Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 285 bits (729), Expect = 3e-81 Identities = 166/474 (35%), Positives = 265/474 (55%), Gaps = 10/474 (2%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 + K F AL+ ++ V PG ALVG NGAGKST++ +LTG+ D G + + G Sbjct: 10 IDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETT 69 Query: 80 SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGVIDWQAMRRDARALLDHW 138 + + + ++Q +I L++AEN+F+ R+ + R G IDW+ M +A LL Sbjct: 70 FTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADKLLAKL 129 Query: 139 KIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQR 198 + + D GDLS+ +Q+VEIA+ LS+ ++ II+DEPT L E + LFR I EL+ Sbjct: 130 NLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKS 189 Query: 199 EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADA 258 +G ++ISH ++E++EIC VTV RD + I V++L + LIE M G + + D Sbjct: 190 QGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK----LEDQ 245 Query: 259 AAR-GALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317 P D + L++ L G VSFT+++GE++G++G +GRT + + + G Sbjct: 246 YPHLDKAPGD--IRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALP 303 Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377 G +++DG + LA+GI + +DR +GLVL SV EN S+T R + G Sbjct: 304 RTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAG 363 Query: 378 IAAP-AKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPT 436 + A + I + E + LSGGNQQKV +AR L T P VL+L +PT Sbjct: 364 GSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPT 423 Query: 437 AGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEF 489 GVDV +K+ + ++++ + +G ++++VS E+ + L DR++VM G ++ EF Sbjct: 424 RGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEF 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: 549 Number of extensions: 31 Number of successful extensions: 8 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