Align Fructose import permease protein FrcC (characterized)
to candidate WP_108223269.1 C8J29_RS11820 ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >NCBI__GCF_003046325.1:WP_108223269.1 Length = 363 Score = 522 bits (1345), Expect = e-153 Identities = 267/362 (73%), Positives = 306/362 (84%), Gaps = 8/362 (2%) Query: 6 TAAQPSQEFEKVLADSSTDVASFDAHDKTLLQKLQHFLHSSPAAVPLIVLVLSLIAFGVI 65 T Q FE L S VA F+ ++ +Q+ +H LH +P+ VPLIVLV+S+ FG + Sbjct: 3 TETHGPQGFEAALNRSPDSVAEFEQR-RSFVQQARHLLHQTPSLVPLIVLVVSVSIFGAL 61 Query: 66 LGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSVIMGQFTFRYG 125 LG KFFSAFT+TLILQQVAIVGIVGAAQTLV+LTAGIDLSVGAIMVLSSVIMGQFTFRYG Sbjct: 62 LGQKFFSAFTLTLILQQVAIVGIVGAAQTLVVLTAGIDLSVGAIMVLSSVIMGQFTFRYG 121 Query: 126 FPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRAQD 185 P LSV+CGL GA G++NGTLVARMKLPPFIVTLGMWQIVLA+NFLYSANETIR+QD Sbjct: 122 IPAPLSVLCGLAAGAGIGFVNGTLVARMKLPPFIVTLGMWQIVLAANFLYSANETIRSQD 181 Query: 186 ISANASILQFFGQNFRI-------GNAVFTYGVVVMVLLVCLLWYVLNRTAWGRYVYAVG 238 ISA A ILQFFG FR+ G AVFTYG V+++LLV ++ YVL +TAWGR+VYAVG Sbjct: 182 ISAQAPILQFFGNTFRLGADEAGRGGAVFTYGAVLLILLVLVIAYVLRQTAWGRHVYAVG 241 Query: 239 DDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITAVVI 298 DDP+AA+LAGV +L+++YTLSGLICALAGW +IGR+GSVSPTAGQFANIESITAVVI Sbjct: 242 DDPDAAELAGVQTRNVLVTVYTLSGLICALAGWVMIGRLGSVSPTAGQFANIESITAVVI 301 Query: 299 GGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAIDQWIRKV 358 GGISLFGGRGS++GMLFGALIVGVFSLGL+LMGTDPQWTYLLIG+LII AVA+DQWIRK Sbjct: 302 GGISLFGGRGSVLGMLFGALIVGVFSLGLKLMGTDPQWTYLLIGMLIIAAVAVDQWIRKA 361 Query: 359 AA 360 AA Sbjct: 362 AA 363 Lambda K H 0.327 0.141 0.420 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: 561 Number of extensions: 27 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: 360 Length of database: 363 Length adjustment: 29 Effective length of query: 331 Effective length of database: 334 Effective search space: 110554 Effective search space used: 110554 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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