Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 240 bits (612), Expect = 4e-68 Identities = 137/290 (47%), Positives = 183/290 (63%), Gaps = 13/290 (4%) Query: 36 SNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSVGSILGFSGAVTAKLLKYGLI 95 ++ F + EN ILRQ A+NL +A GMTFVILT GIDLSVGS+L S + + Sbjct: 52 TSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQ------- 104 Query: 96 LSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITRFNIPPFVATLGTMTAVRGFIMLLT 155 V L P A + + +G +G+ NG ++ NI FV TLGTMTA RG LL Sbjct: 105 -----VSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLA 159 Query: 156 KGHPITRLG-DSFDFIGSGWFLGIPMPVWIAAIATGVGIFILRKTQFGRYVYAVGGNEKA 214 G + SF++IG+G FL +P +W+A + ILRKT G ++YA+GGN +A Sbjct: 160 DGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQA 219 Query: 215 AVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQPNAGLMYELDAIAATVIGGASL 274 A L+G+ L L+VY+ISG+ S +AG + +RL A N G YELDAIAA V+GG SL Sbjct: 220 ARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSL 279 Query: 275 SGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGFIIIAAVIAEK 324 GG G++ GTVVGALIIGV+N+GL ++G+S FWQ VAKG +I+ AVI +K Sbjct: 280 MGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDK 329 Lambda K H 0.327 0.144 0.427 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: 424 Number of extensions: 31 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: 331 Length of database: 339 Length adjustment: 28 Effective length of query: 303 Effective length of database: 311 Effective search space: 94233 Effective search space used: 94233 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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