Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate BPHYT_RS22740 BPHYT_RS22740 ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__BFirm:BPHYT_RS22740 Length = 328 Score = 144 bits (364), Expect = 3e-39 Identities = 103/340 (30%), Positives = 171/340 (50%), Gaps = 13/340 (3%) Query: 25 MTTPTVVEIAPSVEAPGLRTRLARNPEWFTVALIVVTCLIVGAINPRFFQFATLFDLLHS 84 M+TP+ AP+ + R+ E + +V+ C + + RF F L +L Sbjct: 1 MSTPS----APAGHSRSFAERMPSLAEVGPLIALVLACGFFISQSSRFLSFQNLSLILQQ 56 Query: 85 ATTMSLFALGTLVVLASGGIDVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGV 144 +++ A+G +++ +GGID+S + A +TK FA P L ++ G Sbjct: 57 TMVVAVIAIGQTLIVLTGGIDLSCGMVMAFGSIIMTK--FAVTLGVPPVLAILCGVGASA 114 Query: 145 VLGMVNGLLVHRLKAPSLIVTIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYH 204 + G +NG+L+ R+K P+ IVT+GT + L + N+P ++ G F Sbjct: 115 LFGALNGVLITRIKLPAFIVTLGTLNIAFALTQIYSNAESVSNLPDAIMFLGNT--FKLG 172 Query: 205 TADGLRAVLPVSVLALVAAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFV 264 AD V +VL L+ + TW++L T+ GR +YA+G + A +G + + I L V Sbjct: 173 PAD----VTYGTVLTLLMY-LATWFVLRDTVPGRHLYALGNNPEAARLMGLSSQKILLTV 227 Query: 265 FGYTGMLAGIAGILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVV 324 + G + GIA +L VS + +P LD I AV+LGG + GG G++ GTLLG + Sbjct: 228 YSLAGAIYGIAALLSVSRTGVGDPQAGQTENLDSITAVVLGGTSLFGGRGSISGTLLGAL 287 Query: 325 LVTLIKSVLILVGVPSTWQKVIIGAFILLAGTLFALQRKR 364 +V + ++ L L+GV S +Q +I G ++LA L +R Sbjct: 288 IVGVFRNGLTLIGVSSVYQVLITGMLVILAVAADKLSHRR 327 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: 294 Number of extensions: 12 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: 328 Length adjustment: 29 Effective length of query: 335 Effective length of database: 299 Effective search space: 100165 Effective search space used: 100165 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 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