Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 195 bits (495), Expect = 2e-54 Identities = 115/309 (37%), Positives = 178/309 (57%), Gaps = 16/309 (5%) Query: 39 VVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGS 98 ++L L+F+ + F +N + IL+ A+N VLA TFVI+T GIDLSVG+ Sbjct: 38 LILLLVFFSFA-------SPAFMQMDNMLGILQATAVNGVLAIACTFVIITGGIDLSVGT 90 Query: 99 VLAVSAVL-GMQVSLGAAPGWA-IPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAF 156 ++ +AV+ G+ ++ P W + I +G + G V+G + A + I F+ TLG M Sbjct: 91 LMTFTAVICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTAKMKIPPFIATLGMMMLL 150 Query: 157 RGAAYLLADGTTVLNNDIPSFEWIGN----GDFLH---VPWLIWVAVAVVLLSWVILRKT 209 +G + +++ + D +F I GD L VP + + + ++S + L +T Sbjct: 151 KGLSLVVSADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAVLILFFLAVVSSITLNRT 210 Query: 210 VLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGY 269 LG + +A+G N +A RL+G+ V + +Y +SG G+AG + ASRL A G GY Sbjct: 211 ALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIASRLNSAQPALGQGY 270 Query: 270 ELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLA 329 EL+AIAAVV+GGTSL GG G+I GT++GA I+ V+ NGL I+ ++ WQ V G +I+LA Sbjct: 271 ELEAIAAVVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIIILA 330 Query: 330 VILDKWRQK 338 V D R+K Sbjct: 331 VYGDILRRK 339 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: 322 Number of extensions: 25 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: 341 Length adjustment: 29 Effective length of query: 315 Effective length of database: 312 Effective search space: 98280 Effective search space used: 98280 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