Align Fructose import binding protein FrcB (characterized)
to candidate RR42_RS03370 RR42_RS03370 ABC transporter
Query= SwissProt::Q9F9B2 (341 letters) >FitnessBrowser__Cup4G11:RR42_RS03370 Length = 325 Score = 103 bits (257), Expect = 6e-27 Identities = 96/297 (32%), Positives = 137/297 (46%), Gaps = 32/297 (10%) Query: 7 SAAFGALAMGVAFASPSQAAEVSACL---ITKTDT------NPFFVKMKEGAAAKAKELG 57 +AA L G A S AA SA + K NP+FV + GA A AK++ Sbjct: 11 TAALSLLCTGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKIN 70 Query: 58 VTLKSYAGKIDGDSESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALD 117 K D D Q + I++ I ILI A+D + I P V+KAR AG++V+A+D Sbjct: 71 PDAKVTVLSADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVD 130 Query: 118 TPLEPLDAADATFATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVL-RDQ 176 ADAT TDN AG+L + A LG L + P VL R + Sbjct: 131 VAAA---GADATVQTDNTRAGELACAFLAGRLGGRGN------LIIQNGPPVSAVLDRVK 181 Query: 177 GFMIGFGIDPKDPNKIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEP 236 G + G P + + D+ D + G+ EGG M+ L + P I+ V TIN+P Sbjct: 182 GCKMVLGKHP-GIHVLSDDQDGK--------GSREGGLNVMQLYLTRFPKIDAVFTINDP 232 Query: 237 AAAGAYEALKSVGREKDVLIVSVDGGCPGVKNV--AEGVIGATSQQYPLMMAALGIE 291 A GA A + + R +LI SVD G P ++ A ++ A++ Q P +A +E Sbjct: 233 QAVGADLAARQLNR-GGILIASVD-GAPDIEAALKANTLVQASASQDPWAIARTAVE 287 Lambda K H 0.313 0.132 0.372 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: 227 Number of extensions: 10 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: 341 Length of database: 325 Length adjustment: 28 Effective length of query: 313 Effective length of database: 297 Effective search space: 92961 Effective search space used: 92961 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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