Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910 Length = 325 Score = 204 bits (520), Expect = 2e-57 Identities = 123/329 (37%), Positives = 186/329 (56%), Gaps = 10/329 (3%) Query: 17 NTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVL 76 NTAS G R+ F LA A LL MI+ FS S +F+ D ++ VL Sbjct: 2 NTASYAGKRSGNFYGLGTYLGLAGA-LLAMIVLFSVLSSHFLSYDTFSTLANQIPDLMVL 60 Query: 77 AIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMV 136 A+ T+V+I GIDLSVG+++ A V + WG + + AL+G I+G + Sbjct: 61 AVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGWGWGVLPAALLGMAVAALAGTITGSI 120 Query: 137 IAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPN 196 ++P FI +LG++ + +G++ ++G+R Y D F+ ++ G + PS I Sbjct: 121 TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDA--FAWLSNPIAFG-ISPSFII-- 175 Query: 197 AVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIA 256 A+LI+F+ A +L +TVFGRY +G+NEEA+RL+G+ +KV V++ G + G+A Sbjct: 176 ALLIIFV----AQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKVLVFSLMGLLAGVA 231 Query: 257 GLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRI 316 L SRL +A P G G EL IAAVVIGGTSL GG G+++ T G I+SVL GL Sbjct: 232 ALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQ 291 Query: 317 MSVAQEWQTVVTGVIIILAVYLDILRRRR 345 + + + ++TG +I++AV LD R +R Sbjct: 292 IGATEPTKRIITGAVIVVAVVLDTYRSQR 320 Lambda K H 0.326 0.139 0.398 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: 245 Number of extensions: 14 Number of successful extensions: 2 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: 347 Length of database: 325 Length adjustment: 28 Effective length of query: 319 Effective length of database: 297 Effective search space: 94743 Effective search space used: 94743 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