Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate HSERO_RS22215 HSERO_RS22215 branched-chain amino acid ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__HerbieS:HSERO_RS22215 Length = 323 Score = 145 bits (367), Expect = 1e-39 Identities = 99/306 (32%), Positives = 160/306 (52%), Gaps = 15/306 (4%) Query: 57 LIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAALTM 116 L VV L+VG P F ++ +LL + + AL ++V+ + GID+S + AL+ Sbjct: 5 LTVVLILLVGVRAPVFLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNLALS- 63 Query: 117 YGITKAVFAW-WPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYLYRGL 175 G+ A+ A +P P + ++ L G++LG++NG L+ L+ P ++VT+G+ +YRG+ Sbjct: 64 -GMMSALLAMHFPALPVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGM 122 Query: 176 LLTFIGTTFFM--NIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLLNR 233 + G + N+P F L GL ++ + LA+VA W+L Sbjct: 123 VFVLSGGAWVSSRNMPADFIAFPLARL------GGLTHLVWLGALAVVAI----WFLARH 172 Query: 234 TMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLVG 293 T GR +YA+G A A +G R L+ +G +G +AG+AG L V+ +A G Sbjct: 173 TRFGRDLYAIGNDPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYG 232 Query: 294 SELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFILL 353 EL VIAA ++GG I GG G V G +LG + +++I + L ++ + WQ + G IL Sbjct: 233 FELTVIAACVIGGVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILC 292 Query: 354 AGTLFA 359 A L A Sbjct: 293 AVVLNA 298 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: 245 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: 323 Length adjustment: 29 Effective length of query: 335 Effective length of database: 294 Effective search space: 98490 Effective search space used: 98490 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