Align galactose kinase (characterized)
to candidate BWI76_RS08615 BWI76_RS08615 galactokinase
Query= CharProtDB::CH_024146 (382 letters) >FitnessBrowser__Koxy:BWI76_RS08615 Length = 382 Score = 701 bits (1808), Expect = 0.0 Identities = 342/382 (89%), Positives = 366/382 (95%) Query: 1 MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRD 60 MSLKE TQ+LFA FGYPA+H IQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVI+CAPRD Sbjct: 1 MSLKENTQALFAEKFGYPASHVIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVIACAPRD 60 Query: 61 DRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGN 120 DR VRV+AADY NQ DEFSLD+PI +H+ QW+NYVRGVVKHLQ RNN+FGG D++ISGN Sbjct: 61 DRTVRVIAADYANQTDEFSLDSPITSHDTQQWSNYVRGVVKHLQQRNNAFGGADLLISGN 120 Query: 121 VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL 180 VPQGAGLSSSASLEVAVGTV QQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL Sbjct: 121 VPQGAGLSSSASLEVAVGTVFQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL 180 Query: 181 GKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP 240 GKKDHALLIDCR+LGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP Sbjct: 181 GKKDHALLIDCRTLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP 240 Query: 241 ALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHAS 300 ALRDVT++EFNAVAHELDP+VAKRVRH+LTENARTVEAA+ALE+GDL+RMGELMAESHAS Sbjct: 241 ALRDVTLQEFNAVAHELDPVVAKRVRHVLTENARTVEAAAALEKGDLQRMGELMAESHAS 300 Query: 301 MRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQY 360 MRDDFEITVPQIDTLV+IVKA IGDKGGVRMTGGGFGGCIVAL+PE+LV VQQAVA++Y Sbjct: 301 MRDDFEITVPQIDTLVDIVKATIGDKGGVRMTGGGFGGCIVALVPEDLVDTVQQAVAKEY 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: 526 Number of extensions: 11 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 BWI76_RS08615 BWI76_RS08615 (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.13548.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-174 566.3 0.2 1.8e-174 566.1 0.2 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS08615 BWI76_RS08615 galactokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS08615 BWI76_RS08615 galactokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 566.1 0.2 1.8e-174 1.8e-174 2 388 .] 5 382 .] 4 382 .] 0.99 Alignments for each domain: == domain 1 score: 566.1 bits; conditional E-value: 1.8e-174 TIGR00131 2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnkl 72 e+++ +Fa+++++++ +v++aPGRvnliGeh+DYndg+vlP+aid++t++a++ rdd++v++++a++ n++ lcl|FitnessBrowser__Koxy:BWI76_RS08615 5 ENTQALFAEKFGYPASHVIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVIACAPRDDRTVRVIAADYANQT 75 7899******************************************************************* PP TIGR00131 73 aerkldlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlg 143 +e++ld p++ +++++W+nYv+gv+k+lq+R+n+++ G+d++isg+vP+gaGLsssa+levav++v ++l+ lcl|FitnessBrowser__Koxy:BWI76_RS08615 76 DEFSLDSPITSHDTQQWSNYVRGVVKHLQQRNNAFG-GADLLISGNVPQGAGLSSSASLEVAVGTVFQQLY 145 ************************************.********************************** PP TIGR00131 144 kleldskeillriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvk 214 +l+ld+++i+l++q++e++fvG+ncG+mDql+s+lG++dhall+++r+L +++v++p+ ++a+vi+n+n+k lcl|FitnessBrowser__Koxy:BWI76_RS08615 146 HLPLDGAQIALNGQEAENQFVGCNCGIMDQLISALGKKDHALLIDCRTLGTKAVSMPK-GVAVVIINSNFK 215 **********************************************************.************ PP TIGR00131 215 snlapseYnlRrqeveeaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlka 285 ++l++seYn+Rr+++e++a+++++ aLrDv+ +ef+ a +++l+++v+k R++hv++en+R+++a lcl|FitnessBrowser__Koxy:BWI76_RS08615 216 RTLVGSEYNTRREQCETGARFFQQP----ALRDVTLQEFN---AVAHELDPVVAK-RVRHVLTENARTVEA 278 *************************....***********...************.*************** PP TIGR00131 286 vkllkdedlkelGkLmnesqasldddyeitvpeidelvesialvnG.siGsRltGaGfGGCtvalvpnenv 355 + +l+++dl+++G+Lm+es+as++dd+eitvp+id+lv ++++++G ++G+R+tG+GfGGC+valvp++ v lcl|FitnessBrowser__Koxy:BWI76_RS08615 279 AAALEKGDLQRMGELMAESHASMRDDFEITVPQIDTLVDIVKATIGdKGGVRMTGGGFGGCIVALVPEDLV 349 **********************************************9************************ PP TIGR00131 356 ekvrkalaekYekktdlklefavivskealgel 388 ++v++a+a++Ye+kt++k++f+v+++++++g++ lcl|FitnessBrowser__Koxy:BWI76_RS08615 350 DTVQQAVAKEYEAKTGIKETFYVCKPSQGAGQC 382 *******************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 6.89 // [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