Align Xylulose kinase; Xylulokinase; EC 2.7.1.17 (uncharacterized)
to candidate SMc02335 SMc02335 pentose kinase
Query= curated2:P21939 (501 letters) >FitnessBrowser__Smeli:SMc02335 Length = 509 Score = 251 bits (641), Expect = 4e-71 Identities = 149/485 (30%), Positives = 247/485 (50%), Gaps = 12/485 (2%) Query: 6 LGIDLGTSAVKVSAIDKQGNVVAQASAKYALQQPHPGYSEQDPEDWVTQTTQAIRELLQQ 65 L ID+GT +V+ + ID +G +V A+ ++ P G++EQ P DW A+R +L + Sbjct: 7 LAIDVGTGSVRAALIDTRGKIVEIAAREHDQIVPQFGWAEQRPLDWWEGACTAVRTVLDK 66 Query: 66 SEVTADQIEGLSYSGQMHGLVLLDESATVLRP-AILWNDTRTTSQCRELESQFG-DDFIK 123 +E ++I ++ GQMHGLVL+D++ + R A LWND RT + R E++ D ++ Sbjct: 67 AEGARERISIIAVCGQMHGLVLIDDAGQLTRDTAPLWNDKRTLNLVRRFEAENEPDSYLA 126 Query: 124 ITGNRPLEGFTLPKLLWVKENEPNIWKRARTFLLPKDYLRYRMTGKLAMDKSDATGTVLL 183 +GN P + KL WV++ +P ++R+ ++PKDY+ +R+TG++AMD DA+ + L+ Sbjct: 127 ESGNTPTPAWPGFKLQWVRDADPGAYRRSAVAIMPKDYINFRLTGEIAMDTGDASCSFLM 186 Query: 184 DITTSQWSETLCNQLDIPLTLCPPLIESTAYVGHINQTYAQLSGLSVNTKVFGGAADNAA 243 + T WS + ++ + L PP+ +G + A +GL+ T V G AD Sbjct: 187 NPATLAWSPAMIERMGLDARLLPPIRNPLEIIGRVTDQAALATGLTAGTPVMVGGADYPM 246 Query: 244 GAVGAGILSSDKALVSIGTSGVVLKYEDNAQTD--YRGVLQYERHAFPGKYYSMGVTLAA 301 +G+G+ S GT +V D D V E G + + Sbjct: 247 ALLGSGVCRPGLGSDSTGTGAIVTMIADKPLLDPEISNVATIE-----GNWAPFVLLETG 301 Query: 302 GYSLNWFKQTFAPDE-DFGTVVASAEQSTIGANGLLFAPYIVGERAPYADATIRGSFIGV 360 G + W ++ F +G +VA AE++ G LLF P++ GER R F G+ Sbjct: 302 GDGMRWARRAFHDGALSYGDIVARAEKAPAGCEALLFMPFLTGERLG-QHRNARAQFFGL 360 Query: 361 DGSHQRADFVRAVLEGIIFSFEDLIKLYQH-NGAEFKTIVSIGGGAKSALWLQIQADIFN 419 H RA+LEGI F+ I++ +H +G + +++ GGGA++ LWL+I+A +F+ Sbjct: 361 GAGHGMEHLHRAILEGIAFAMARHIRIMEHSSGKRLERMIAAGGGARTKLWLKIKASVFD 420 Query: 420 CKVVSLKNEQGPGMGAAMIAATGLGWFKTLADCAQTFVHYGKAYYPVTAHVAQYQEMYRL 479 V+ + + MG A +AAT G F D A +V Y P A V Y + + Sbjct: 421 TPVLVPQEPECGLMGCAAMAATATGRFSRPDDAADAYVRYADEIAPDPAWVEVYSHVQPV 480 Query: 480 YQQIY 484 + ++Y Sbjct: 481 FDRLY 485 Lambda K H 0.318 0.133 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: 578 Number of extensions: 26 Number of successful extensions: 6 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: 509 Length adjustment: 34 Effective length of query: 467 Effective length of database: 475 Effective search space: 221825 Effective search space used: 221825 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: 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