Align Amino acid ABC transporter, membrane protein (characterized, see rationale)
to candidate 8500098 DvMF_0861 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:Q88GX2 (236 letters) >FitnessBrowser__Miya:8500098 Length = 263 Score = 121 bits (304), Expect = 1e-32 Identities = 72/208 (34%), Positives = 117/208 (56%), Gaps = 12/208 (5%) Query: 25 DGLLVTAKLVAISFSLGAVLGLLLALARLSRSLVLQRMAAGYVYFFRGSPLLAQLFLLYY 84 DG+ VT K+ +S +GL+ L RLSR+ ++ +A+ YV RG PLL QLF +YY Sbjct: 61 DGIAVTFKVTVLSILCSIPIGLITGLGRLSRNRLINLVASTYVEVVRGIPLLVQLFYIYY 120 Query: 85 GLGSLKGFWQDVGLWWFFRDAWFCTLLAFTLNTAAYQAEIFRGSLMAVAPGQHEAARALN 144 LG F + L ++A ++ AY E+FR + +++ GQ EAAR+L Sbjct: 121 ALGR---FLKVPDL--------LAAIIALSVCYGAYMGEVFRAGIDSISKGQTEAARSLG 169 Query: 145 LKRSTTFFKVILPQSLLVAIGPLGNELILMIKASAIASLVTIYDLMGVTKLAFSRSF-DF 203 R+ T F VILPQ+ + P+GNE I M+K +++ S++ + D++ + S SF F Sbjct: 170 FNRAETMFMVILPQAWRTILPPVGNEFIAMLKDTSLVSIIAVADILRRGREFASESFLYF 229 Query: 204 QIYLWAAVLYLVIVELVRRLLKHLEARL 231 + Y A++YL+I + + + +E+RL Sbjct: 230 ETYTMVALIYLLITLFLSKGVSIMESRL 257 Lambda K H 0.331 0.144 0.433 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: 110 Number of extensions: 5 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: 236 Length of database: 263 Length adjustment: 24 Effective length of query: 212 Effective length of database: 239 Effective search space: 50668 Effective search space used: 50668 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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