Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate BWI76_RS07870 BWI76_RS07870 carbohydrate kinase
Query= CharProtDB::CH_003784 (484 letters) >FitnessBrowser__Koxy:BWI76_RS07870 Length = 495 Score = 181 bits (460), Expect = 4e-50 Identities = 156/502 (31%), Positives = 244/502 (48%), Gaps = 45/502 (8%) Query: 2 YIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGD 61 Y+GID+GTS VK +L +++ + A+ + +EQD Q WQ+ ++ + Sbjct: 4 YLGIDIGTSRVKAVLFDQRFQACASAAQNTGPRLSANGDAEQDMAQLWQSVVAILRDIAR 63 Query: 62 QHSLQD--VKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVI- 118 +LQ+ ++A+G+AGQ G L DA+ + P ILW+D R + + L +R R Sbjct: 64 HPALQNGRLRAIGLAGQGEGVWLSDAEGEPVGPGILWSDTRSRELMSELLSRPGFDRRFF 123 Query: 119 --TGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMW 176 TG + P T+ +L W++ H+PE + KD++R R+TG A D++DA+ T Sbjct: 124 DDTGTHLQPCNTSMQLCWLKHHQPERLAAARYLFFAKDWIRFRLTGVAALDLTDAS-TSL 182 Query: 177 LDVAKRDWSDVMLQACDLSRDQ--MPALYEGSEITGALLPEVAKAWGM-ATVPVVAGGGD 233 L+ S V+L L+ Q P L GAL EVA G+ A PV AG D Sbjct: 183 LNQQSGKLSTVVLNEMGLADLQHLFPPLLAPDAQAGALREEVAALTGLPADTPVAAGALD 242 Query: 234 NAAGAVGVGMVDANQAMLSLGTS---GVYF----AVSEGFLSKPESAVHSFCHALPQRWH 286 + A+G G V+ LGT+ G+ +V+EG + SF + P Sbjct: 243 VCSAALGCGAVNDGDIYTILGTTCCTGIVCHGRQSVNEGTRYVTHTEAGSFINLFP---- 298 Query: 287 LMSVMLSAASCLDWAAKLTGLSNVPALIAAAQQADESAEP----VWFLPYLSGERTPHNN 342 M + +DW + L P L +Q S EP V++ PYL+GER P + Sbjct: 299 ----MQAGTPNIDWLQQQISLE--PDL-RQLEQNIASVEPGSGGVFWQPYLNGERAPFFS 351 Query: 343 PQAKGVFFGLTHQHGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYW 402 P+A+ +FG++ EL RAV EG+ YA+ D + G + L GGGA S W Sbjct: 352 PEARAGYFGISQHTTRAELQRAVFEGLAYAIVDSLQGYPQGG----ELYLTGGGAASATW 407 Query: 403 RQMLADISGQQLDYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLP-LEQS-HLPDAQ 460 QM+AD +G+ + ++ A GAA LA + ++ L + P LEQ+ + P+ Q Sbjct: 408 LQMIADCTGRTVVSSPFNELS-ARGAAILAARS-------VDALSRYPALEQTRYRPNPQ 459 Query: 461 RYAAYQPRRETFRRLYQQLLPL 482 ++ Y +R L +Q+LP+ Sbjct: 460 AHSRYAALYPVYRLLREQMLPV 481 Lambda K H 0.319 0.134 0.409 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: 579 Number of extensions: 30 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: 484 Length of database: 495 Length adjustment: 34 Effective length of query: 450 Effective length of database: 461 Effective search space: 207450 Effective search space used: 207450 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 (21.8 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