Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PP_2760 PP_2760 putative ribose transport permease protein
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Putida:PP_2760 Length = 327 Score = 133 bits (335), Expect = 6e-36 Identities = 107/325 (32%), Positives = 162/325 (49%), Gaps = 21/325 (6%) Query: 25 AQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMT 84 AQWLL R +L +L L LS NF + N +N+L Q AI LA G+T Sbjct: 15 AQWLLRRGALLAFAAIL------LAFALSAP---NFLTLSNLVNVLAQSAILGSLAFGLT 65 Query: 85 FVIL-------TAGIDLSVGSVLAVSAVLGMQVS-LGAAPGWAIPMFIFSGLVMGMVNGA 136 VI+ + G+DLS+ + L +SA + ++ G +I + +GL +G +N Sbjct: 66 TVIIGGGSNVVSGGLDLSLAANLGLSAAVYASLNNAGFGDVVSIAATLGTGLAIGTLNAL 125 Query: 137 MVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAV 196 +V + + TL TM G +L + T VL + P E + G ++ VP L WV + Sbjct: 126 VVVGFRLPPLLATLATMNLVAGLELVLTENT-VLPSTSPLLEGLAFGSWVGVPALAWVLL 184 Query: 197 AVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSAS 256 AV + V+ + T G+ +YAIG +AA G+ V + Y ISGL LA SA+ Sbjct: 185 AVGGVLIVLTQYTPFGLRLYAIGEYPEAANAAGLSVRGYVFASYLISGLCGSLAAFCSAA 244 Query: 257 RLYGANGNWGSGYELDAIAAVVLGGTSLMGGV-GSIWGTVVGALIIGVMNNGLTILGLSS 315 G+ GSG L ++ A+ G + SI GT++ L++GV+ NG +L +SS Sbjct: 245 WFSGS--TTGSGEMLLSVVAIAFLGVIFSQRLQPSIGGTLLATLLVGVLINGFQLLNISS 302 Query: 316 FWQYVAKGAVIVLAVILDKWRQKDA 340 FW +G +I+L V L R K+A Sbjct: 303 FWVDGVQGVLILLVVALSGLRNKEA 327 Lambda K H 0.324 0.138 0.417 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: 304 Number of extensions: 12 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: 344 Length of database: 327 Length adjustment: 28 Effective length of query: 316 Effective length of database: 299 Effective search space: 94484 Effective search space used: 94484 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