Align Xylulose kinase; Xylulokinase; EC 2.7.1.17 (uncharacterized)
to candidate H281DRAFT_04146 H281DRAFT_04146 xylulokinase
Query= curated2:P39211 (499 letters) >FitnessBrowser__Burk376:H281DRAFT_04146 Length = 514 Score = 249 bits (636), Expect = 2e-70 Identities = 166/517 (32%), Positives = 267/517 (51%), Gaps = 26/517 (5%) Query: 1 MKYVIGIDLGTSAVKTILVNQNGKVCAETSKRYPLIQEKAGYSEQNPEDWVQQTIEALAE 60 M YVIG+D+GT + K +LV+Q+G + A + Y + ++EQ P W + E +A Sbjct: 1 MDYVIGVDIGTQSTKALLVDQHGAIVAHHASSYQPDTPRPLWAEQWPAVWFKAVTECIAA 60 Query: 61 LV---SISNVQAKDIDGISYSGQMHGL-VLLDQDRQVLRNAILWNDTRTTPQCIRMTEKF 116 V + V A I + S G + +D D + L ++W D R T Q + Sbjct: 61 CVRKAKEAGVAANSIKAVCVSSLYGGSGIPVDSDMRPLYPCLIWMDRRATDQVEWVRNNV 120 Query: 117 G-DHLLDITKNRVLEGFTLPKMLWVKEHEPELFKKTAVFLLPKDYVRFRMTGVIHTEYSD 175 D L IT N V + KMLW+++HEP+++ +T FL P YV + +TG I ++S Sbjct: 121 DLDRLYTITGNGVDSYYGYTKMLWLRDHEPDVWAQTRYFLPPNAYVIYMLTGEIAVDHS- 179 Query: 176 AAGTL--LLHITRKEWSNDICNQIGISADICPP-LVESHDCVGSLLPHVAAKTGLLEKTK 232 +AG + + I +++WS++ + +GI A + P LVES + VGSLL + GL T Sbjct: 180 SAGNIGGIYDIAKRDWSDEALDMLGIPATMMPERLVESSEVVGSLLSQWTEELGLAAGTA 239 Query: 233 VYAGGADNACGAIGAGILSSGKTLCSIGTSGV--ILSYEEEKERDFKGKVHFFNHGKKDS 290 + AGG D A AG+ +G+ + IGTS ++ + H FN G++D Sbjct: 240 IVAGGVDAAVATFAAGVSRAGQHVAMIGTSMCWGYINQTVDARHGLISMPHVFN-GQRD- 297 Query: 291 FYTMGVTLAAGYSLDWFKRTFA----------PNESFEQLLQGVEA-IPIGANGLLYTPY 339 Y G + AG S+ W++ F P+ +LL+ A +P G++G+++ PY Sbjct: 298 IYVFGGAITAGASVTWYRDQFCHAEIEAARATPHGDPHRLLEDNAAKVPAGSDGVMFLPY 357 Query: 340 LVGERTPHADSSIRGSLIGMDGAHNRKHFLRAIMEGITFSLHESIELFREAGKSVH-TVV 398 L+GER+P D+ G+ +G+ H R H RA++EG++F+L +IE R+ +S+ +V Sbjct: 358 LMGERSPVWDAKASGAFVGLSLFHTRAHLYRAVLEGVSFALKHNIEAGRKGAQSLEDKLV 417 Query: 399 SIGGGAKNDTWLQMQADIFNTRVIKLENEQGPAMGAAMLAAFGSGWFESLEECAEQFIRE 458 +GG A +D W+Q+ ADI V +E E AMGAA+LAA G G S E ++ Sbjct: 418 VVGGAAHSDLWMQIIADITGYPVYTIEQEVEAAMGAALLAALGVG-LVSQEAAQGGWVTL 476 Query: 459 AAAFYPKAQNVQKYKTLFDLYKNIYTHTKDLNTALKS 495 P A + Y+ F +Y ++Y K + L++ Sbjct: 477 VERAQPDAARMALYEQRFGIYTDLYPALKPVMHRLQT 513 Lambda K H 0.319 0.135 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: 647 Number of extensions: 29 Number of successful extensions: 8 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: 499 Length of database: 514 Length adjustment: 34 Effective length of query: 465 Effective length of database: 480 Effective search space: 223200 Effective search space used: 223200 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: 52 (24.6 bits)
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