Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate WP_002723190.1 RSPH17029_RS17455 autoinducer 2 ABC transporter substrate-binding protein
Query= reanno::Burk376:H281DRAFT_01114 (334 letters) >NCBI__GCF_000015985.1:WP_002723190.1 Length = 348 Score = 268 bits (685), Expect = 1e-76 Identities = 148/350 (42%), Positives = 207/350 (59%), Gaps = 18/350 (5%) Query: 1 MKLTRLGAALAAAALTVGVIA--------------AAQAATNETIVTVVKVTGINWFNRM 46 MK+ AALA + L +A + +I TVVKV GI WF+RM Sbjct: 1 MKIMLTSAALALSVLAAPAVAQDIVDVSKVNKELITTKDGKEYSIATVVKVDGIAWFDRM 60 Query: 47 DEGVKEFAKDNPGVTAYQTGPGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKK 106 +G+ +F KD G + GP +ADAA Q+++IE+LIA+ V+AI VVP+ +EP LKK Sbjct: 61 RDGITQFQKDT-GHDVWMVGPSQADAAAQVQLIENLIAQGVDAICVVPFSVEAVEPVLKK 119 Query: 107 AMDRGIKVVTHEADNAKNTMVDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRS 166 A DRGI V+THEA N +NT D+EAFDN AYGA L + LA M +GK+ VGSL S+S Sbjct: 120 ARDRGIVVITHEASNIQNTDFDLEAFDNLAYGANLMKELAKSMGEKGKYVATVGSLTSKS 179 Query: 167 QVQWADGGIGNAKAKYAKMNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDV 226 Q++W DG + K Y +M+LV +LET +D Y KE + +PD+ G G+ Sbjct: 180 QMEWIDGAVAYQKEHYPEMSLVGDRLETADDAAIDYTKLKEAMTTYPDITGILGAPMPTS 239 Query: 227 IGIGRAVEEAGMQGKICVYGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVD 286 G GR + E+G++ K+ GTGLP+ AG++L++G I I FWDP +AG AMN +A ++ Sbjct: 240 AGAGRLIAESGLKDKVFFAGTGLPSVAGEYLQNGDIQYIQFWDPAVAGYAMNMLAVAALE 299 Query: 287 GK--TVENGADLGIPGYTKVTVAKGPGKGIIVRGQGWVNVDKSNYKQYPF 334 GK ++ G +LG+ GY ++T A ++ G GWV V K N Y F Sbjct: 300 GKKDEIKPGLNLGLAGYEELT-APDAANPHLLYGAGWVGVTKDNMADYDF 348 Lambda K H 0.314 0.133 0.385 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: 330 Number of extensions: 17 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: 334 Length of database: 348 Length adjustment: 29 Effective length of query: 305 Effective length of database: 319 Effective search space: 97295 Effective search space used: 97295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. 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