Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 189 bits (481), Expect = 6e-53 Identities = 111/304 (36%), Positives = 174/304 (57%), Gaps = 7/304 (2%) Query: 34 GMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSIL 93 G+L L IGF++ F N + + ++I V+A G+TFV+++G +DLSVGS++ Sbjct: 17 GILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSMM 76 Query: 94 SISAVVAMLVSLMPQLG-MLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRG 152 S S +V + L +LG L++PA L G + G LV ++KL IVTLG L+A+ G Sbjct: 77 SFSTIVVL--DLHDKLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSAIHG 134 Query: 153 LARLVGNDSTIYNPD---IGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIY 209 L + D FA G G +LG+ ++I A+ A+ +L +T G ++Y Sbjct: 135 LTLTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIALAALLGIILAKTPFGRKVY 194 Query: 210 AVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIA 269 AVGGN AA SGI+ V+ Y +S L G++ ++R + +GQ EL+ +A Sbjct: 195 AVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNT-VGQGLELEVLA 253 Query: 270 AVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSY 329 AVILGG S +GG+G+I T++G LI+ + NGL+L+G+ QY++ ++II AV LD Sbjct: 254 AVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWLDIA 313 Query: 330 RRKG 333 ++G Sbjct: 314 AKRG 317 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: 361 Number of extensions: 25 Number of successful extensions: 6 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: 324 Length adjustment: 28 Effective length of query: 309 Effective length of database: 296 Effective search space: 91464 Effective search space used: 91464 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