Align Ribose import permease protein RbsC (characterized)
to candidate H281DRAFT_00427 H281DRAFT_00427 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Burk376:H281DRAFT_00427 Length = 341 Score = 239 bits (609), Expect = 9e-68 Identities = 130/315 (41%), Positives = 196/315 (62%), Gaps = 9/315 (2%) Query: 10 RYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILT 69 R F+ L + + +L++L+ S SP F ++N+ ILQ T+VN ++A+ T VI+T Sbjct: 22 RIFSPTALQKLLAFASLILLLVFFSFASPAFMQMDNILGILQATAVNGVLAIASTFVIIT 81 Query: 70 SGIDLSVGSLLALTGAVAASIVGI-EVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFI 128 GIDLSVG+L+ T + + + + V AA+ GA G ++G + AK ++ FI Sbjct: 82 GGIDLSVGTLMTFTAVICGVFLTYWHLPMWLGVIAAIGTGAICGTISGTLTAKMKIPPFI 141 Query: 129 ATLVMMLLLRGVTMVYTNGSPVNTGFTENA------DLFGWFGIGRPLGVPTPVWIMGIV 182 ATL MMLLL+G+++V + P+ TEN L G+ P +P V I+ + Sbjct: 142 ATLGMMLLLKGLSLVVSADKPIYFTDTENFYMISQDSLIGYLVPSLP--IPNAVLILFFL 199 Query: 183 FLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARL 242 + + L+ T LGRY +ALG NE A RLSG+NV++ KI +Y L G + +AG++ +RL Sbjct: 200 AIVSSVTLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLGGAICGIAGLLIASRL 259 Query: 243 SSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQ 302 +SAQP G GYEL+AIAAVV+GGTSL+GG G I+GT+IGA I+ L NGL ++ V+ +Q Sbjct: 260 NSAQPALGQGYELEAIAAVVIGGTSLSGGSGTILGTIIGAFIMSVLTNGLRIMSVAQEWQ 319 Query: 303 MIVKAVVILLAVLVD 317 ++V ++I+LAV D Sbjct: 320 IVVTGLIIILAVYAD 334 Lambda K H 0.324 0.139 0.393 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: 260 Number of extensions: 12 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: 321 Length of database: 341 Length adjustment: 28 Effective length of query: 293 Effective length of database: 313 Effective search space: 91709 Effective search space used: 91709 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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