Align xylulokinase (EC 2.7.1.17) (characterized)
to candidate WP_011779842.1 MVAN_RS13185 carbohydrate kinase
Query= BRENDA::Q9WXX1 (492 letters) >NCBI__GCF_000015305.1:WP_011779842.1 Length = 505 Score = 215 bits (548), Expect = 3e-60 Identities = 134/448 (29%), Positives = 225/448 (50%), Gaps = 14/448 (3%) Query: 5 VGLDVGTTGVKGILV---------NEKGEILATANERLTMFTPQPAWAEQDPLSWWEAVK 55 +G+D+GTTG+K +L+ N I+ATAN T+++P P +AE DP W+ V Sbjct: 6 IGVDIGTTGIKTVLLDTTAAGRASNTTAGIVATANRENTLYSPGPGFAEADPAQWYRNVV 65 Query: 56 KILKNLSERSKEMGGKIRAISTSGQMHSLVAIDDNGKVLRNAILWCDQRTYKECEEATQI 115 + ++ + S +I A++TSG + ++VA+D GK LR AIL D R ++E Sbjct: 66 ESIREVLAVSGVAPDQIGALATSGMVPAVVAVDQTGKPLRRAILQNDARAHREVAGLAAK 125 Query: 116 LGGEENVLKLVGNPILPGFTLPKILWIRKHEPEIYGKISKIMLPKDFINYMLTGEVKTEH 175 L + ++ L G+ + P +W+R HEP +Y + + + D++ L + E Sbjct: 126 LASVD-LVTLTGSALTQQSVAPTTVWLRDHEPGVYARTAHWIGSYDWVLSALGAPIHVEQ 184 Query: 176 SDASGTVMYSVSKMEWNKDVLKELNIPESVLPEIIPSNGVVGNVKPEVASDLGLSEDTLV 235 + A + ++ + + DV++ + L + VG + A + GL T + Sbjct: 185 NWALESGLFEIDG-DVATDVVQAAALEPVTLAPVRRPGTQVGELSRRAADETGLRAGTAL 243 Query: 236 IGGGADNACAALGIAVVEPGDVMVSLGTSGTVLAPTKGNQPDPKGRVHFFAHTVPETRYH 295 + GGAD+ +A V +PGD +V LG +G +L + D R++ AH +P Sbjct: 244 VVGGADHVLSAYAAGVNDPGDALVKLGGAGDILVASDTQVVDE--RLYLDAHPIPGHWLP 301 Query: 296 MGVMLSATYSLEWFKEKFLSEDYETINEEVDKIPAGSNG-IIFLPYLNGERTPHRDPFAR 354 G M ++ + WF+ + + D+ S ++ LPY GE++P DP R Sbjct: 302 NGCMATSGSLIRWFQALIGGPEAVELTTLDDEAALRSPAEVLCLPYFLGEKSPIHDPDLR 361 Query: 355 GVFFGISSYNTKWDMVRAIFEGVAFGIKDSFDILRELKVVLNSVRITGGGSKSRVWNKML 414 GVF G+ +T+ DM R++ E +AFG + D+ E+ + L V IT GGSKS +W ++ Sbjct: 362 GVFAGMHLGHTRADMYRSVLEAIAFGFRHHVDVFAEIGIPLRRVMITNGGSKSTLWKQIH 421 Query: 415 ADMTGLRIQKPAVDEGASYGAAILAVSG 442 AD+ G + GAS GAA++A G Sbjct: 422 ADVLGQEMHPVRGHPGASLGAAVIAAIG 449 Lambda K H 0.316 0.135 0.397 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: 605 Number of extensions: 32 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: 492 Length of database: 505 Length adjustment: 34 Effective length of query: 458 Effective length of database: 471 Effective search space: 215718 Effective search space used: 215718 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 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