Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Koxy:BWI76_RS00275 Length = 501 Score = 287 bits (734), Expect = 7e-82 Identities = 168/473 (35%), Positives = 264/473 (55%), Gaps = 8/473 (1%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 + K F AL+ S+ V PG ALVG NGAGKST++ +LTG+ D G + + G Sbjct: 10 IDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGSLLWLGKETT 69 Query: 80 SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGVIDWQAMRRDARALLDHW 138 + + + ++Q +I L++AEN+F+ R+ + R G IDW+ M +A LL Sbjct: 70 FNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADKLLAKL 129 Query: 139 KIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQR 198 + GDLS+ +Q+VEIA+ LS+ ++ II+DEPT L E + LFR I EL+ Sbjct: 130 NLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKS 189 Query: 199 EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADA 258 +G ++ISH ++E++EIC VTV RD + I V++L + LIE M G + + D Sbjct: 190 QGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGRK----LEDQ 245 Query: 259 AARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRAA 318 R A AV L++ L G+ E +SF +++GE++G+ G +GRT + + + G Sbjct: 246 YPR-LDKAPGAVRLKVDNLCGSGVENISFILRQGEILGVAGLMGAGRTELMKVLYGALPR 304 Query: 319 KRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFGI 378 G++++DG + LA+GI + +DR +GLVL SV EN S+T R + G Sbjct: 305 SSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRGGG 364 Query: 379 AAPAK-KNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTA 437 + K + I + E + LSGGNQQKV +AR L T P VL+L +PT Sbjct: 365 SLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTR 424 Query: 438 GVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEF 489 GVDV +K+ + ++++ + EG ++++VS E+ + L DR++VM G + EF Sbjct: 425 GVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEF 477 Lambda K H 0.318 0.134 0.377 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: 538 Number of extensions: 26 Number of successful extensions: 7 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: 510 Length of database: 501 Length adjustment: 34 Effective length of query: 476 Effective length of database: 467 Effective search space: 222292 Effective search space used: 222292 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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