Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate WP_051378618.1 H566_RS24095 hypothetical protein
Query= reanno::Phaeo:GFF1384 (478 letters) >NCBI__GCF_000482785.1:WP_051378618.1 Length = 458 Score = 127 bits (318), Expect = 1e-33 Identities = 138/456 (30%), Positives = 191/456 (41%), Gaps = 43/456 (9%) Query: 3 LGIDLGTSGLRALMTDAAGKPVASAEAQYDVQTPHPGWSEQDPGDWITALDQAMAQLQGS 62 +GIDLGTSG+RA+ D A VA+A A + Q P DW A +A L Sbjct: 13 IGIDLGTSGVRAVAIDTALDVVATASAALPPSRRDGAAATQSPDDWWNATWAVLAGLCAG 72 Query: 63 PGYSD--ICGIAVAGHMHGAVLLDGSDQVLRPCILWNDTRSAAEAAELDAAEKVRDLSGN 120 G + IAV G +L D + L P ++++DT A EAA + A + Sbjct: 73 LGRRGGRVAAIAVDGTSGSLLLTDARLRPLTPGLMYDDTSCADEAARVAAIVPEDSAARG 132 Query: 121 IVFPGFTAPKLLWVQRHEPEIFANTAKVLLPAAYLNLHLTGRHVADMSDSAGTS------ 174 P A L W + A VL A ++ L D+ S +S Sbjct: 133 PASP--LARLLRW------QATPGAAHVLHQADWITARLRAEGATDLPASLASSDENNAL 184 Query: 175 --WLDVGARDWSEWLLEAGHMRRDQMPDLVEGSAAAGTLRPELAVRWGLTGPVTIAGGAG 232 D ARDW W G +RR +P + +A G + PELA+ GL+ V IA G Sbjct: 185 KLGYDPVARDWPGWFDALG-VRRALLPAVRPPGSAIGAIAPELAMHMGLSPEVLIAAGTT 243 Query: 233 DNAAAACGTGVMAPGQGFVSLGTSGVVLTARDGFRPDPATAVHTFCHAIPDRWYQMGVML 292 D AA TG PG SLG++ V+ D RP A A + H + D W G Sbjct: 244 DGVAAFLATGACEPGDAVSSLGSTLVLKLLTD--RPVNAPAFGVYSHRLGDMWLVGGASN 301 Query: 293 SATDCMNWLGRITGQSPADLTAGLGEELQPPGPVTFMPYL----SGERTPHNSASL--RG 346 S + L + L A L PG T + Y +GER P L R Sbjct: 302 SGGAAL--LRHFSVGRMRALEAQL-----RPGHPTGLDYYPLAGTGERFPFADPDLVSRD 354 Query: 347 GFQGLSIATTAEDLAR--AVMEGVCYGLRDCLEALRKTGAEIDSCLVIGGGSKSAYWVKL 404 G + +S AT + L A +EG+ Y L A+ T +GGG+ +A W + Sbjct: 355 GPRPISDATHFQALLEGIAAIEGLGYRRLGELGAITPT-----RVFSVGGGAANAAWQDI 409 Query: 405 LATILDLPLQLPKDGEFGAALGAARLARLAVTGDDP 440 A L +P+ + + AA+GAARLA A+ +P Sbjct: 410 RAQHLGVPVIRSRHAD--AAVGAARLALAALPPHEP 443 Lambda K H 0.318 0.135 0.419 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: 625 Number of extensions: 35 Number of successful extensions: 4 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: 478 Length of database: 458 Length adjustment: 33 Effective length of query: 445 Effective length of database: 425 Effective search space: 189125 Effective search space used: 189125 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 (21.7 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