp 80 e+++++Fa+a++++++++++aPGRvnliGeh+DYndg+vlP+aid++t+++++ rdd++v++++a+++n+l+e++ld+p lcl|FitnessBrowser__Keio:14882 5 EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKVRVMAADYENQLDEFSLDAP 83 789**************************************************************************** PP TIGR00131 81 ldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldskeillriqkv 159 ++++e+++WanYv+gv+k+lq R+ns++ G+d+visg+vP+gaGLsssa+levav++vl++l++l+ld+++i+l++q++ lcl|FitnessBrowser__Keio:14882 84 IVAHENYQWANYVRGVVKHLQLRNNSFG-GVDMVISGNVPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEA 161 ****************************.************************************************** PP TIGR00131 160 eehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaakvlak 238 e++fvG+ncG+mDql+s+lG++dhall+++r+L +++v++p+ ++a+vi+n+n+k++l++seYn+Rr+++e++a+++++ lcl|FitnessBrowser__Keio:14882 162 ENQFVGCNCGIMDQLISALGKKDHALLIDCRSLGTKAVSMPK-GVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQ 239 ******************************************.************************************ PP TIGR00131 239 ksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldddyeitvp 317 aLrDv+ eef+ a +++l+++v+k R++h+++en+R+++a+++l+++dlk++G+Lm+es+as++dd+eitvp lcl|FitnessBrowser__Keio:14882 240 P----ALRDVTIEEFN---AVAHELDPIVAK-RVRHILTENARTVEAASALEQGDLKRMGELMAESHASMRDDFEITVP 310 *....***********...************.*********************************************** PP TIGR00131 318 eidelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskealgel 388 +id+lve++++v+G ++G+R+tG+GfGGC+val+p+e v++v++a+ae+Ye+kt++k++f+v+++++++g++ lcl|FitnessBrowser__Keio:14882 311 QIDTLVEIVKAVIGdKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQYEAKTGIKETFYVCKPSQGAGQC 382 **************9*******************************************************98 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.02 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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