Align Xylulose kinase; Xylulokinase; EC 2.7.1.17 (uncharacterized)
to candidate WP_086008539.1 MVAN_RS26630 xylulose kinase
Query= curated2:P12867 (466 letters) >NCBI__GCF_000015305.1:WP_086008539.1 Length = 461 Score = 560 bits (1443), Expect = e-164 Identities = 284/455 (62%), Positives = 331/455 (72%), Gaps = 1/455 (0%) Query: 4 VAGIDSSTQSCKVVIRDAETGALVRQGRASHPDGTEVHPDAWWSALQSAIEEAGGLDDVA 63 +AG+DSSTQSCKVV+ D+ TG +VR + HPDGTE+HPD WW ALQ IE GG DDVA Sbjct: 1 MAGVDSSTQSCKVVVCDSATGQVVRSASSPHPDGTEIHPDRWWEALQRTIEAVGGFDDVA 60 Query: 64 AASVAGQQHGMVALDENGEVVRPALLWNDTRSAGAAADLIAELGGGEKWAEAVGIVPVAS 123 A SV QQHGM+ LD G+VVR ALLWNDTRSA AA L+ ELGG WAE +G+VPVA+ Sbjct: 61 AVSVGAQQHGMICLDSAGQVVRDALLWNDTRSAEAAEQLVDELGGPAAWAERIGVVPVAA 120 Query: 124 FTLTKLRWLARNEPANAAKVAAVCLPHDWLTWKLSGSTDIADIKTDRSDASGTLYWSAKT 183 T KLRWLA +EP +A AAVCLPHDWLTW+LSGSTDIAD+ TDRSDASGT Y+SA+T Sbjct: 121 VTAAKLRWLADHEPVHADATAAVCLPHDWLTWRLSGSTDIADLCTDRSDASGTGYYSAET 180 Query: 184 NEYRRDLLELGF-GRDLVLPEVLGPTGIAGHLPNGAPLGPGAGDNAAAALGTGALPGDVI 242 + Y+ DLL L GR + P VLGP AG P+GA LGPGAGDNAAAALG GA GD + Sbjct: 181 DGYQYDLLALALRGRIPLAPRVLGPRESAGATPHGAALGPGAGDNAAAALGLGAASGDCV 240 Query: 243 VSIGTSGTVFVSSDVAPVDGRGTVAGFADTTGRFLPIVVTLNAARVLDAAAKLLGVDHDE 302 VS+GTSG V AP D G VAGFAD TG LP+V TLN A VL A++L VD DE Sbjct: 241 VSLGTSGVVSAVGRAAPHDPEGIVAGFADATGHQLPLVCTLNGAPVLATVAEMLQVDFDE 300 Query: 303 LSRLALSAPAGADGMVLVPYLEGERTPNRPDATGAIHGLTLKTSDPAHLARAAVEGMLCA 362 RLALSAPAGADG+VLVPY GER+PN P A GA+HG+T++ PA++ARAAVEG+L + Sbjct: 301 FDRLALSAPAGADGLVLVPYFAGERSPNLPQAAGALHGMTMRNLHPANIARAAVEGLLSS 360 Query: 363 LADGLDALVAHGAEANRIVLVGGGARSEAVRRIAPALFGKPVLVPPPGEYVADGAARQAA 422 +A +D + G A RI+LVGG +RSEAVRRIAPA+ G V VP P EYVA GAARQAA Sbjct: 361 MAFCIDKIGDQGVAAERIILVGGASRSEAVRRIAPAVLGATVYVPTPAEYVALGAARQAA 420 Query: 423 WVARGGDTPPAWSAASPEVYEDDPVPLIREQYAAA 457 WV G DTPP WS P Y+ D P + E+Y AA Sbjct: 421 WVLSGQDTPPPWSVGEPARYDADATPQVLERYRAA 455 Lambda K H 0.315 0.133 0.398 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: 747 Number of extensions: 36 Number of successful extensions: 2 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: 466 Length of database: 461 Length adjustment: 33 Effective length of query: 433 Effective length of database: 428 Effective search space: 185324 Effective search space used: 185324 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 (21.6 bits) S2: 51 (24.3 bits)
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