Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate 18256 b4231 putative transport system permease protein (VIMSS)
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Keio:18256 Length = 331 Score = 125 bits (315), Expect = 1e-33 Identities = 95/322 (29%), Positives = 152/322 (47%), Gaps = 28/322 (8%) Query: 50 PEWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFT 109 P T+ + V+ L P F + ++L + + A+G V+ SGGID+S Sbjct: 7 PLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVG 66 Query: 110 AIAALTMYGITKAV--FAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIG 167 ++ A T + K + F P F L+LV G G +G LL+ LK P+ I+T+ Sbjct: 67 SVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMG----LLIDALKIPAFIITLA 122 Query: 168 TQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLP------VSVLALV 221 + RG+ + +N P Y T L +P L ++ Sbjct: 123 GMFFLRGVSYLVSEESIPINHP------------IYDTLSSLAWKIPGGGRLSAMGLLML 170 Query: 222 AAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVS 281 A V+ +L +RT G VYA+GG+ A +G + R+ + ++ + LA +AGI+ Sbjct: 171 AVVVIGIFLAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSI 230 Query: 282 NNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVG-VPS 340 + VG ELD IA+V++GG ++GG GTV+GTL GV + LI++ + G + S Sbjct: 231 YTQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSS 290 Query: 341 TWQKVIIGAFILLAGTLFALQR 362 W K+ IG + + ALQR Sbjct: 291 WWTKIAIGILLFI---FIALQR 309 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: 289 Number of extensions: 18 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: 364 Length of database: 331 Length adjustment: 29 Effective length of query: 335 Effective length of database: 302 Effective search space: 101170 Effective search space used: 101170 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