Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate WP_012385426.1 BIND_RS12460 xylulokinase
Query= reanno::Smeli:SMc03164 (484 letters) >NCBI__GCF_000019845.1:WP_012385426.1 Length = 484 Score = 723 bits (1865), Expect = 0.0 Identities = 351/480 (73%), Positives = 397/480 (82%) Query: 1 MYLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLR 60 MYLGLDLGTSGVKA+L+D Q+++GSAS L+V RP PGWSEQDP +W+RAA+ A+A ++ Sbjct: 1 MYLGLDLGTSGVKALLIDANQQVVGSASSPLNVSRPQPGWSEQDPVEWVRAAQAAMAGVK 60 Query: 61 ETHAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDGDPQFRALT 120 H +A A+RGIGLSGQMHGATLLD D VLRPCILWND RS R+AAALD D +FR +T Sbjct: 61 AAHPEAFKALRGIGLSGQMHGATLLDADDKVLRPCILWNDVRSHRQAAALDADSRFRVIT 120 Query: 121 GNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDT 180 GNIVFPGFTAPKL WV E+EPEIFAR+ VLLPKDYLRLWLTGE S+MSD+AGT+WLDT Sbjct: 121 GNIVFPGFTAPKLVWVAEHEPEIFARIHRVLLPKDYLRLWLTGESFSDMSDAAGTAWLDT 180 Query: 181 GKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASA 240 G RKWS LLAAT ++ERQMP LVEG + AG LR LAA WG+G G+VVAGGAGDNAA+A Sbjct: 181 GGRKWSPELLAATGMDERQMPALVEGVEPAGVLRSGLAAEWGLGAGIVVAGGAGDNAAAA 240 Query: 241 CGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDAL 300 CGMG + EG AFVSLGTSGVLFAAN SY P P SAVH FCHALP TWHQMGVIL ATDAL Sbjct: 241 CGMGVIDEGAAFVSLGTSGVLFAANDSYRPQPASAVHTFCHALPGTWHQMGVILCATDAL 300 Query: 301 NWHSGVTGRSAAELTSELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGHESSRA 360 NWHSG+TG SAAEL +E G+SLKAP SVTFLPYLSGERTPHNDA+ RG F GLG ES RA Sbjct: 301 NWHSGLTGLSAAELIAEQGDSLKAPSSVTFLPYLSGERTPHNDASARGAFVGLGRESDRA 360 Query: 361 VLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPVDLPAD 420 LTQAVLEGV+FAIRD+L ALR+AG ++ RV A GGG++S YWLS++ATAL +PVD PAD Sbjct: 361 ALTQAVLEGVAFAIRDNLVALRSAGAQITRVMATGGGAQSSYWLSALATALEIPVDRPAD 420 Query: 421 GDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRLYPAIK 480 GDFGAAFGAARLGLIAATGA P +CTAP AET P L AY DAY RYR LYPA++ Sbjct: 421 GDFGAAFGAARLGLIAATGAMPKKICTAPAIAETFEPITPLAQAYADAYARYRALYPALR 480 Lambda K H 0.317 0.132 0.401 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: 746 Number of extensions: 26 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: 484 Length of database: 484 Length adjustment: 34 Effective length of query: 450 Effective length of database: 450 Effective search space: 202500 Effective search space used: 202500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_012385426.1 BIND_RS12460 (xylulokinase)
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))
# 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/TIGR01312.hmm # target sequence database: /tmp/gapView.27935.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01312 [M=481] Accession: TIGR01312 Description: XylB: xylulokinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-175 570.4 0.0 1.6e-175 570.2 0.0 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012385426.1 BIND_RS12460 xylulokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012385426.1 BIND_RS12460 xylulokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 570.2 0.0 1.6e-175 1.6e-175 1 480 [. 3 476 .. 3 477 .. 0.97 Alignments for each domain: == domain 1 score: 570.2 bits; conditional E-value: 1.6e-175 TIGR01312 1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeik 69 lG+DlgTs+vKall+d++++v++s+s++l+v++p+pgwsEqdp ew++a + a++ +++++ e k+++ lcl|NCBI__GCF_000019845.1:WP_012385426.1 3 LGLDLGTSGVKALLIDANQQVVGSASSPLNVSRPQPGWSEQDPVEWVRAAQAAMAGVKAAHPEAFKALR 71 7******************************************************************** PP TIGR01312 70 aisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvr 138 +i++sGQmHg++lLD+++kvlrp+iLWnD+r++++++ l+++ +++ +tgn++++gfTapKl+Wv lcl|NCBI__GCF_000019845.1:WP_012385426.1 72 GIGLSGQMHGATLLDADDKVLRPCILWNDVRSHRQAAALDADS---RFRVITGNIVFPGFTAPKLVWVA 137 ***************************************9987...7********************** PP TIGR01312 139 khepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklves 207 +hepe+fari+ vlLPkDylr++Ltge +++sDA+GT+++d+ r+ws ell+a+ ++e+++P+lve+ lcl|NCBI__GCF_000019845.1:WP_012385426.1 138 EHEPEIFARIHRVLLPKDYLRLWLTGESFSDMSDAAGTAWLDTGGRKWSPELLAATGMDERQMPALVEG 206 ********************************************************************* PP TIGR01312 208 sekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpega 276 e aG +r+ +a+++Gl +g+ va+G+gdnaa+A+G+g+++eg+++vslGtSGv++a++d+++++p++a lcl|NCBI__GCF_000019845.1:WP_012385426.1 207 VEPAGVLRSGLAAEWGLGAGIVVAGGAGDNAAAACGMGVIDEGAAFVSLGTSGVLFAANDSYRPQPASA 275 ********************************************************************* PP TIGR01312 277 vhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhld 345 vh+Fchalpg+w+++gv+l at+al+w + l+g + e ++e+ + ++ +v++lPylsGERtPh+d lcl|NCBI__GCF_000019845.1:WP_012385426.1 276 VHTFCHALPGTWHQMGVILCATDALNWHSGLTGLSAAELIAEQGDSLKAP-SSVTFLPYLSGERTPHND 343 *********************************77777777777777777.89**************** PP TIGR01312 346 pqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladil 414 ++arg ++Gl ++ ra l++Avlegvafa+rd l +l++ +g +i++++++GGGa+s++w+ la+ l lcl|NCBI__GCF_000019845.1:WP_012385426.1 344 ASARGAFVGLGRESDRAALTQAVLEGVAFAIRDNLVALRS-AGAQITRVMATGGGAQSSYWLSALATAL 411 ****************************************.67************************** PP TIGR01312 415 glevvvpe.eeegaalGaAilAaialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480 + +v+ p+ + gaa+GaA+l++ia++ + + c++ ++++ + pi+ ++ay+++y+ry++ly lcl|NCBI__GCF_000019845.1:WP_012385426.1 412 EIPVDRPAdGDFGAAFGAARLGLIAATGAMPKKICTAPAIAETFE--PITPLAQAYADAYARYRALY 476 *******999*****************988888899888887766..*****************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (484 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: 7.89 // [ok]
This GapMind analysis is from Sep 24 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