Align L-fuculokinase; L-fuculose kinase; EC 2.7.1.51 (characterized)
to candidate WP_034410950.1 H566_RS0106830 xylulokinase
Query= SwissProt::P11553 (472 letters) >NCBI__GCF_000482785.1:WP_034410950.1 Length = 488 Score = 123 bits (309), Expect = 1e-32 Identities = 126/451 (27%), Positives = 188/451 (41%), Gaps = 26/451 (5%) Query: 6 ILVLDCGATNVRAIAVNRQGKIVARAST----PNASDIAMENNTWHQW-SLDAILQRFAD 60 +L +D G + ++ + ++ + +IVA A + E N W +LD L R A Sbjct: 3 VLGIDLGTSELKVLLLDARQRIVASAGERLMLQRPRPLWSEQNPADWWIALDRALLRLA- 61 Query: 61 CCRQINSELTECHIRGIAVTTFGVDGALVDKQGNLLYPIISWKCPRTAAVMDNIERLISA 120 +R I ++ L+D +L P I W R+A +ER + Sbjct: 62 ----AGQPAAMAAVRAIGLSGQMHGAVLLDAADAVLRPAILWNDGRSADACVALER--AE 115 Query: 121 QRLQAISGVGAFSFNTLYKLVWLKENHPQLLERAHAWLFISSLINHRLTGEFTTDITMAG 180 RL+AI+G A T KL WL+E+ P L R L + LTGE +D++ A Sbjct: 116 PRLRAIAGNLAMPGFTAPKLGWLREHEPALFARVACVLLPKDWLRLGLTGEKASDLSDAS 175 Query: 181 TSQMLDIQQRDFSPQILQATGIPRRLFPRLVEAGEQIGTLQNSAAAMLGLPVGIPVISAG 240 + LD+ +R +SP++L A G+ R PRLVE E G L AA GLP G+PV G Sbjct: 176 GTLWLDVGRRRWSPELLGACGLDERHMPRLVEGCEVAGRLDARLAARWGLPAGVPVAGGG 235 Query: 241 HDTQFALFGAGAEQNEPVLSSGTWEILMVRSAQVDTSLLSQYAGSTCELDSQAGLYNPGM 300 D A+ E LS GT ++ V S + + L A + + Sbjct: 236 GDNAAAVGIGAVRPGEGFLSLGTSGVIFVVSDGFRPNPAAAVHAFCHAL--PATWHQMSV 293 Query: 301 QWLASGVLEWVRKLFWTAETPWQMLIEEARLIAPGADGVKMQCDLLSCQNAGW-----QG 355 A+ L W +L + +L ARL + L + QG Sbjct: 294 MLNAASALRWACELLGQPDEA-TLLDRVARLTPAQRAAAPIFLPYLGGERTPHNDPHAQG 352 Query: 356 VTLNTTRGH----FYRAALEGLTAQLQRNLQMLEKIGHFKASELLLVGGGSRNTLWNQIK 411 V GH A +EG+ L+ L L + + L LVGGG+R+ LW + Sbjct: 353 VLFGLGAGHDAASVGHAVIEGVGFGLRDGLASL-GLAPGALARLSLVGGGARSPLWAGLL 411 Query: 412 ANMLDIPVKVLDDAETTVA-GAALFGWYGVG 441 A++L +P+ D E A GAA W +G Sbjct: 412 ASILGVPLVTHDGGEAGAALGAARLAWLALG 442 Lambda K H 0.320 0.134 0.410 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: 604 Number of extensions: 26 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 472 Length of database: 488 Length adjustment: 34 Effective length of query: 438 Effective length of database: 454 Effective search space: 198852 Effective search space used: 198852 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: 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