Align ABC transporter permease (characterized, see rationale)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= uniprot:A0A165KPZ4 (293 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 137 bits (345), Expect = 3e-37 Identities = 88/270 (32%), Positives = 134/270 (49%), Gaps = 5/270 (1%) Query: 11 PKLVVAPAFV-LGFAFIYGLM--VWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRWWVA 67 P+ + PA + + F Y L+ W + +L ++ L + GLA Y+RLW R+W Sbjct: 5 PRWLTIPALLTITGVFAYPLLRAAWLSLQALNLNTQLQPV-FIGLANYQRLWGDSRFWGD 63 Query: 68 LKNLGIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLN 127 L N +F V V L++G+ +A+LL Q R G LRTI L P L V W W+ N Sbjct: 64 LFNTTVFTVTSVSLELVLGLAIALLLHQPSRWRGPLRTIALLPWVLPTAVMALGWAWIFN 123 Query: 128 PGLGI-EKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSI 186 G+ ++ G+ WL + A +V A +W++ F L LAG + I + + Sbjct: 124 DPYGVWNDWLQQLGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLLAGRQAIPEDL 183 Query: 187 IKAAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVP 246 +A ++GA+ + +W+I LP LRP L+ S A FDLV +T GGP +T+ Sbjct: 184 YEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMTGGGPANSTETL 243 Query: 247 ATFMYTMSFSRGQIGLGAASATMMLATVAA 276 A + YT + G GA A + A +AA Sbjct: 244 ALYAYTTALRYLDFGYGATLAIVTAAILAA 273 Lambda K H 0.327 0.141 0.451 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: 332 Number of extensions: 12 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: 293 Length of database: 292 Length adjustment: 26 Effective length of query: 267 Effective length of database: 266 Effective search space: 71022 Effective search space used: 71022 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: 48 (23.1 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