Align Sugar ABC transporter permease (characterized, see rationale)
to candidate 3608007 Dshi_1415 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__Dino:3608007 Length = 294 Score = 155 bits (391), Expect = 1e-42 Identities = 96/292 (32%), Positives = 145/292 (49%), Gaps = 14/292 (4%) Query: 2 NLRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWI---------- 51 N+ + LRL W ++ + L+ A FPF + + S K F W Sbjct: 4 NIATRRSMPLRLFLWGVVLLWLMLAAFPFLWTLWGSFKVQGDFFSREDWTNALTGVRTLA 63 Query: 52 ENPDF---SNYAAVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTV 108 E + YA Q F RA N+++V L VV ++L YAL R F+ + Sbjct: 64 ETGGYFTGGGYAGAWVQEEFWRAGLNTMIVTLSVVAISLTFGTLGGYALSRSSFKYTFWI 123 Query: 109 LMMVLGVSMFPQVAVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPH 168 LM L P + ++SG L ++ I+ PFT+W+L +F +P Sbjct: 124 LMAALIFRAMPHITLVSGYLLPFFELNIWGILPTTIIVLVAINQPFTLWMLRSFFMNIPK 183 Query: 169 ELEEAAIMDGASPWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVP 228 +L+E+A++DG + + RV++P++WP ++TTGL +F+ A+N+F T D Q +P Sbjct: 184 DLDESAMVDGCTRFQAFRRVIIPVMWPGVITTGLFSFLLAYNDFAVTATLLSQDNQTMIP 243 Query: 229 VAIALISGGSPHELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALKG 280 IA G + E ++A V T PL ILVL FQR+IVSGLTAGA+KG Sbjct: 244 -KIASFLGTTQQEGNVMFAVSAVVSATAPLFILVLFFQRQIVSGLTAGAVKG 294 Lambda K H 0.329 0.141 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: 248 Number of extensions: 17 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: 280 Length of database: 294 Length adjustment: 26 Effective length of query: 254 Effective length of database: 268 Effective search space: 68072 Effective search space used: 68072 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 (21.8 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