Align galactose kinase (characterized)
to candidate 199882 SO0694 galactokinase (NCBI ptt file)
Query= CharProtDB::CH_024146 (382 letters) >FitnessBrowser__MR1:199882 Length = 381 Score = 311 bits (797), Expect = 2e-89 Identities = 157/377 (41%), Positives = 233/377 (61%), Gaps = 4/377 (1%) Query: 5 EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKV 64 ++ LF FG A QAPGRVNLIGE+TDYNDGFVLP AI++ TVI+ R+D K Sbjct: 6 QRATKLFVQTFGTKADDLYQAPGRVNLIGEYTDYNDGFVLPAAINFHTVIAVKRREDSKF 65 Query: 65 RVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGNVPQG 124 R +A + Q+ E++ H W NY++G + G+D+ + G+VP Sbjct: 66 RAVADAFPGQIKEWTFGKETEIHPEDGWVNYLKGFTAAMANTGLIAKGLDLAVVGDVPLA 125 Query: 125 AGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISALGKKD 184 AGLSSS +L VA GT + L L +A Q E ++V C IMD ++ A+G+ D Sbjct: 126 AGLSSSGALVVAFGTAISDSSQLHLSPMAVAQLAQRGEYRYVASACSIMDHMVCAMGEPD 185 Query: 185 HALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQPALRD 244 HALLIDC L ++A+++P+ ++++II+++ ++ + + RRE+C A FF ALR Sbjct: 186 HALLIDCLDLDSEAIAIPENLSLIIIDAHIEKQRLATISQQRREECAQAAEFFGLDALRH 245 Query: 245 VTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHASMRDD 304 + + + + ++LD + +R +H++TEN RT AA ALEQ ++ + LMA+SH S+RDD Sbjct: 246 LDLRQLESAKNKLDETLYRRAKHVVTENKRTQSAARALEQNNISKFSLLMAQSHQSLRDD 305 Query: 305 FEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQYEAKT 364 FE+T+P+ DTLV+IV VIG++GG+RMT GC+VAL+ EL AV AV + + +T Sbjct: 306 FEVTLPEFDTLVDIVSQVIGERGGIRMT----DGCVVALVDHELTDAVVSAVEQAFFEQT 361 Query: 365 GIKETFYVCKPSQGAGQ 381 GI T Y+C S GAG+ Sbjct: 362 GIDATVYLCSASSGAGR 378 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: 334 Number of extensions: 16 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: 381 Length adjustment: 30 Effective length of query: 352 Effective length of database: 351 Effective search space: 123552 Effective search space used: 123552 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 199882 SO0694 (galactokinase (NCBI ptt file))
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.11850.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-96 309.1 0.0 2.4e-96 308.9 0.0 1.0 1 lcl|FitnessBrowser__MR1:199882 SO0694 galactokinase (NCBI ptt f Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:199882 SO0694 galactokinase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 308.9 0.0 2.4e-96 2.4e-96 3 387 .. 7 378 .. 5 379 .. 0.96 Alignments for each domain: == domain 1 score: 308.9 bits; conditional E-value: 2.4e-96 TIGR00131 3 evkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldlpl 81 +++k+F++++++k+d +aPGRvnliGe++DYndg+vlP ai+++t++avk r+d + + +++ + +++e + + lcl|FitnessBrowser__MR1:199882 7 RATKLFVQTFGTKADDLYQAPGRVNLIGEYTDYNDGFVLPAAINFHTVIAVKRREDSKFRAVADAFPGQIKEWTFGKET 85 67899************************************************************************** PP TIGR00131 82 dksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldskeillriqkve 160 + + + W nY+kg + + +Gld+ + gdvP +aGLsss al va ++ + + +l+l+ ++ +q+ e lcl|FitnessBrowser__MR1:199882 86 EIHPEDGWVNYLKGFTAAMANTGLI-AKGLDLAVVGDVPLAAGLSSSGALVVAFGTAISDSSQLHLSPMAVAQLAQRGE 163 ***99*********98888776655.55*************************************************** PP TIGR00131 161 ehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaakvlakk 239 ++v c +mD ++ ++Ge dhall+++ L+ +++ +p+ +++l+i+++ ++++ + Rr+e+ +aa+++ lcl|FitnessBrowser__MR1:199882 164 YRYVASACSIMDHMVCAMGEPDHALLIDCLDLDSEAIAIPE-NLSLIIIDAHIEKQRLATISQQRREECAQAAEFFGLD 241 *****************************************.**************8889999**************99 PP TIGR00131 240 sekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldddyeitvpe 318 aLr + + + +kl++ + Rakhvv+en+R+ a+++l+++++ ++ Lm++s++sl+dd+e+t pe lcl|FitnessBrowser__MR1:199882 242 ----ALRHLDLRQLE---SAKNKLDETLYR-RAKHVVTENKRTQSAARALEQNNISKFSLLMAQSHQSLRDDFEVTLPE 312 ....9**99998888...777888888888.************************************************ PP TIGR00131 319 idelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskealge 387 d+lv ++ +v+G +G R+t GC+valv +e ++v a+ + + ++t++ ++ +++ ++ ++g+ lcl|FitnessBrowser__MR1:199882 313 FDTLVDIVSQVIGeRGGIRMTD----GCVVALVDHELTDAVVSAVEQAFFEQTGIDATVYLCSASSGAGR 378 *************999*****5....9****************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (388 nodes) Target sequences: 1 (381 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: 9.03 // [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