Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate H281DRAFT_01221 H281DRAFT_01221 monosaccharide ABC transporter membrane protein, CUT2 family
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Burk376:H281DRAFT_01221 Length = 338 Score = 125 bits (313), Expect = 2e-33 Identities = 96/303 (31%), Positives = 156/303 (51%), Gaps = 14/303 (4%) Query: 19 LLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVG 78 L+IV +L + + LS F+ NL ++ L E+ L+AL + L +V+ IDLS Sbjct: 23 LVIVLILSIALGRVLSP-VFLTGANLSNVLADLTEIALMALPMTLIIVAAE--IDLS--- 76 Query: 79 LANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILCT 138 +A++ G +A++ G PV+ A+VL+ G L GLLNG+VI +L L + T Sbjct: 77 VASVLGASSALMGVLWHMGLPMPVVI-----ALVLVAGALAGLLNGLVIVKLNLPSLAVT 131 Query: 139 LGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTV--LQVPIAFCIFLAAVIVLGWLLK 196 +GT LF G A V+ +V D+ + G T+ VP+ F I + ++ LL+ Sbjct: 132 IGTLALFRGLAYVLLGDQAV-ADFPPAYTAFGMDTLGGTFVPLPFAIVMVGAVLFTVLLQ 190 Query: 197 RSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDYGN 256 + FG LY +G NP AA ++GI ++ + + + G++ +LAG++ +SA+ D G Sbjct: 191 STAFGRSLYAIGANPTAAAFSGIEVTKIRLRLFVLSGLMGALAGVVYTLRFTSARGDNGE 250 Query: 257 SYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFLLL 316 + L I + GGV+ GG G +I V + ++ L + L VS G LLL Sbjct: 251 GFELSVIAAVLFGGVSIFGGRGSMIGVLLSLLIIGVLKNALTLDDVSSETLTIVTGVLLL 310 Query: 317 LSL 319 S+ Sbjct: 311 ASV 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: 295 Number of extensions: 26 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