Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate 3607827 Dshi_1235 xylulokinase (RefSeq)
Query= reanno::Smeli:SMc03164 (484 letters) >FitnessBrowser__Dino:3607827 Length = 480 Score = 351 bits (901), Expect = e-101 Identities = 202/482 (41%), Positives = 261/482 (54%), Gaps = 10/482 (2%) Query: 1 MYLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLR 60 M+LGLD+GTS VK ++ DG R++G+AS L V P PG SEQDP W R A L Sbjct: 1 MFLGLDIGTSAVKGLVWDGA-RVLGAASAPLKVQVPVPGASEQDPEAWWRGILAVCAEL- 58 Query: 61 ETHAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDGDPQFRALT 120 + A V IGLSGQMHGA L AVLRP ILWND R+ REAA + P A Sbjct: 59 -SAQPGWAEVSAIGLSGQMHGAVCLGPDGAVLRPAILWNDNRAVREAAEMAALPGLAARV 117 Query: 121 GNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDT 180 G PGF APKLAW+ EPE+ A V+ KD++ + L G ++E S++AGT WLD Sbjct: 118 GVPPMPGFPAPKLAWLARTEPELHAATTMVMQAKDWVGMRLHGRAVTEYSEAAGTLWLDQ 177 Query: 181 GKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASA 240 R W LA + LE QMP L GTD AG L AA G+ PGV V G GD A Sbjct: 178 AARDWDREALAFSGLERAQMPALGAGTDLAGPLSAAAAAALGLKPGVPVIRGGGDAMVGA 237 Query: 241 CGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDAL 300 G+G V GQA +SLGTSG A+ ++ PNP VH+F H +P + QM +L+ + Sbjct: 238 AGIGVVAPGQAMISLGTSGQYLVASEAHRPNPAGLVHSFAHCVPGAYIQMAAMLNGAAPM 297 Query: 301 NWHSGVTGRSAAEL--TSELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGHESS 358 W +GV GRS +L +E + P FLPYL+GERTPH D R F GL H S Sbjct: 298 AWLAGVLGRSVPDLLAAAETADPAHVP---LFLPYLTGERTPHGDPEARAGFEGLSHGSG 354 Query: 359 RAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPVDLP 418 + +AV++ ++++ D+ L AG + AIGGG+RS L ++A L +PV P Sbjct: 355 PGEMMRAVVDAIAYSFADAQAVLGEAGVRAASPLAIGGGARSDLVLQTLADVLEVPVQRP 414 Query: 419 ADGDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRLYPA 478 A D G A GAA+L + + A + PE P S + RYR LY Sbjct: 415 ASADLGPALGAAKLAAVGSGAMPAARLADPPEIGAVFHPRPS--ARHGARLARYRALYSE 472 Query: 479 IK 480 ++ Sbjct: 473 LR 474 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: 657 Number of extensions: 34 Number of successful extensions: 4 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: 480 Length adjustment: 34 Effective length of query: 450 Effective length of database: 446 Effective search space: 200700 Effective search space used: 200700 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 3607827 Dshi_1235 (xylulokinase (RefSeq))
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.697235.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-134 435.6 0.0 1.2e-134 435.3 0.0 1.0 1 FitnessBrowser__Dino:3607827 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Dino:3607827 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.3 0.0 1.2e-134 1.2e-134 1 452 [. 3 446 .. 3 475 .. 0.94 Alignments for each domain: == domain 1 score: 435.3 bits; conditional E-value: 1.2e-134 TIGR01312 1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQmHglv 81 lG+D+gTs+vK l+ d +v++ +sa+l+v+ p pg sEqdpe+w++ + +++el+++ ++e++ai++sGQmHg+v FitnessBrowser__Dino:3607827 3 LGLDIGTSAVKGLVWDG-ARVLGAASAPLKVQVPVPGASEQDPEAWWRGILAVCAELSAQPG--WAEVSAIGLSGQMHGAV 80 7**************95.57**************************************9977..8**************** PP TIGR01312 82 lLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariakvlLPkDylrykL 162 L +g vlrpaiLWnD r+++e++e+ + g l++++g +++gf apKl+W+ + epe a ++ v+ kD++ ++L FitnessBrowser__Dino:3607827 81 CLGPDGAVLRPAILWNDNRAVREAAEMAALPG---LAARVGVPPMPGFPAPKLAWLARTEPELHAATTMVMQAKDWVGMRL 158 *****************************999...99******************************************** PP TIGR01312 163 tgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiG 243 g++vteys A+GTl++d + r+w++e l+ le++++P+l ++++ aG +++++a++lGl+ gv+v+ Gggd ++gA G FitnessBrowser__Dino:3607827 159 HGRAVTEYSEAAGTLWLDQAARDWDREALAFSGLERAQMPALGAGTDLAGPLSAAAAAALGLKPGVPVIRGGGDAMVGAAG 239 ********************************************************************************* PP TIGR01312 244 lgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekve 324 +g+v++g++++slGtSG +l+++++++++p+g vhsF+h++pg++ +++ +l+ ++ + wl+ +lg v +l+++ae+++ FitnessBrowser__Dino:3607827 240 IGVVAPGQAMISLGTSGQYLVASEAHRPNPAGLVHSFAHCVPGAYIQMAAMLNGAAPMAWLAGVLG-RSVPDLLAAAETAD 319 ******************************************************************.99**********99 PP TIGR01312 325 vgaegvlllPylsGERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksev 405 ++ + l+lPyl+GERtPh dp+ar+ + Gl++ + +++rAv++++a++++d+ +l e +g++ ++ +iGGGa+s++ FitnessBrowser__Dino:3607827 320 PA-HVPLFLPYLTGERTPHGDPEARAGFEGLSHGSGPGEMMRAVVDAIAYSFADAQAVLGE-AGVRAASPLAIGGGARSDL 398 97.999*******************************************************.67***************** PP TIGR01312 406 wrqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseav 452 ++q+lad+l+++v+ p+ ++ g+alGaA lAa+++g + + +++ FitnessBrowser__Dino:3607827 399 VLQTLADVLEVPVQRPAsADLGPALGAAKLAAVGSGAMPAARLADPPE 446 ****************98999**************9766555554444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (480 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: 00:00:00.00 # Mc/sec: 28.95 // [ok]
This GapMind analysis is from Apr 09 2024. 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