Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate SMc02334 SMc02334 pentose kinase transmembrane protein
Query= reanno::Koxy:BWI76_RS27020 (484 letters) >FitnessBrowser__Smeli:SMc02334 Length = 515 Score = 208 bits (530), Expect = 3e-58 Identities = 150/484 (30%), Positives = 229/484 (47%), Gaps = 26/484 (5%) Query: 6 DLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALGAQHSL 65 DLGT GVKA + G +A P P EQ PE WW A ++++ L ++ Sbjct: 9 DLGTGGVKAAIFRPDGTCIAEEVVSYRTFYPSPSCHEQRPEDWWEAICASLRTLFENTAV 68 Query: 66 RA--VKALGIAGQMHGATLLDKQQRVLRPAI-LWNDGRCGEECALLEEKVSRSR--QITG 120 +A ++A+ ++G G LD+ +L+ + +W+DGR E +V + TG Sbjct: 69 KAGDIRAIAVSGHSLGCLPLDENGALLQEFVPIWSDGRAVAEAEDFFTRVDPDTWYRTTG 128 Query: 121 N-LMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDV 179 N P +T K +W++R+ P+IF + ++ KDY+ LR+TG A+D S A+GT D+ Sbjct: 129 NGFPAPLYTVFKAMWLRRNAPDIFARTRTIIGTKDYINLRLTGRIATDPSYASGTGVYDL 188 Query: 180 ARRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNM-PEVLVVAGGGDNAAGA 238 +S E++ A GLSR+ P + +V G + P +A+ + P V VVAGG DN+ A Sbjct: 189 KAGRYSAELVEAAGLSRELFPPIVASTDVLGDVLPEIAERLGLFPGVKVVAGGVDNSCMA 248 Query: 239 VGVGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAASCL 298 +G G A S+G+S + L F H PG + + + S+ + Sbjct: 249 LGGRTFLEGDAYASMGSSSWITVSASEPLLDDRVRPFVFAHVAPGMFISATSIFSSGTSF 308 Query: 299 DW-----------AATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKG 347 +W AA + G+ AL A A A + F+P L G + P +G Sbjct: 309 NWVTDTLLPDVKHAAKVAGMDVHDALFRLAGEAPAGARGLIFVPTLGGGTSFEGGPAVRG 368 Query: 348 VFFGLTHQHGPAELARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLA 407 F GL QHG A++ RA LEGV L +D + + ++GGGARSA+WRQ+ A Sbjct: 369 GFVGLDLQHGRADILRATLEGVALGLRIALDELRRMTAIGPEMIIVGGGARSAFWRQVFA 428 Query: 408 DISGQQLDFRTGGDVGPALGAARLAQLALHRNVAFSDLLPQLPLEQAH-----LPDAERF 462 D+ + ALGAA LA + + + D LP L A P+A + Sbjct: 429 DVFDCAIVKTRVDQQAAALGAAALAFVGMG---LWEDFLPIRTLHVAEGRTEPAPEARKV 485 Query: 463 ARYA 466 R A Sbjct: 486 YRAA 489 Lambda K H 0.320 0.134 0.417 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: 609 Number of extensions: 38 Number of successful extensions: 3 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: 515 Length adjustment: 34 Effective length of query: 450 Effective length of database: 481 Effective search space: 216450 Effective search space used: 216450 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