Align Ribose import permease protein RbsC (characterized)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 236 bits (603), Expect = 5e-67 Identities = 134/321 (41%), Positives = 200/321 (62%), Gaps = 7/321 (2%) Query: 4 QTVSG--RRYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAV 61 +T SG R FT L + + +L++L+ S SP F ++N+ ILQ T+VN ++A+ Sbjct: 14 KTFSGLRARVFTPTALQKLLAFGSLILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAI 73 Query: 62 GMTLVILTSGIDLSVGSLLALTGAVAASIVGI-EVNALVAVAAALALGAAIGAVTGVIVA 120 T VI+T GIDLSVG+L+ T + + + V AA+ GA G V+G + A Sbjct: 74 ACTFVIITGGIDLSVGTLMTFTAVICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTA 133 Query: 121 KGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPL--GVPTPVWI 178 K ++ FIATL MM+LL+G+++V + P+ TEN + + L +P P + Sbjct: 134 KMKIPPFIATLGMMMLLKGLSLVVSADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAV 193 Query: 179 MGIVFLA--AWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGI 236 + + FLA + L+ T LGRY +ALG NE A RLSG+NV++ KI +Y L G + +AG+ Sbjct: 194 LILFFLAVVSSITLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGL 253 Query: 237 IEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLG 296 + +RL+SAQP G GYEL+AIAAVV+GGTSL+GG G I+GT+IGA I+ L NGL ++ Sbjct: 254 LIASRLNSAQPALGQGYELEAIAAVVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMS 313 Query: 297 VSSYYQMIVKAVVILLAVLVD 317 V+ +Q++V ++I+LAV D Sbjct: 314 VAQEWQIVVTGLIIILAVYGD 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: 250 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