Align Ribose import permease protein RbsC (characterized)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 176 bits (447), Expect = 5e-49 Identities = 103/298 (34%), Positives = 169/298 (56%), Gaps = 6/298 (2%) Query: 23 LIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82 + A+L+L+A++++ P F +NL ++ TS ++A+G +VILT IDLSV + LAL Sbjct: 14 IAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANLAL 73 Query: 83 TGAVAASIVGIEVNAL---VAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRG 139 TG V S+V + L V +A A+ LG +G G++V K ++ + TL M + RG Sbjct: 74 TGMVV-SMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFRG 132 Query: 140 VTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYI 199 + + ++G VN+ E + F F LG+P WI + + ++ T LGR Sbjct: 133 IIFLISDGKWVNSH--EMSPAFKAFPRAELLGLPVLSWIAILAVILFTIVMTRTTLGRAF 190 Query: 200 YALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIA 259 YA GGN A +GI+V K + +++ G LA L G + V+R + + G+ELD +A Sbjct: 191 YAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFELDVVA 250 Query: 260 AVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317 A V+GG S+ GG G + G L+GAL LG + N L ++ +S ++Q+ + I++AV ++ Sbjct: 251 ACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAVALN 308 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: 229 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: 327 Length adjustment: 28 Effective length of query: 293 Effective length of database: 299 Effective search space: 87607 Effective search space used: 87607 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