Align Ribose import permease protein RbsC (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 211 bits (538), Expect = 1e-59 Identities = 123/301 (40%), Positives = 178/301 (59%), Gaps = 14/301 (4%) Query: 24 IALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLALT 83 IAL++ A +T S F + N ILQQ V A++A+G TLVILT+GIDLS G ++AL Sbjct: 18 IALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMALG 77 Query: 84 GAVAASIVG-IEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTM 142 G V + ++A VA+A +A+ G + G++V K ++ FI TL + + T Sbjct: 78 GIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFAATQ 137 Query: 143 VYTNGSPVN---TGFTENADLFGWFGIGRPLGVPTPVW---IMGIVFLAAWYMLHHTRLG 196 +Y+ + G T + F LG VW +M ++L W+ L T G Sbjct: 138 LYSGAQTITDIPAGMTALGNTF-------QLGQTAIVWGAVLMLALYLVTWFALRETAPG 190 Query: 197 RYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELD 256 R++YA+G + ATRL+GI +K+ + VY L GL +A ++ VAR + P AG LD Sbjct: 191 RHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLD 250 Query: 257 AIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLV 316 AI+AVVLGGTSL GG+G I+GTL+GALI+G NGL L+GVSS YQ++V ++++LAV Sbjct: 251 AISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVAT 310 Query: 317 D 317 D Sbjct: 311 D 311 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: 236 Number of extensions: 13 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: 321 Length of database: 319 Length adjustment: 28 Effective length of query: 293 Effective length of database: 291 Effective search space: 85263 Effective search space used: 85263 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: 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