Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate Pf6N2E2_524 Inositol transport system permease protein
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524 Length = 340 Score = 212 bits (540), Expect = 1e-59 Identities = 140/329 (42%), Positives = 192/329 (58%), Gaps = 35/329 (10%) Query: 31 RALGMLPV---LVLLCIGFSVLTENFAGW-----------QNLSIIAQQASINMVLAAGM 76 RA LP + L+ IG ++ E F GW Q L ++ Q SI +LA G+ Sbjct: 15 RARRRLPTELSIFLVLIGIGLVFEMF-GWIMRDQSFLMNSQRLVLMILQVSIIGLLAIGV 73 Query: 77 TFVILTGGIDLSVGSILSISAVVAMLVS--------LMPQLGMLSV----PAALLCGLLF 124 T VI+T GIDLS GS+L++SA++A ++ + P L L V A L GLL Sbjct: 74 TQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVVAGLGVGLLA 133 Query: 125 GIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWL 184 G +NG+++A +PPFI TLG + + RGLAR + + IG+G + Sbjct: 134 GAINGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGA------M 187 Query: 185 VIIAFAVVAVSWFV-LRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLG 243 +I F VVAV + + LR T G YA+GGN +AAR SGI V L+ VY+++GLLAGL Sbjct: 188 PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLA 247 Query: 244 GVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLV 303 GV++SAR A +G SYELDAIAA ++GGTS GG G I GT++GALI+ V+++G Sbjct: 248 GVVASARA-ATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFT 306 Query: 304 LLGVSDIWQYIIKGLVIIGAVALDSYRRK 332 +GV Q IIKGL+I+ AV +D YR K Sbjct: 307 FVGVDAYIQDIIKGLIIVVAVVIDQYRNK 335 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: 349 Number of extensions: 20 Number of successful extensions: 4 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: 340 Length adjustment: 28 Effective length of query: 309 Effective length of database: 312 Effective search space: 96408 Effective search space used: 96408 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