Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate BPHYT_RS16155 BPHYT_RS16155 carbohydrate kinase
Query= reanno::Smeli:SMc03164 (484 letters) >FitnessBrowser__BFirm:BPHYT_RS16155 Length = 493 Score = 229 bits (585), Expect = 1e-64 Identities = 163/499 (32%), Positives = 238/499 (47%), Gaps = 37/499 (7%) Query: 2 YLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLRE 61 +LG+DLGT +K ++D R AS A ++ P GW+E W RA EA ARL + Sbjct: 3 FLGIDLGTGSLKVAIVDENGREQAVASVAYPIETPQAGWAETSVQTWWRALCEAAARLPD 62 Query: 62 THAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDGDPQFRALTG 121 + VR IG SGQMHG L+D +RP +LW DTR+ A L+ P+ + Sbjct: 63 GLRRD---VRAIGFSGQMHGVVLIDAAGEAVRPAMLWPDTRAL---ALLEAWPEPQP--- 113 Query: 122 NIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDTG 181 N V PG P L W+ +EP+ +R RW L PKD+LR+ L G ++ SD+ T+ D Sbjct: 114 NPVAPGMAGPLLRWIVLHEPQSASRTRWALQPKDWLRVALGGAVATDPSDACATALADPA 173 Query: 182 KRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASAC 241 W A+LL + L A G L A G+ G+V+A GA D +A Sbjct: 174 G-VWDAALLDRLEIPHEWFAPLAPSYAAGGVLSESAARALGLRAGIVLATGAADTPCAAL 232 Query: 242 GMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDALN 301 G G +G A ++ GT G + A + P +H + A + W++M + + AL Sbjct: 233 GSGLAHDGDALLTTGTGGQIVVL-AEHAPAAVKGLHRY-RAASDHWYRMAAMQNVGIALE 290 Query: 302 ----WHS-------------GVTGRSAAELTSELGESLKAPGSVTFLPYLSGERTPHNDA 344 W S +A T+ + A +TFLPYL+GERTP + Sbjct: 291 RARGWLSYEWADAYRDAFGDATNATNATNATATFSANTAAASGLTFLPYLTGERTPWLNP 350 Query: 345 TIRGVFAGLGHESSRAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWL 404 RG + GL + +R + +A EGV+F++R L+A+RA+G + + GGGS W Sbjct: 351 MARGGWLGLALDHTRGTMMRAAFEGVAFSLRAGLDAIRASGATVTALKLAGGGSVDARWR 410 Query: 405 SSIATALNLPVDLPADGDFGAAFGAARLGLIAA---TGADPAAVCTAPETAETIAPEASL 461 +A ALN+ + D A GAA LG +A+ D AA+ AP P+ Sbjct: 411 QLLADALNVELH-AVDCPNAAPRGAAILGGLASGHWHARDLAAL--APGATRVAGPQGD- 466 Query: 462 VPAYEDAYQRYRRLYPAIK 480 A + Y+R+ LY I+ Sbjct: 467 -AALAERYERFLDLYGRIE 484 Lambda K H 0.317 0.132 0.401 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: 672 Number of extensions: 34 Number of successful extensions: 4 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: 493 Length adjustment: 34 Effective length of query: 450 Effective length of database: 459 Effective search space: 206550 Effective search space used: 206550 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