Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate HSERO_RS17030 HSERO_RS17030 xylulokinase
Query= reanno::Smeli:SMc03164 (484 letters) >FitnessBrowser__HerbieS:HSERO_RS17030 Length = 493 Score = 485 bits (1248), Expect = e-141 Identities = 259/486 (53%), Positives = 313/486 (64%), Gaps = 9/486 (1%) Query: 2 YLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLRE 61 YLG+DLGTS VK +L D + +I S S L VD PHP WSEQ P W A +AIA LR Sbjct: 3 YLGIDLGTSEVKLVLTDEDSNVIASTSARLRVDNPHPLWSEQAPQSWWNATLDAIAALRT 62 Query: 62 THAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDG-DPQFRALT 120 QA A+RGIGLSGQMHGATLLD VLRP ILWND R+ E L+ P A+T Sbjct: 63 QAPQAFQALRGIGLSGQMHGATLLDRNGNVLRPAILWNDMRAHAECVELEALVPDAVAIT 122 Query: 121 GNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDT 180 GN PGFTAPKL W+ + EP ++ + VLLPKD+L LTGE +SEMSD+AGT WLD Sbjct: 123 GNRAMPGFTAPKLLWLSKYEPAVYRAIDKVLLPKDFLGWKLTGEFVSEMSDAAGTLWLDV 182 Query: 181 GKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASA 240 +R WS +L AT L+ MP LVEG+ AG LR EL WG+ VVVAGGAGDNAASA Sbjct: 183 ARRDWSERMLGATGLDRSHMPRLVEGSAVAGQLRDELRREWGISGPVVVAGGAGDNAASA 242 Query: 241 CGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDAL 300 G+G + G AF+SLG+SGVLFAA A + PN + VHAFCH LP WHQM VILSA +L Sbjct: 243 VGIGVIRAGDAFLSLGSSGVLFAATAHHAPNAQQGVHAFCHCLPGQWHQMSVILSAAASL 302 Query: 301 NWHSGVTGRSAAELTS-----ELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGH 355 +W SGVT R AEL S G+ +AP FLPYL+GERTPHNDA +GV G+ Sbjct: 303 HWLSGVTARPVAELVSGAERLSAGQQAQAP---LFLPYLNGERTPHNDAAAKGVLFGMTP 359 Query: 356 ESSRAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPV 415 A L AV+EGV+FA+ D AL+AAGT L+ +GGGSRS +W ATAL +P+ Sbjct: 360 AHESAHLAYAVMEGVAFAMADGYAALQAAGTTLESAAFVGGGSRSAFWGVLCATALGIPL 419 Query: 416 DLPADGDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRL 475 A + GAA GAARLG +A TG D A+VC PE E P+A+ + +YRRL Sbjct: 420 RRHAGAEVGAALGAARLGRLARTGEDAASVCIPPEVLEWYRPDAARQAQLQRRLAQYRRL 479 Query: 476 YPAIKE 481 Y ++ + Sbjct: 480 YRSLAD 485 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: 655 Number of extensions: 35 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: 484 Length of database: 493 Length adjustment: 34 Effective length of query: 450 Effective length of database: 459 Effective search space: 206550 Effective search space used: 206550 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 HSERO_RS17030 HSERO_RS17030 (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.14674.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-171 556.1 0.0 3.4e-171 555.9 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS17030 HSERO_RS17030 xylulokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS17030 HSERO_RS17030 xylulokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 555.9 0.0 3.4e-171 3.4e-171 1 480 [. 4 480 .. 4 481 .. 0.99 Alignments for each domain: == domain 1 score: 555.9 bits; conditional E-value: 3.4e-171 TIGR01312 1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkei 68 lGiDlgTs+vK +l de +vias+sa+l v +p+p wsEq p++w++a+ +a+++l+++a + +++ lcl|FitnessBrowser__HerbieS:HSERO_RS17030 4 LGIDLGTSEVKLVLTDEDSNVIASTSARLRVDNPHPLWSEQAPQSWWNATLDAIAALRTQAPQAFQAL 71 7******************************************************************* PP TIGR01312 69 kaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllW 136 ++i++sGQmHg++lLD +g+vlrpaiLWnD r+++ec ele+ ++ ++++tgn a++gfTapKllW lcl|FitnessBrowser__HerbieS:HSERO_RS17030 72 RGIGLSGQMHGATLLDRNGNVLRPAILWNDMRAHAECVELEALVP--DAVAITGNRAMPGFTAPKLLW 137 ********************************************9..999****************** PP TIGR01312 137 vrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPkl 204 + k+ep v++ i+kvlLPkD+l +kLtge+v+e+sDA+GTl++dv++r+ws+ +l a+ l++s +P+l lcl|FitnessBrowser__HerbieS:HSERO_RS17030 138 LSKYEPAVYRAIDKVLLPKDFLGWKLTGEFVSEMSDAAGTLWLDVARRDWSERMLGATGLDRSHMPRL 205 ******************************************************************** PP TIGR01312 205 vessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesd 272 ve+s++aG++r+e+ +++G++ v va+G+gdnaa+A+G+g++++g++++slG+SGv++a++ ++ ++ lcl|FitnessBrowser__HerbieS:HSERO_RS17030 206 VEGSAVAGQLRDELRREWGISGPVVVAGGAGDNAASAVGIGVIRAGDAFLSLGSSGVLFAATAHHAPN 273 ******************************************************************** PP TIGR01312 273 pegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevg..aegvlllPylsG 338 ++ vh+Fch+lpg+w++++v+lsa+++l+wl+ +++ v+el+ ae+ ++g a++ l+lPyl+G lcl|FitnessBrowser__HerbieS:HSERO_RS17030 274 AQQGVHAFCHCLPGQWHQMSVILSAAASLHWLSGVTA-RPVAELVSGAERLSAGqqAQAPLFLPYLNG 340 *************************************.9**********9999877999********* PP TIGR01312 339 ERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevw 406 ERtPh+d++a+g+l+G+t +++ a+la+Av+egvafa++d+ +l++ +g+++++ +GGG++s++w lcl|FitnessBrowser__HerbieS:HSERO_RS17030 341 ERTPHNDAAAKGVLFGMTPAHESAHLAYAVMEGVAFAMADGYAALQA-AGTTLESAAFVGGGSRSAFW 407 **********************************************9.67****************** PP TIGR01312 407 rqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseavvkqkesvepiaenveayeely 473 + a+ lg +++ ++ +e gaalGaA+l+ +a + +d +++c v ++ + p+a+++++ ++++ lcl|FitnessBrowser__HerbieS:HSERO_RS17030 408 GVLCATALGIPLRRHAgAEVGAALGAARLGRLARTGEDAASVCIPPEVLEWYR--PDAARQAQLQRRL 473 ***************98999***************999******999999988..************* PP TIGR01312 474 erykkly 480 ++y++ly lcl|FitnessBrowser__HerbieS:HSERO_RS17030 474 AQYRRLY 480 *****98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (493 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: 11.84 // [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