Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate SM_b20497 SM_b20497 L-xylulose kinase
Query= reanno::Phaeo:GFF1384 (478 letters) >FitnessBrowser__Smeli:SM_b20497 Length = 509 Score = 177 bits (448), Expect = 1e-48 Identities = 147/489 (30%), Positives = 224/489 (45%), Gaps = 30/489 (6%) Query: 3 LGIDLGTSGLRALMTDAAGKPVASAEAQYDVQTPHPGWSEQDPGDWITALDQAMAQLQGS 62 LG+D G + ++A++ D GK +ASA A+ + P+PG E+D + + + + Sbjct: 6 LGLDAGNTVIKAVIFDRKGKEIASAAAEGHSRMPYPGHVERDLDELWENARRVIRKCIDE 65 Query: 63 PGYS--DICGIAVAGHMHGAVLLDGSDQVLRPCILWNDTRSAAEAAELDA---AEKVRDL 117 G ++ I AGH +G LD + L I DTR+AA E + ++ + Sbjct: 66 AGIDAGELAAIGCAGHGNGLYALDHEGRPLLG-IQSLDTRAAALVEEWTSQGVGDRTYPI 124 Query: 118 SGNIVFPGFTAPKLLWVQRHEPEIFANTAKVLLPAAYLNLHLTGRHVADMSDSAGTSWLD 177 +P T L W++R+ PE+FA+ + L ++ LTG V+D+SD G L+ Sbjct: 125 GQQRPWPSQTPTLLAWMKRYRPEVFASIGTIFLCKDFIVNRLTGARVSDVSDMTGCGLLN 184 Query: 178 VGARDWSEWLLEAGHM--RRDQMPDLVEGSAAAGTLRPELAVRWGLTGPVTIAGGAGDNA 235 V R + L+ A + D +P LVE + AG + A GL + GG D Sbjct: 185 VAGRHYDRELMAAYGLCESMDLLPPLVESAEIAGRITEAAAAGTGLAAGTPVVGGLFDVV 244 Query: 236 AAACGTGVMAPGQGFVSLGTSGVVLTARDGFRPDPATAVHTFCHAIPDRWYQMGVMLSAT 295 A+A G+GV G + GT + + RP+ V F + DR M + SAT Sbjct: 245 ASAIGSGVTRTGAASIIAGTWSINQVIIE--RPELQGPV--FMSSTFDRDRYMAIESSAT 300 Query: 296 DCMN--WLGR-------ITGQSPADLTAGLGEELQPP--GPVTFMPYLSGERTPHNSASL 344 N WL R G+SP DL L P P+ + PYL G + S Sbjct: 301 SAANLEWLVREFFSEVRSDGRSPFDLCCELASSSDPAFDDPI-YHPYLYGAQ---QDGSA 356 Query: 345 RGGFQGLSIATTAEDLARAVMEGVCYGLRDCLEALRKTGAEIDSCLVIGGGSKSAYWVKL 404 R GF G++ T L RAV+EGV +G R +E +RK GA D ++ GGGS+S W ++ Sbjct: 357 RAGFYGIAGWHTKGHLVRAVLEGVAFGHRQHIETMRKAGAAFDEAVLSGGGSRSLIWPQI 416 Query: 405 LATILDLPLQLPKDGEFGAALGAARLAR--LAVTGDDPADVLTAPESAMTVAPDPLLRDG 462 A ++ +P+ + E G ALGAA A + + D ++ P+ L Sbjct: 417 FADVIGVPVSVAGSRETG-ALGAAIAAATGVGIFSDFAEGAAAMVKTERHYLPNRALEAH 475 Query: 463 YEAGYAAFR 471 Y YA +R Sbjct: 476 YARRYALYR 484 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: 581 Number of extensions: 26 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: 478 Length of database: 509 Length adjustment: 34 Effective length of query: 444 Effective length of database: 475 Effective search space: 210900 Effective search space used: 210900 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