Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate WP_011654713.1 RL_RS25585 ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >NCBI__GCF_000009265.1:WP_011654713.1 Length = 329 Score = 213 bits (542), Expect = 6e-60 Identities = 122/320 (38%), Positives = 189/320 (59%), Gaps = 4/320 (1%) Query: 45 RLARNPEWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGI 104 R R+ E++ +A+++V L + A F LFDLL S + + A G LVVL GGI Sbjct: 7 RWTRSHEFWLLAVVIVLSLFLTAATDSFLTLQNLFDLLTSTSFAGILAAGLLVVLVFGGI 66 Query: 105 DVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIV 164 D+SFTAIA++ Y + + +P F + LV G++ G+ N ++H+++ S+IV Sbjct: 67 DISFTAIASVAQY-VALMIAKTYPIGWFGVFLVA-CCTGILCGLFNAAIIHKVRISSVIV 124 Query: 165 TIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAA 224 TI T ++ GLL+ + ++P S R G I F + ++G + L LV A Sbjct: 125 TISTLNIFYGLLIYITRGDYITSLP-SYFREG-IWWFEFTDSNGFPYAINFQALLLVVAF 182 Query: 225 VVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNR 284 +TW LLN+T +GR +YAMGG+ AERLG+++ + V+GY G +A IA I + Sbjct: 183 FMTWVLLNKTNIGRQIYAMGGNEIAAERLGFHVFGLRCLVYGYMGFMAAIASISQAQLAQ 242 Query: 285 LANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQK 344 P L+G EL+V+AAV+LGGA + GG G+V G +LGV+L+ ++++ LIL+GV S W + Sbjct: 243 SVTPTTLIGKELEVLAAVVLGGASLAGGNGSVFGAVLGVMLIAILQNGLILLGVSSYWNQ 302 Query: 345 VIIGAFILLAGTLFALQRKR 364 +G ILLA + AL ++R Sbjct: 303 FFVGCVILLAVSATALSQRR 322 Lambda K H 0.328 0.141 0.426 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: 256 Number of extensions: 8 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: 364 Length of database: 329 Length adjustment: 29 Effective length of query: 335 Effective length of database: 300 Effective search space: 100500 Effective search space used: 100500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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