Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 101 bits (251), Expect = 2e-26 Identities = 79/258 (30%), Positives = 127/258 (49%), Gaps = 9/258 (3%) Query: 11 WGVG-IVLVLVAVFPLLWALLNSVKTLLDIVT-PTPRFLFTPTLENYRQVIG-SPEVLVG 67 W + + L L ++ P+LW LL S+K DI PT + T+E+Y+ + +P Sbjct: 7 WAIAALALSLFSLAPILWQLLTSIKVNADIAAIPTIYWPRQWTVEHYQALWQQTPAFGRY 66 Query: 68 LTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLSLRFLPPVAVAIPLIAI- 126 L NSAV+ A L +G P AY IAR + + LL + P V + L+ + Sbjct: 67 LLNSAVVSAIATLAALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLLFQGLLEVV 126 Query: 127 -WVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYGPYAVFWKIA 185 W+ G + +++V Y L + L F+++P E+EEAA +DG W I Sbjct: 127 RWLQWG--NNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQRLWLIL 184 Query: 186 LPNCATTLLGGIIFSFVLVWNELMIALALTSSNS-ATLPVVASAFTSMG-QEVPWGVINA 243 +P A L+ I +F+ WNE ++AL+ S + T+P+ + + +VP+G I A Sbjct: 185 VPLTAPALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPYGDIAA 244 Query: 244 STVLLALPPLIFVGVLSR 261 +TV+ LP + V V R Sbjct: 245 ATVVATLPLIGLVLVAQR 262 Lambda K H 0.327 0.142 0.434 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: 263 Number of extensions: 13 Number of successful extensions: 4 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: 270 Length of database: 275 Length adjustment: 25 Effective length of query: 245 Effective length of database: 250 Effective search space: 61250 Effective search space used: 61250 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: 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