Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate WP_083529392.1 AS188_RS10230 ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >NCBI__GCF_001482365.1:WP_083529392.1 Length = 327 Score = 179 bits (453), Expect = 1e-49 Identities = 117/326 (35%), Positives = 184/326 (56%), Gaps = 10/326 (3%) Query: 6 TRPAASTGAPLPAGTLGRLTTQERLRALGMLPVLVL--LCIGFSVLTENFAGWQNLSIIA 63 T + + AP+ GT R + + + ++++ +C+ F + FA +NL I Sbjct: 3 TTTSTPSPAPVQEGTAARKAPLDWRNYIIYIGIVLVYGICVLF-LHDSGFATTENLLNIF 61 Query: 64 QQASINMVLAAGMTFVILTGGIDLSVGSILSISAVVAML--VSLMPQLGMLSVPAALLCG 121 +Q ++ ++A +TFVI IDLSVG++ +++V A + + P +G L A + G Sbjct: 62 RQTAMIALMAVAVTFVIAAAEIDLSVGAVAGLASVTAAMGVAAGGPVVGAL---AGIGTG 118 Query: 122 LLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGF-AFIGNGEVLG 180 +L G+VNG+LVAF K+P F+VTLG + G+A + + GF AF G G + Sbjct: 119 VLVGLVNGSLVAFAKIPSFLVTLGMMGIAMGVAMWITGSAPQPILSPGFNAFFGGGSLGP 178 Query: 181 VPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLA 240 +P L+I + V+ RT G ++ A GGN +AA SG++ ++ V S + A Sbjct: 179 IPALLIWVIIATVIGAIVMHRTAYGRRVLATGGNEQAAIYSGVRTRRIIFSVLLTSAVAA 238 Query: 241 GLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSN 300 L G++ + RL + Q G EL IAAVILGGTS GG G++VG++VGAL+I V++N Sbjct: 239 SLAGMLYAGRLESGR-YQWGSGDELSVIAAVILGGTSLFGGRGAVVGSVVGALLIGVINN 297 Query: 301 GLVLLGVSDIWQYIIKGLVIIGAVAL 326 LVL G+ Q I++G++II AVAL Sbjct: 298 ALVLAGLETSQQNIVRGIIIILAVAL 323 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: 399 Number of extensions: 25 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: 327 Length adjustment: 28 Effective length of query: 309 Effective length of database: 299 Effective search space: 92391 Effective search space used: 92391 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 24 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