Align Xylulose kinase; Xylulokinase; EC 2.7.1.17 (uncharacterized)
to candidate GFF3460 PS417_17715 actin
Query= curated2:Q9CFG8 (501 letters) >FitnessBrowser__WCS417:GFF3460 Length = 510 Score = 231 bits (590), Expect = 4e-65 Identities = 154/511 (30%), Positives = 260/511 (50%), Gaps = 21/511 (4%) Query: 1 MTYVLGIDLGTSSLKGILMDEVGNLITTKSAEYQIDTPKQGYSEQRPEYWIVALESVLTG 60 M YV+G+D+GT S K +L+D G +I S Y++DTPK ++EQ P+ W+ A+E+ + Sbjct: 1 MNYVMGVDIGTQSTKALLVDGQGTIIAQHSQGYRVDTPKVRWAEQWPQVWLDAVEACVAQ 60 Query: 61 LSVEISDFGQQLAGISFSGQMH-SLVVLDDNNKPVYPAILWNDVRTSKQCQEITDRLG-Q 118 + +Q+ + S S + +D P++P ++W D R +Q + +++ Sbjct: 61 CMAKAGVAAEQVKALCISSLYGGSGIAVDAQITPLHPCLIWMDRRAGEQVAWVREQVDLD 120 Query: 119 RLLEITKNIALEGFTLPKILWLQENEPEVWSRVKKIMLPKDYLSLWLTGNIYTEFSDAAG 178 RL IT N + K+LWL++++PEVW+ + ++ P Y++ LTG + + S +AG Sbjct: 121 RLFAITGNSVDSYYGFTKMLWLKQHQPEVWANTRYLLPPNSYINWCLTGELAVDHS-SAG 179 Query: 179 TL--LLDIEKKQWSEEITDAFNIDRRILPE-LIESTDRTGFVKAEIAERYKLTNEVKVFA 235 + + D++ + WS E+ DA I + ++P+ L+ S + G + A R L + A Sbjct: 180 NIGGVYDVKARDWSGEMLDALGIPQTMMPQRLVYSGEVVGGLLDTWATRLGLQAGTPLLA 239 Query: 236 GGADNAAAALGVGLINEEVGLISMGTSGVVSAYEPKIADYKGKLHFFNHTVPGA--CYSM 293 GG D A A L G+ + +GTS ++ + G L H G Y Sbjct: 240 GGVDAAMATLAAGVTQPGNHVAMIGTSMCWGYLNQQVDAHHG-LVSMPHVYNGHRDLYIF 298 Query: 294 GVTLAAGNSLNWYKETFGKGL----------SFNELLSEVYTVSPGSEGLLFTPYIVGER 343 G + AG S++W++E F + S L + GSEGLLF PY++GER Sbjct: 299 GGAITAGASVSWFREQFCQAEEQQAKVTGQDSLVLLEQRAMNLPAGSEGLLFLPYLMGER 358 Query: 344 TPHFDSKIRGSFIGISAHHEQKHFSRAVLEGITFSLRDSKDIMEKTKNKKFKRLISVGGG 403 +P +D + GSF+G++ +H + H RAVLEG++F+LR + + + + RLI VGG Sbjct: 359 SPVWDDRASGSFVGLNLYHGRIHLYRAVLEGVSFALRHNIEAGTRGAHSLDPRLIVVGGA 418 Query: 404 AQNPDIMQMQADIFNSEMIRLTVEQGPGLGACMIAAFGCGLFDSLEAVTKAFVHYKEASF 463 + + MQ+ ADI + + E LGA ++AA GL E + K +V + Sbjct: 419 SHSDLWMQIIADITQYPVYTIVQEVEAALGAALLAAHSVGLVSDGE-MDKGWVQLALRA- 476 Query: 464 IPNPKNVARYEQIYQIWKQVYKNTSEISHQL 494 P +NV Y++ + + ++Y I H L Sbjct: 477 EPKVENVGVYDRAFAEYLKLYPALKPIMHNL 507 Lambda K H 0.317 0.135 0.394 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: 612 Number of extensions: 23 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: 501 Length of database: 510 Length adjustment: 34 Effective length of query: 467 Effective length of database: 476 Effective search space: 222292 Effective search space used: 222292 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 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