Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 214 bits (545), Expect = 2e-60 Identities = 128/304 (42%), Positives = 185/304 (60%), Gaps = 7/304 (2%) Query: 29 RLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLS 88 RL ALG LLC+ +V ++ F N+ + +QAS+ +LA+G+T VILTGG+DLS Sbjct: 20 RLFALG------LLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLS 73 Query: 89 VGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLT 148 VG+ +++SA VA V ML V A L G L G+ NG LVA +++PPFI T G L Sbjct: 74 VGANVAMSACVAATVMKATGSTMLGVGAGLGTGALIGLANGLLVAMLRIPPFIATYGMLW 133 Query: 149 AVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQI 208 + G+ TI+ F IG+G + GVP V + + + ++T G +I Sbjct: 134 VLHGVTYWFMAGETIHGFPPAFRAIGSGYLWGVPIPVYLMLVFLVAGTAMSQKTTYGQEI 193 Query: 209 YAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAI 268 YA+G N AARLSG+ V L+ VY VSG +AG+ ++ ARL +A G +G++ L AI Sbjct: 194 YAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEG-DIGEALTLPAI 252 Query: 269 AAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDS 328 AAV++GGTS GG G + GTLVGA+I+ ++ NG+ LL VS WQ ++ G++++ AV LD+ Sbjct: 253 AAVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVIVVLAVFLDT 312 Query: 329 YRRK 332 RK Sbjct: 313 LSRK 316 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: 342 Number of extensions: 19 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: 337 Length of database: 322 Length adjustment: 28 Effective length of query: 309 Effective length of database: 294 Effective search space: 90846 Effective search space used: 90846 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