Align deoxynucleoside transporter, ATPase component (characterized)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456 Length = 518 Score = 300 bits (768), Expect = 8e-86 Identities = 181/515 (35%), Positives = 298/515 (57%), Gaps = 23/515 (4%) Query: 11 LSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPD-- 68 +S L++ G+ K F GV AL G+ + + G+ L GENG GKSTL+K++S P Sbjct: 1 MSDYLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTW 60 Query: 69 EGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTF 128 +G+++ +G P S E AAGI ++Q+L+L+P++SVAEN+ + EL GR+ Sbjct: 61 DGEILWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRM---- 116 Query: 129 DRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTT 188 + + A + + +P + S + Q +QLV IA+A+ +A+ +I+DEP++ Sbjct: 117 NYPAMIHRAEALMRELKVPDMNV--SLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSS 174 Query: 189 SLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTK 248 +LT+ E++ L+ ++ +L+A+GV +++SHKLDE A+ + V+RDG+ +A +A+ + Sbjct: 175 ALTRSEIEVLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSI 234 Query: 249 AQISELMTGRHLSNERYRESAHAQDIVLDVRGFT-------RAGQFSDVSFKLHGGEILG 301 +I M GR +SN E +++ + R FT R + D+SF L GEILG Sbjct: 235 PKIITQMVGREMSNLYPTEPHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILG 294 Query: 302 VTGLLDSGRNELARALAGVAPAQ-SGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGL 360 + GL+ +GR EL AL G P + G+V L+GQQI RTP + R + VPEDR +G+ Sbjct: 295 IAGLVGAGRTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGI 354 Query: 361 FLDKPIRDNVITAMISSLRDRFGQIDRTRAQA---LAEQTVKELQIATPGVDKPVQSLSG 417 D + N+ A++ D + ++ R A+A ++ + + + T P+ SLSG Sbjct: 355 IPDLGVGQNITLAVL----DNYSKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSG 410 Query: 418 GNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPEL 477 GNQQ+ ++ + L PRVLIL PT GVDVG+K IY++M L+ G+ II++S +L E+ Sbjct: 411 GNQQKAVLAKMLLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEV 470 Query: 478 LQNCDRILMMKKGHVSAEYRADELSEADLYHALLS 512 L DR+L++ G + ++ EL++ + A LS Sbjct: 471 LGVSDRVLVIGDGQLRGDFINHELTQEQVLAAALS 505 Lambda K H 0.319 0.135 0.376 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: 620 Number of extensions: 36 Number of successful extensions: 9 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: 515 Length of database: 518 Length adjustment: 35 Effective length of query: 480 Effective length of database: 483 Effective search space: 231840 Effective search space used: 231840 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 (21.7 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