Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 223 bits (567), Expect = 7e-63 Identities = 136/326 (41%), Positives = 196/326 (60%), Gaps = 10/326 (3%) Query: 18 AGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMT 77 +G R+ T L+ L L+LL + FS + F N+ I Q ++N VLA T Sbjct: 17 SGLRARVFTPTALQKLLAFGSLILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAIACT 76 Query: 78 FVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLS-VPAALLCGLLFGIVNGALVAFMK 136 FVI+TGGIDLSVG++++ +AV+ + L M + V AA+ G + G V+G L A MK Sbjct: 77 FVIITGGIDLSVGTLMTFTAVICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTAKMK 136 Query: 137 LPPFIVTLGTLTAVRGLARLVGNDSTIYNPDI-GFAFIGNGEVLG-------VPWLVIIA 188 +PPFI TLG + ++GL+ +V D IY D F I ++G VP V+I Sbjct: 137 IPPFIATLGMMMLLKGLSLVVSADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAVLIL 196 Query: 189 FAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSS 248 F + VS L RT LG +A+G N EA RLSG+ V + +Y +SG + G+ G++ + Sbjct: 197 FFLAVVSSITLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIA 256 Query: 249 ARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVS 308 +RL +A LGQ YEL+AIAAV++GGTS GG G+I+GT++GA I++VL+NGL ++ V+ Sbjct: 257 SRLNSAQPA-LGQGYELEAIAAVVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVA 315 Query: 309 DIWQYIIKGLVIIGAVALDSYRRKGS 334 WQ ++ GL+II AV D RRK S Sbjct: 316 QEWQIVVTGLIIILAVYGDILRRKKS 341 Lambda K H 0.325 0.141 0.409 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: 360 Number of extensions: 23 Number of successful extensions: 5 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: 337 Length of database: 341 Length adjustment: 28 Effective length of query: 309 Effective length of database: 313 Effective search space: 96717 Effective search space used: 96717 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