Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate BPHYT_RS28205 BPHYT_RS28205 ATPase
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__BFirm:BPHYT_RS28205 Length = 338 Score = 126 bits (316), Expect = 9e-34 Identities = 96/307 (31%), Positives = 155/307 (50%), Gaps = 13/307 (4%) Query: 15 QLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDL 74 Q LL++ +++ L L F+ NL ++ L E+ L+AL + L +V+ IDL Sbjct: 18 QWEVLLVIVLILSLALGRLLSPVFLTGANLSNVLADLTEIALMALPMTLIIVAAE--IDL 75 Query: 75 SGVGLANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTP 134 S +A++ G +A++ G P L +VL+ G L GLLNG+VI +L L Sbjct: 76 S---VASVLGASSALMGVLWHMGLPMP-----LVIVLVLVAGALAGLLNGLVIVKLNLPS 127 Query: 135 ILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTV--LQVPIAFCIFLAAVIVLG 192 + T+GT LF G A V+ +V D+ + G T+ +P+ F I + IV Sbjct: 128 LAVTIGTLALFRGLAYVLLGDQAV-ADFPPAYTAFGMDTLGGSFIPLPFVIVIVGAIVFT 186 Query: 193 WLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKW 252 LL+ + FG LY +G NP AA ++GI A++ + + + G +++LAG++ +SA+ Sbjct: 187 VLLQSTAFGRSLYAIGANPTAAAFSGIEVAKIRLRLFVLSGAMSALAGVVYTLRFTSARG 246 Query: 253 DYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWG 312 D G + L I + GGV+ GG G +I V + ++ L + L VS G Sbjct: 247 DNGEGFELSVIAAVLFGGVSIFGGRGSMIGVLLSLLIIGVLKNALTLDDVSSETLTIVTG 306 Query: 313 FLLLLSL 319 LLL S+ Sbjct: 307 VLLLASV 313 Lambda K H 0.327 0.143 0.429 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: 281 Number of extensions: 24 Number of successful extensions: 2 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: 357 Length of database: 338 Length adjustment: 29 Effective length of query: 328 Effective length of database: 309 Effective search space: 101352 Effective search space used: 101352 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