Align ABC-type sugar transport system, permease component, component of Maltose transporter, MusEFGKI (characterized)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= TCDB::Q8NMV4 (281 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 114 bits (284), Expect = 3e-30 Identities = 83/273 (30%), Positives = 132/273 (48%), Gaps = 20/273 (7%) Query: 11 VFVLPTLLAFMIAFLVPFIVGFFLSFTKF-----TTITNAKWVGIDNYVKAFSQREGFIS 65 +F+ P LL + FL+P I LS T + I + ++V + NY + R F S Sbjct: 9 LFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELL-HRPLFWS 67 Query: 66 AFGFTVLVVIVSVITVNIFAFLLAWLLTRKL-RGTNFFRTVFFMPNLIGGIVLGYTWQTM 124 A G T+ V+V V + + A LL L R FRT F P + + + W+ + Sbjct: 68 ALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIWRYL 127 Query: 125 INAV--LSHYAT----TISADW----KFGYAGLIMLLNWQLIGYMMIIYIAGLQNVPPEL 174 N L++YA DW ++ +I+ W+ GY MII++A LQ +P +L Sbjct: 128 FNTKYGLANYALGGLGIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQAIPADL 187 Query: 175 IEAAELDGVNKWEMLRHVTIPMVMPSITICLFLTLSNSFKLFDQNLALTNGAPGGQTEMV 234 EAA +DG + RH+T+PM+ P++ + LT+S F+LF + +T G P T V Sbjct: 188 YEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGPLQSTTSV 247 Query: 235 ALNIINTLFNRMNVEGVGQAKAVIFVVVVVVIA 267 + F N +G A AV F++ +++ A Sbjct: 248 LYLMYEEGFKWWN---LGSASAVAFLLFLIMFA 277 Lambda K H 0.331 0.142 0.431 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: 233 Number of extensions: 18 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: 281 Length of database: 292 Length adjustment: 26 Effective length of query: 255 Effective length of database: 266 Effective search space: 67830 Effective search space used: 67830 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: 47 (22.7 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