Align xylulokinase (EC 2.7.1.17) (characterized)
to candidate WP_026090363.1 C792_RS0112905 gluconokinase
Query= BRENDA::Q9WXX1 (492 letters) >NCBI__GCF_000330705.1:WP_026090363.1 Length = 501 Score = 231 bits (589), Expect = 4e-65 Identities = 137/447 (30%), Positives = 229/447 (51%), Gaps = 16/447 (3%) Query: 5 VGLDVGTTGVKGILVNEKGEILATANERLTMFTPQPAWAEQDPLSWWEAVKKILKNLSER 64 +GLD+GTT VK +L + G + + TP AEQDP E + L+ L R Sbjct: 2 IGLDIGTTAVKAVLFDMDGTFIDKETGDYPLHTPDAKTAEQDPEEILERTLQALRLLISR 61 Query: 65 SKEMGGKIRAISTSGQMHSLVAIDDNGKVLRNAILWCDQRTYKECEEATQILGGEENVLK 124 + G I IS S MHS++ +D G+ L I W D R + + + G E + Sbjct: 62 NG-CGDSIEFISFSSAMHSMILLDRKGERLTECITWADSRAAEYADRLNEADGLE--IYH 118 Query: 125 LVGNPILPGFTLPKILWIRKHEPEIYGKISKIMLPKDFINYMLTGEVKTEHSDASGTVMY 184 G PI P L K+ + EPE+Y +I +IM K+++ ++GE + S AS + Sbjct: 119 RTGTPIHPMNPLVKLFHFKNEEPELYAQIGRIMGIKEYVFAEISGEYAVDRSIASSMGLM 178 Query: 185 SVSKMEWNKDVLKELNIPESVLPEIIPSNGVVGNVKPEVASDLGLSEDTLVIGGGADNAC 244 ++ EW+ ++L L + LPE++ + + ++ + A D+G+S+DT ++ G +D Sbjct: 179 NLEASEWDTELLSMLELSADQLPELVDTTEIF-SMDEDAAGDIGISQDTKLVIGASDGVL 237 Query: 245 AALGIAVVEPGDVMVSLGTSGTVLAPTKGNQPDPKGRVHFFAHTVPETRYHMGVMLSATY 304 A LG+ + GDV +++GTSG + + D K R F H P G + + Sbjct: 238 ANLGVNAIHEGDVAITVGTSGAIRTVIDRPRTDVKMRT-FCYHLTPGAFVIGGPVNNGGV 296 Query: 305 SLEWFKEKFLSED-----------YETINEEVDKIPAGSNGIIFLPYLNGERTPHRDPFA 353 L W +++ ++ YE + E + +PAGS+G+IF PYL GER P D A Sbjct: 297 ILRWIRDELCQQEISEADTCSRDPYEIMTEAAESVPAGSDGLIFHPYLAGERAPLWDAKA 356 Query: 354 RGVFFGISSYNTKWDMVRAIFEGVAFGIKDSFDILRELKVVLNSVRITGGGSKSRVWNKM 413 G F+G++ + + M+RA EGV + + F LRE + + S++ +GG ++S +W ++ Sbjct: 357 VGSFYGLTISHERKHMIRAAMEGVVYNLYSVFLALREQMMEVRSIKASGGFARSALWKQL 416 Query: 414 LADMTGLRIQKPAVDEGASYGAAILAV 440 +AD+ G + P E +++GA IL + Sbjct: 417 MADVFGEALHVPESYESSAFGACILGL 443 Lambda K H 0.316 0.135 0.397 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: 566 Number of extensions: 18 Number of successful extensions: 5 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: 492 Length of database: 501 Length adjustment: 34 Effective length of query: 458 Effective length of database: 467 Effective search space: 213886 Effective search space used: 213886 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: 52 (24.6 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